14,400-Year-Old Woolly Rhinoceros Genome Reveals No Signs of Recent Inbreeding

Posted on January 15, 2026 by Igor Mitreski

The Woolly Rhino (Coelodonta antiquitatis) is a fascinating cold-adapted herbivore that went extinct approximately 14,000 years ago. Despite its extinction, little is understood about the factors leading to its population decline. A recent study by scientists from the Center for Paleogenetics and Stockholm University successfully generated a high-coverage genome from one of the last known woolly rhinoceros specimens, recovered from the stomach of a frozen wolf pup in Siberian permafrost. This genomic analysis, when combined with data from two other late Pleistocene woolly rhinoceroses, reveals that the population was stable, lacking any genomic evidence of rapid declines before extinction—contrasting sharply with other endangered and extinct species.

This depiction of a Pleistocene landscape in northern Spain features woolly mammoths (Mammuthus primigenius), equids, woolly rhinoceros (Coelodonta antiquitatis), and the European cave lion (Panthera leo spelaea) alongside reindeer carcasses. Image credit: Mauricio Anton.

The woolly rhino, a cold-adapted herbivore, first appeared around 350,000 years ago and thrived across northern Eurasia until its extinction roughly 14,000 years ago.

Its habitat began to contract eastward approximately 35,000 years ago, likely due to adverse environmental conditions in Western Europe.

This species persisted in northeastern Siberia and showcased complex range shifts in response to changing environments until disappearing from the fossil record.

Earlier genomic studies have shown no signs of recent inbreeding in individuals dating back 18,400 and 48,500 years; however, this is the first time an entire genome has been successfully recovered from a specimen so close to the extinction timeline.

“Recovering genomes from individuals that lived just before extinction is challenging but crucial for understanding a species’ decline, which can inform current conservation efforts for endangered species,” stated Dr. Camilo Chacon-Duque, the lead author of the study.

The newly sequenced woolly rhinoceros genome was sourced from muscle tissue found within a permafrost-preserved wolf pup recovered from northeastern Siberia.

Radiocarbon dating indicates that both the wolf and the tissue are about 14,400 years old, making it one of the youngest known woolly rhino remains.

“Sequencing the entire genome of an Ice Age animal found in another animal’s stomach is unprecedented,” Dr. Chacon-Duque commented.

By comparing this genome with two previously published late Pleistocene woolly rhinoceros genomes, researchers assessed genome-wide diversity, inbreeding, genetic load, and population size changes before extinction.

Results indicated a lack of long homozygous segments typically seen in populations experiencing recent inbreeding, suggesting stability in population size just centuries before extinction.

“DNA extraction from such a rare sample was both thrilling and immensely challenging,” said Solveig Gjonsdottir, the lead study author.

Researchers also mapped changes in effective population size and found no decline at the beginning of the Inter-Bolling-Allerod warm period, starting around 14,700 years ago.

The data imply that woolly rhinoceros extinction likely happened rapidly during this climate change period, or over a timeframe that left no detectable genomic evidence.

“Our analysis reveals an unexpectedly stable genetic pattern, showcasing unaltered inbreeding levels over tens of thousands of years prior to the woolly rhino’s extinction,” said co-author Dr. Edana Lord.

“Our findings indicate that woolly rhinos maintained viable populations for 15,000 years following the arrival of the first humans in northeastern Siberia. This suggests that climate warming, rather than human hunting, was the primary driver of their extinction,” co-author Professor Rab Dalen concluded.

For further details, refer to the study results published in Genome Biology and Evolution.

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Solveig M. Gudjonsdottir et al. 2026. Genome reveals no recent inbreeding in endangered woolly rhinoceros sample found in ancient wolf stomach. Genome Biology and Evolution 18 (1): evaf239; doi: 10.1093/gbe/evaf239

Source: www.sci.news

Ancient Woolly Rhinoceros Genome Found in Frozen Wolf Pup’s Stomach Meat

Posted on January 14, 2026 by Igor Mitreski

Woolly Rhinoceros: Icon of the Last Ice Age

History Collection / Alamy

Woolly Rhinoceros - an ancient herbivore — Woolly Rhinoceros: Icon of the Last Ice Age

History Collection / Alamy

A recently reconstructed genome from a piece of flesh found in the stomach of a wolf pup, dated to 14,400 years ago, reveals that the woolly rhinoceros was genetically robust despite its close proximity to extinction.

While the exact cause of the young female wolf pup’s death, near present-day Tumato in northern Siberia, remains a mystery, it is believed she and her sister, referred to as Tumat puppies, had recently consumed woolly rhinoceros meat (Coelodonta antiquitatis). Their mother inadvertently caused their burial in permafrost when their burrow collapsed.

The first puppy was discovered on-site in 2011, with the second found in 2015. Examination of one puppy’s stomach contents revealed remnants of woolly rhino meat.

Edana Road, a member of the research team at Stockholm University, remarked that the preserved material resembled “fluffy jerky.”

“It was astonishing to see hair still intact,” Lord commented.

Lord stated that the preservation of the tissue was almost miraculous.

“It’s remarkable that, thousands of years later, we retrieved a beautifully preserved mummified wolf pup, analyzed its stomach contents, and uncovered this woolly rhinoceros tissue, shedding light on a previously different species,” Lord adds.

Tumat Wolf Pup: Evidence of Woolly Rhinoceros Diet

Mietje Germonpre

Lord’s team successfully reconstructed the woolly rhinoceros genome, identifying it as a female with no signs of inbreeding.

This groundbreaking finding is significant because it marks the first time DNA has been recovered from a woolly rhinoceros close to the time of its extinction.

The cause behind the woolly rhinoceros’ extinction remains a topic of debate, encompassing the impacts of human hunting, climate change, and inbreeding.

Another researcher on the team, Darren Love, noted that the sample’s hair was yellowish, leading to initial thoughts that it belonged to a cave lion carcass (Panthera spelaea) until DNA analysis was performed.

“As far as I know, sequencing an entire ancient genome from stomach contents has never been accomplished before,” Darren stated.

The research team compared the new genome with two others from the woolly rhinoceros, dating back 18,000 and 49,000 years, discovering no evolution in genetic diversity or inbreeding levels over time.

“Had populations dwindled, we would expect a drop in genetic diversity among woolly rhinoceroses, alongside an increase in inbreeding,” Darren explained.

The researchers concluded that the most probable driver behind the woolly rhinoceros extinction was a rapid climate shift between 14,700 and 12,900 years ago, during the Bølling-Allerød Interstadial, which drastically altered the species’ habitat.

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Source: www.newscientist.com

Scientists Decode 200,000-Year-Old Denisovan Genome: Unraveling Ancient Human Ancestry

Posted on January 2, 2026 by Igor Mitreski

A groundbreaking research team at the Max Planck Institute for Evolutionary Anthropology has successfully generated a high-quality Denisovan genome assembly using ancient DNA extracted from molar teeth found in the Denisovan Cave. This genome, dating back approximately 200,000 years, significantly predates the only previously sequenced Denisovan specimen. The findings are prompting a reevaluation of when and where early human groups interacted, mixed, and migrated throughout Asia.

Artist’s concept of Penghu Denisovans walking under the bright sun during the Pleistocene in Taiwan. Image credit: Cheng-Han Sun.

Dr. Stéphane Peregne, an evolutionary geneticist from the Max Planck Institute for Evolutionary Anthropology, along with his team, recovered this Denisovan genome from molars excavated in the Denisova Cave, located in the Altai Mountains of southern Siberia. This cave is historically significant as it was the site where Denisovans were first discovered in 2010 through DNA analysis of finger bones.

This cave continues to be pivotal in the study of human evolution, revealing repeated occupations by Denisovans, Neanderthals, and even offspring resulting from the interbreeding of these groups.

“The Denisovans were first identified in 2008 based on ancient DNA sourced from Denisova 3, a phalanx found in the Denisova Cave,” Dr. Peregne and his colleagues noted.

“This analysis confirms that Denisovans are closely related to Neanderthals, an extinct human group that thrived in Western Eurasia during the mid-to-late Pleistocene.”

Since then, twelve fragmentary remains and a single skull have been associated with Denisovans through DNA or protein analysis, with Denisova 3 being the only specimen yielding a high-quality genome.

The newly studied molars, belonging to a Denisovan male who lived approximately 200,000 years ago, are predating modern humans’ migration out of Africa.

“In 2020, a complete upper left molar was found in Layer 17, one of the oldest cultural layers within the southern chamber of the Denisova Cave, dating between 200,000 and 170,000 years old based on photostimulated luminescence,” the scientists elaborated.

“Designated as Denisova 25, this molar resembles others found at Denisova Cave, specifically Denisova 4 and Denisova 8, and exhibits larger dimensions compared to Neanderthal and most post-Middle Pleistocene hominid molars, indicating it likely belonged to a Denisovan.”

“Two samples of 2.7 mg and 8.9 mg were extracted by drilling a hole at the cement-enamel junction of the tooth, with an additional 12 subsamples varying from 4.5 to 20.2 mg collected by carefully scraping the outer root layer using a dental drill.”

Thanks to excellent DNA preservation, researchers successfully reconstructed the genome of Denisova 25 with high coverage, matching the quality of the 65,000-year-old female Denisova 3 genome.

Denisovans likely had dark skin, in contrast to the pale Neanderthals. The image depicts a Neanderthal. Image credit: Mauro Cutrona.

Comparisons between the genomes indicate that Denisovans were not a singular, homogeneous population.

Instead, at least two distinct Denisovan groups inhabited the Altai region at various intervals, with one group gradually replacing the other over millennia.

Earlier Denisovans possessed a greater amount of Neanderthal DNA than later populations, suggesting that interbreeding was a regular event rather than an isolated occurrence in the Ice Age landscape of Eurasia.

Even more intriguing, the study uncovered evidence that Denisovans engaged in interbreeding with “hyperarchaic” hominin groups that diverged from the human lineage before the ancestors of Denisovans, Neanderthals, and modern humans branched off.

“This second Denisovan genome illustrates the recurrent admixture between Neanderthals and Denisovans in the Altai region, suggesting these mixed populations were eventually supplanted by Denisovans from other regions, reinforcing the notion that Denisovans were widespread and that populations in the Altai may have existed at the periphery of their geographic range,” the researchers explained.

The Denisovan 25 genome presents valuable insights into the long-standing mysteries regarding the Denisovan ancestry in contemporary populations.

People in Oceania, parts of South Asia, and East Asia all carry Denisovan DNA, albeit from different Denisovan sources.

Through genetic comparison, scientists have identified at least three separate Denisovan origins, highlighted by their genetic segments found in thousands of modern genomes.

One lineage closely relates to the later Denisovan genome and is linked to widespread ancestry across East Asia and beyond.

A second, more distantly related Denisovan population contributed independently to Oceanian and South Asian ancestry.

Notably, East Asians do not share this highly divergent Denisovan ancestry, implying their ancestors may have taken a different route into Asia, potentially from the north, whereas Oceanian ancestors likely migrated through South Asia.

“Neanderthal-like DNA fragments appear in all populations, including Oceanians, aligning with a singular out-of-Africa migration; however, the distinct Denisovan gene flow points to multiple migrations into Asia,” the researchers stated.

Reconstruction of a young Denisovan woman based on skeletal profiles derived from ancient DNA methylation maps. Image credit: Maayan Harel.

The researchers believe certain Denisovan genetic traits offered advantages that increased their prevalence in modern human populations through the process of natural selection.

By analyzing both Denisovan genomes, the authors pinpointed numerous regions in present-day populations that appear to have originated from Denisovan introgression, particularly in Oceania and South Asia.

Genetic alterations observed in other Denisovans provide intriguing insights into their physical appearances.

Several unique mutations in Denisovans influence genes connected to cranial shape, jaw protrusion, and facial characteristics—attributes that align with the limited fossil record associated with Denisovans.

A shift in regulatory mechanisms is on the horizon. The Fox P2 gene, implicated in brain development and language in modern humans, raises important questions regarding the cognitive capabilities of Denisovans, although researchers emphasize that genetic data cannot replace direct fossil or archaeological evidence.

“The impact of Denisovan alleles on modern human phenotypes might also shed light on Denisovan biology,” the researchers pointed out.

“Examining alleles linked to contemporary human traits, we identified 16 associations with 11 Denisovan alleles, covering aspects like height, blood pressure, cholesterol levels, and C-reactive protein levels.”

“Additionally, we recognized 305 expressed quantitative trait loci (QTL) and 117 alternative splicing QTLs that affect gene expression across 19 tissues in modern humans, with the most significant effects observable in the thyroid, tibial artery, testis, and muscle tissues.”

“These molecular effects can be utilized to explore additional phenotypes that are not retained in the fossil record. This updated catalog provides a more reliable foundation for investigating Denisovan traits, adaptations, and disease susceptibilities, some of which may have influenced modern humans through admixture.”

A Preprint of the team’s research paper was published in bioRxiv.org on October 20, 2025.

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Stephane Peregne et al. 2025. High coverage genome of Denisovans from 200,000 years ago. BioRxiv doi: 10.1101/2025.10.20.683404

Source: www.sci.news

Scientists Uncover the Genome Sequence of the Vampire Squid

Posted on November 29, 2025 by

The genome of the vampire squid (Vampirotutis sp.) is among the largest of any animal, containing over 10 billion base pairs.

The vampire squid (Vampirotutis sp.) is among the deep sea’s most enigmatic creatures. Image credit: Steven Haddock/MBARI.

The vampire squid, often referred to as a “living fossil,” inhabits ocean basins worldwide at depths ranging from 500 to 3,000 meters.

This creature is soft-bodied and has a size, shape, and color reminiscent of a football.

It features a dark red body, large blue eyes, and cloak-like webbing connecting its eight arms.

When threatened, the squid can turn itself inside out, displaying rows of menacing “siri.”

In contrast to other squid species that reproduce in a single event later in life, vampire squids exhibit signs of multiple reproductive cycles.

“Modern cephalopods, including squids, octopuses, and cuttlefish, diverged into two main lineages over 300 million years ago: the 10-armed Decapoda (cuttlefish and cuttlefish) and the eight-armed Octopoda (octopuses and vampire squids),” explained biologist Masaaki Yoshida from Shimane University and his team.

“Despite its name, the vampire squid has eight arms similar to those of an octopus, yet it shares significant genomic characteristics with cuttlefish and cuttlefish.”

“It occupies a unique position between these two lineages, and for the first time, its relationship has been revealed at the chromosomal level through genome analysis.”

“Although classified within the octopus lineage, it retains features of a more ancestral squid-like chromosomal structure, shedding light on the evolutionary history of early cephalopods.”

A recent study sequenced the genome of a vampire squid from specimens gathered in the Western Pacific Ocean.

“With over 11 billion base pairs, the vampire squid’s genome is nearly four times larger than the human genome and represents the largest cephalopod genome analyzed to date,” the researchers noted.

“Despite its vast size, the chromosomes share a surprisingly conserved structure.”

“Thus, Vampirotutis is termed a ‘living fossil of the genome,’ embodying modern-day descendants of ancient lineages that retain essential features from their evolutionary background.”

The study revealed that while modern octopuses have undergone significant chromosome fusions and alterations during evolution, octopuses have managed to preserve some decapod-like karyotypes.

This conserved genome structure provides fresh insights into how cephalopod lineages branched apart.

“Vampire squids exist right on the boundary between octopuses and squids,” commented Dr. Oleg Simakov, a researcher at the University of Vienna.

“The genome unfolds deep evolutionary narratives about how these distinctly different lineages emerged from a shared ancestor.”

By comparing the vampire squid with other sequenced species, including the pelagic octopus Argonauta hians, scientists could trace the trajectory of chromosomal changes throughout evolution.

“The genome sequence of Argonauta hians reveals, for the first time, a ‘bizarre’ pelagic octopus (paper nautilus) where females have secondarily acquired shell-like calcified structures,” the researchers stated.

“The analysis suggests that early coleoids had a squid-like chromosomal organization that subsequently fused and compacted into the modern octopus genome, a process termed mixed fusion.”

“These irreversible rearrangements may have instigated significant morphological innovations, including weapon specialization and the loss of the outer shell.”

“Although the vampire squid is classified among octopuses, it preserves an older genetic lineage than both groups,” added Dr. Emese Todt, a researcher at the University of Vienna.

“This enables us to study the early phases of cephalopod evolution directly.”

“Our research provides the clearest genetic evidence to date indicating that the common ancestor of octopuses and squids was more squid-like than previously recognized.”

“This study underscores that large-scale chromosomal rearrangements, rather than the emergence of new genes, have primarily driven the extraordinary diversity of modern cephalopods.”

The findings are detailed in a study published in the Journal on November 21, 2025 iscience.

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Masaaki Yoshida et al. 2025. The extensive genome of a vampire squid unveils the derived state of modern octopod karyotypes. iscience 28 (11): 113832; doi: 10.1016/j.isci.2025.113832

Source: www.sci.news

Analyzing Hitler’s Genome Offers No Insight into His Crimes

Posted on November 13, 2025 by

DNA of Adolf Hitler Sequenced for Documentary

Smith Archives/Alamy

Many individuals find it challenging to discuss Adolf Hitler without losing the argument. If you feel the need to sequence Hitler’s DNA to grab attention for your TV program, you’ve likely lost the plot.

Yet, this is precisely what Britain’s Channel 4 has undertaken. The documentary Hitler’s DNA: The Dictator’s Blueprint is set to air this Saturday. While I’m reluctantly preparing to watch it, feel free to skip it.

DNA comes from a piece of cloth soaked in blood, cut from the sofa where Hitler shot himself in 1945 and now housed in a museum in the United States. Although the resulting genome contains gaps due to the sample’s age, the Y chromosome reportedly matches that of a male relative of Hitler, suggesting its authenticity.

If this endeavor had been purely academic, aimed at expanding our knowledge—perhaps to verify if Hitler had a rumored Jewish grandfather (he didn’t, according to DNA)—it might have been acceptable. Instead, we are presented with a sensational two-part documentary claiming this DNA evidence “will change the way we perceive Hitler.”

The issue lies in the implication of genetic determinism, suggesting Hitler was predestined to commit horrific acts due to his genes. While this documentary does not directly assert this claim, it comes perilously close. What else could the phrase “dictator’s blueprint” imply?

This line of reasoning is akin to arguing that cloning Hitler would lead to the emergence of numerous murderers. While ethically we disdain such an experiment, the world contains clones in the form of identical twins sharing the same DNA. Studies on twins have been used to assess the degree to which various traits and conditions arise from genetics instead of the environment.

Now, there are numerous challenges with twin research. It’s impossible to entirely disentangle genetic influences from environmental ones, especially as twins generally grow up in similar surroundings. Nonetheless, the best estimates indicate that the heritability of criminal behavior, which likely aligns closely with that of genocidal dictators, is less than 50%. Thus, there is no basis to expect that most clones of Hitler would be tyrants.

Additionally, our grasp of the human genome remains primitive. We still lack the ability to predict straightforward traits like eye color with absolute certainty, let alone more complex characteristics arising from brain and environmental interactions.

What we can do is identify genetic variations statistically associated with higher risk for conditions like autism. Individuals receive a “polygenic score” for each condition. However, possessing a high polygenic score for autism does not guarantee a diagnosis. This situation arises from various factors, including the importance of environmental influences, potential misleading associations, and incomplete identification of significant variants.

“It is crucial to emphasize that, in their current form, autism polygenic scores have no clinical applicability due to inconsistent associations and restricted generalizability,” as concluded in a recent meta-analysis.

The documentary claims that Hitler’s genome rates exceptionally high for autism, alongside mental health issues such as schizophrenia, bipolar disorder, and antisocial behavior or psychopathy. His ADHD score is also reported to be above average. However, historical accounts have long suggested that Hitler exhibited such characteristics based on his actions. Genetic data does not yield definitive proof, and established diagnostic criteria do not incorporate genetic information.

More critically, what if he did display these symptoms? Are there alternative explanations for these classifications? As Simon Baron-Cohen from Cambridge University argues in the documentary, the neglect and abuse Hitler faced from his alcoholic father make it “crucial to comprehend why he developed such hatred and anger.”

He further pointed out that traits often linked to schizophrenia might connect with creativity and unconventional thought, possibly accounting for Hitler’s political and military achievements. Is this mere speculation?

For me, this represents the core issue with analyzing Hitler’s genome. We can speculate about potentially valid connections to his personality and behavior, but these could all be entirely incorrect. Moreover, this could worsen the stigma around conditions like autism, schizophrenia, and bipolar disorder.

This documentary undermines its assertions as it largely reiterates established information about Hitler. The main novelty lies in the assertion that Hitler suffered from Kallmann syndrome, a condition affecting sexual development. Yet, this condition’s physical effects are extensive, and there is already documentary evidence suggesting Hitler had undescended testicles. Thus, history proves more enlightening than genetics.

Additionally, the broader question this documentary raises is whether Hitler was uniquely evil or entirely accountable for World War II and the Holocaust. Unfortunately, history reveals that genocidal dictators do not operate in isolation; they need the backing of numerous individuals.

Millions supported Hitler, other politicians enacted laws enabling his rise, and many authorities aided in enforcing the racist legislations that resulted in the Holocaust. We shouldn’t search within our genes for reasons why so many opt to become dictators; the pressing issue lies in why we allow them to do so.

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Source: www.newscientist.com

Scientists Decode the Genome of Oat Bread | Science News

Posted on October 29, 2025 by

Oats (avena sativa) grain are a traditional food rich in dietary fiber, contributing positively to human health. Recent years have seen a rise in interest in oats as they serve as the foundation for plant-based milk alternatives. Unlike many other cereal crops, oat genomic research is still in its early stages, with limited exploration into structural genomic diversity and gene expression variability. Scientists are currently focused on collecting and annotating the genome. An atlas of gene expression across six tissues at various developmental stages in 33 wild and domesticated oat strains is also being developed.

Oats (avena sativa). Image credit: Christian Wynn.

Oats rank as the seventh most cultivated grain globally, esteemed for their high fiber content and notable health benefits.

In 2022 and 2023, global production exceeded 25 million tons.

Advancements in genetically improved varieties hold the promise of enhanced productivity and sustainability in oat farming; however, much of this potential remains untapped, with the first oat reference sequences released only in recent years.

The complexity of the oat genome adds to the slow progress.

“Pangenomes encapsulate the complete genetic diversity of cultivated plants like oats and are essential for our understanding,” remarked lead author Raz Avni, Ph.D., from the Leibniz Institute for Plant Genetics and Crop Research.

“They comprise genes common to all plants and those unique to specific species, providing a kind of roadmap.”

“The pantranscriptome reveals which genes are active across various tissues, such as leaves, roots, and seeds, and at different developmental stages. It serves as a gene expression atlas.”

“However, deciphering how genetic variations influence traits in individual plants poses a challenge, particularly in oats.”

“The oat genome’s complexity arises from its hexaploid nature, having six sets of chromosomes from three ancestral sources.”

During their study, the authors sequenced and analyzed the genomes of 33 oat lines, including cultivated varieties and related wild types.

They also constructed an oat pan transcriptome by scrutinizing gene expression in six tissues across various developmental stages in 23 of these oat lines.

The research aimed to identify structural changes, such as chromosome inversions and translocations.

“Our pangenome illustrates the extensive genetic diversity present in oats,” stated Dr. Avni.

“This insight aids in identifying key genes associated with yield, adaptation, and health.”

The researchers uncovered intriguing findings during their study.

“For instance, we observed the loss of many genes in one of the three subgenomes,” the team noted.

“Nevertheless, other gene copies seem to compensate for the functions, ensuring the plant’s productivity remains intact.”

“Sequencing the oat pangenome highlights how modern genomic methods can propel foundational research and directly influence health, agriculture, and breeding,” commented lead author Dr. Martin Mascher from Murdoch University’s Leibniz Institute for Plant Genetics and Crop Research.

“We also discovered that structural variations in the genome influence the regulation of flowering time.”

The team’s results are published in the journal Nature.

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R. Avni et al. Pangenome and pantranscriptome of hexaploid oat. Nature, published online October 29, 2025. doi: 10.1038/s41586-025-09676-7

Source: www.sci.news

The World’s Oldest Person Had a Youthful Microbiome and an “Extraordinary Genome.”

Posted on September 24, 2025 by Igor Mitreski

Painted alongside scientist Manel Esterer, Maria Blagnas Morela contributed to research aimed at uncovering her secrets of longevity

Manel Esterler

From January 17, 2023, to August 19, 2024, Maria Blañas Morera from Spain was formally recognized as the oldest person in the world until her passing at the age of 117 years and 168 days. To investigate the secrets behind her remarkable longevity, a team of researchers explored her genetics, microbiome, and lifestyle.

When Morera was 116, the researchers gathered samples of her blood, saliva, and stool for genetic analysis. “Her genome was exceptional, enriched with variants known to extend lifespans in other species such as dogs, worms, and flies,” noted team member Manel Esterler at the Josep Carreras Leukemia Research Institute in Barcelona, Spain.

Showing no signs of dementia, Morera also possessed numerous genetic variants that helped maintain low blood lipid levels, protecting her heart and cognitive functions, according to Esteller. “Simultaneously, she lacked genetic mutations linked to conditions such as cancer, Alzheimer’s disease, or metabolic disorders.”

The researchers discovered that her lipid metabolism was one of the most efficient recorded. “Her lipid profile was remarkable, with very low cholesterol,” Esterer mentioned. “This efficiency was tied to her modest diet and genetic traits that enabled the rapid metabolism of damaged molecules.”

Esteller noted that Morela abstained from alcohol and smoking and adhered to a Mediterranean diet comprising vegetables, fruits, legumes, and olive oil, along with three servings of sugar-free yogurt daily.

Further assessments indicated that Morela maintained a robust immune system typically seen in younger individuals, alongside a gut microbiota characteristic of much younger people.

One of the most “astonishing” findings was a high concentration of Actinobacteriota bacteria in her gut, including well-known probiotics like Bifidobacteria. This abundance typically declines with age but tends to increase among centenarians and supercentenarians, offering various anti-aging benefits, such as reducing inflammation.

The researchers believe that her yogurt intake may have continually replenished her levels of Bifidobacteria. “This may suggest that dietary interventions can be linked to prolonged lifespan by influencing gut microbiota, along with preventing obesity and other health issues,” Esterer added.

Lastly, scientists examined whether there was a significant difference between Morela’s biological age and her chronological age by constructing an epigenetic clock based on her DNA methylation. This process involves adding or removing chemical tags that regulate gene expression. “Her biological age appeared 23 years younger than her actual age, contributing significantly to her longevity,” remarked Esterer.

Previous studies indicate that supercentenarians may carry genetic mutations associated with various medical conditions, such as Alzheimer’s disease and cardiovascular issues. Nevertheless, they somehow manage to overcome these obstacles and attain extraordinary lifespans. “There are limited studies on supercentenarians, and many only focus on one aspect, like microbiomes,” explained Esteller. “Our research demonstrates that overcoming such maladies is a blend of advantageous genetics and other elements, including beneficial gut microbiota, delayed biological aging indicated by a youthful epigenome, and lifestyle factors such as avoiding smoking, alcohol, and maintaining a low-fat diet.”

Richard Farragher from the University of Brighton in the UK acknowledged that the study highlights the plethora of assessments available to longevity researchers, cautioning that a case study of one individual could risk being perceived as a scientific “So-So Story.”

He explains that there are two key reasons behind the survival of extremely long-lived individuals: “First, there’s something extraordinary about them, perhaps genetically, and second, survival biases due to their fortunate circumstances,” said Farragher.

If luck plays a role, he asserts that to substantiate her longevity, Morela belonged to a family with a history of long lifespans that wasn’t documented in the study.

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Source: www.newscientist.com

Insights from the Thylacine Genome Reveal Reasons for Its Extinction

Posted on August 27, 2025 by Igor Mitreski

Thylacines were once found throughout Australia and New Guinea

Robert Nickelsberg/Getty Images

SEI 263374247 — Thylacines were once found throughout Australia and New Guinea

Robert Nickelsberg/Getty Images

The extinction of crucial genes over the millennia since humans arrived in Australia may have made the thylacine more prone to extinction.

The thylacine, also known as the Tasmanian tiger (Thylacinus cynocephalus), was the last remaining member of a marsupial family called Thylacinidae, which once thrived in Australia and New Guinea.

It became extinct on mainland Australia around 2000 years ago, primarily due to human hunting and competition with dingoes. After European settlers arrived in Tasmania, the animal was targeted by farmers and government bounties, leading to the last of its kind dying in 1936 at Hobart Zoo.

Nagarjun Vijay and Buddha Bhashan Gilish Salv from the Institute of Science and Education in Bhopal, India, grew fascinated by the Tasmanian tiger’s genome while studying that of the Bengal tiger (Panthera tigris tigris).

“We noticed some parallels between the extinction of thylacines and our own tiger,” Vijay notes. “There’s a significant push to protect Indian tigers.”

The duo theorized that hypercarnivores like the Bengal and Tasmanian tigers may have lost vital genes through their evolutionary journey in response to environmental shifts and emerging diseases.

They examined genetic data previously obtained from thylacine specimens and compared these to the genome of the Tasmanian devil, a close relative (Sarcophilus harrisii), along with other marsupials.

Unlike nearly all other marsupials, including the Tasmanian devil, the thylacine has lost at least four crucial genes: SAMD9L, HSD17B13, CUZD1, and VWA7.

Vijay found it surprising that this genetic loss did not occur after Tasmania’s populace was isolated due to rising sea levels roughly 10,000 years ago.

This genetic loss may have been beneficial under certain historical conditions, but can hinder species health by diminishing antiviral defense, metabolic functions, lactation, as well as increasing susceptibility to cancer and pancreatitis.

Thylacines lost SAMD9L, CUZD1, and VWA7 at least 6 million years ago, coinciding with a significant climatic transition when species sizes increased dramatically, resulting in an oversaturation of carnivores entirely dependent on meat.

“The overarching narrative is that much of the human influence, or artificial changes, has perpetually shaped the extinction of thylacines,” Vijay states. “We speculated that there would be lost genes linked to disease, and that’s exactly what we uncovered.”

Timothy Churchill from the University of New South Wales in Sydney emphasizes that climate change over the course of human history has indeed led to a drastic decrease in genetic diversity among thylacines. He believes that the genetic losses identified in the new study may have rendered the Tasmanian tigers more vulnerable to illnesses, though confirming this requires additional research.

“It’s one of those species that truly survived against the odds for an extended period in that niche,” Churchill explains. “But once dingo-like canids arrived, it was the beginning of the end on the mainland. Then, of course, after creating adversaries in Tasmania, it marked their doom.”

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Source: www.newscientist.com

Scientists Unlock the Genome of Sweet Potatoes

Posted on August 13, 2025 by Igor Mitreski

Researchers have successfully created a chromosomal-level genomic assembly of a sweet potato cultivar known as “Tanzania.”

“Tanzania” sweet potato variety. Image credit: Benard Yada from the National Crop Resources Institute in Uganda.

The sweet potato is a crucial global staple crop that supports millions of people, particularly in sub-Saharan Africa. Its inherent resilience to harsh climates significantly contributes to food security.

Despite its importance, this humble root vegetable has hidden its genetic complexities for many years.

Sweet potato DNA is exceptionally intricate. While humans have two sets of chromosomes from each parent, sweet potatoes possess six sets.

This phenomenon, known as Hexaploidy, involves deciphering genetic codes that aim to piece together a set of six distinct, albeit similar, encyclopedias mixed together.

Utilizing advanced DNA sequencing and other state-of-the-art technologies, Professor Zhangjun Fei and his team at the Boyce Thompson Institute have produced the first complete genetic blueprint of “Tanzania,” which is widely appreciated in Africa for its stress tolerance and high dry matter content.

The key challenge was organizing the 90 chromosomes of the plant into six original sets known as haplotypes.

The researchers succeeded in either completely or incrementally separating this intricate genetic puzzle.

“Having this complete gradual genome provides an unprecedented level of clarity,” Professor Fei noted.

“This allows us to explore remarkable details of the sweet potato’s genetic narrative.”

The research team found that the sweet potato genome is a mosaic formed from various wild ancestors, some of which remain unidentified.

Approximately one-third of the genome is derived from ipomoea aequatoriensis, a wild species from Ecuador believed to be a direct progenitor of sweet potato cells.

Another significant portion is similar to the wild species of Central America, Ipomoea batatas 4x, though actual wild donors have yet to be discovered.

Dr. Shan Wu, a researcher at the Boyce Thompson Institute, stated:

“In sweet potatoes, ancestral sequences are intermixed within the same chromosome, resulting in a unique genomic structure.”

This complex genetic heritage suggests that sweet potatoes can be tentatively classified as segmented allopolyploids—hybrids that effectively function as though derived from a single species while originating from different ones.

This genomic merging and recombination grant sweet potatoes exceptional adaptability and disease resistance, essential for subsistence farmers globally.

“The six sets of chromosomes in sweet potatoes also contribute to their resilience,” Professor Fei added.

“With multiple versions of key genes, these plants can retain backup copies that assist them in surviving droughts, resisting pests, and adapting to diverse environments. This phenomenon is referred to as the polyploid buffer.”

“However, to fully comprehend the genetic capabilities of sweet potatoes, we need to decode multiple varieties from various regions, as each can possess unique genetic traits absent in others.”

Survey results were published this month in the journal Nature Plants.

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S. Woo et al. Gradual chromosomal level assembly provides insight into the genomic architecture of hexaploid sweet potatoes. Nature Plants Published online August 8, 2025. doi:10.1038/s41477-025-02079-6

Source: www.sci.news

The E. coli Genome Redesigned with 101,000 DNA Modifications

Posted on August 1, 2025 by Igor Mitreski

E. coli can lead to serious illnesses, yet is frequently utilized in pharmaceutical development.

Victor Habbick Visions/Science Photo Library

Unlike the natural evolution of life forms, our ability to create life has reached new heights. The genome of an E. coli bacterium has been meticulously redesigned via computer simulations, utilizing just 57 out of the 64 genetic codons. This synthetic genome was built from the ground up and introduced into living bacterial cells.

“This was a massive undertaking,” states Wesley Robertson from the Institute of Medical Research in Molecular Biology, Cambridge, UK.

The objective was to demonstrate the feasibility of this approach, with the 57 codons, termed Syn57, offering commercial applications. Future modifications could enable Syn57 to develop complete resistance to viral infections, a significant benefit for the industrial production of proteins used in pharmaceuticals, food, or cosmetics. Since viral proteins depend on their hosts to produce, altering the genetic code can lead to erroneous viral proteins.

Moreover, additional modifications permit Syn57 to synthesize proteins containing up to 27 amino acids, whereas natural proteins are limited to 20. These synthetic proteins hold potential for functions unattainable with conventional proteins.

A protein is essentially a sequence of amino acids arranged in a specified order determined by a gene. Each triplet of DNA bases, known as a codon, instructs the synthesis machinery on when to add the next amino acid or when to cease the protein assembly.

There are four DNA bases that combine to produce 64 distinct codons. However, organisms on Earth typically utilize only 20 amino acids, leading to considerable redundancy, with multiple codons corresponding to each amino acid.

If all instances of a specific codon for an amino acid were substituted with another codon for the same amino acid, that original codon could then be repurposed. For instance, it could code for non-natural amino acids or alternative chemicals, facilitating the creation of novel protein types.

Theoretically, only 21 unique codons are required, allowing for a biological organism to free up to 43 codons—one for each natural amino acid and one stop codon. However, this is not yet feasible, as increasing genetic alterations raises the likelihood of harmful unintended consequences.

Instead, biologists are taking a more measured approach. In 2011, an edit of 314 genes in E. coli aimed to free one codon.

Because executing thousands of genetic edits is so labor-intensive, Robertson and his team opted to synthesize the DNA from scratch. In 2019, they introduced Syn61, incorporating 18,000 changes across 4 million DNA bases, achieving the release of three codons in the E. coli genome. A derivative company named Constructive.Bio is working on commercial applications.

Currently, researchers are implementing 101,000 modifications to release seven codons within Syn57. This process necessitated testing small sections of the reconstructed genome on live bacterial cultures to identify and rectify harmful changes. This complex procedure was repeated with progressively larger genome fragments until the entire structure was reassembled.

“This marks a significant achievement, resulting from years of effort,” mentions Akos Nyerges at Harvard Medical School. Nyerges’ team is also working to release seven codons in E. coli via different codon reproductions. “Our journey with the 57 codons in E. coli is ongoing,” he adds.

While Syn57 is already fully established, its growth rate is significantly slower than that of typical strains. Enhancements in this aspect are essential for commercial viability. “We anticipate being able to improve the growth rates, making it more beneficial,” remarks Robertson.

For the time being, his focus will be on investigating the potential applications of Syn57 rather than attempting further codon releases. “There’s still a great deal to accomplish before contemplating even more compressed genetic codes,” he concludes.

The first synthetic genome bacteria were created in 2010, but their design aimed more at simplifying organisms than at codon recovery.

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Source: www.newscientist.com

Researchers Decipher the Complete Genome of Ancient Egypt

Posted on July 3, 2025 by Igor Mitreski

A global consortium of researchers has successfully sequenced the complete genome of adult male Egyptians from over four millennia ago, predating the unification of Egypt and enriching our understanding of the early dynastic period and prior kingdoms.

The Nevamun hunt in the swamp with his wife and daughter is part of a mural from Chapelle, the tomb of Nevamun in the New Kingdom, in 1350 BC. Image credit: Werner Forman Archive/Bridgeman Images.

Dr. Pontus Skoglund from the Francis Crick Institute stated:

“While Ancient Egypt offers a rich tapestry of history and archaeology, the challenges of DNA preservation have rendered the genomic records of early Egyptian ancestors largely unparalleled.”

“Recent advances in genetic technology have enabled us to transcend these barriers and mitigate DNA contamination, giving us the first genetic insights into potential migrations of Egyptian populations during this era.”

In this research, scientists obtained and sequenced DNA from individual teeth belonging to Nuway rats from a village located 265 km south of Cairo.

Through analysis of the genetic code, they discovered that a significant portion of the individual’s ancestry traced back to ancient populations in North Africa.

The remaining 20% of ancestry linked to ancient peoples from the fertile crescent, particularly from a region known as Mesopotamia (roughly corresponding to modern Iraq).

These findings provide genetic proof that populations migrated to Egypt, intermingling with the local populace—previously revealed only through archaeological artifacts.

However, researchers caution that additional genomic sequences are required to fully comprehend the variations among Egyptian ancestors during this period.

By examining the chemical markers found in teeth related to diet and environmental factors, they concluded that these individuals likely grew up in Egypt.

They also analyzed skeletal remains to estimate age, gender, height, and gather insights into their ancestry and way of life.

These markers indicated that the skeleton exhibited muscle markings suggestive of prolonged occupations, such as pottery or other trades requiring similar movements.

“By piecing together the evidence from this individual’s DNA, bones, and teeth, we were able to construct a detailed portrait,” remarked Dr. Adeline Mores Jacobs from Liverpool John Moores University.

“We anticipate that future DNA samples from ancient Egypt will enhance our understanding of this migration from West Asia.”

“This individual’s life story is remarkable,” noted Dr. Linus Girdland Flink, co-author from Liverpool John Moores University.

“He lived and died during a pivotal moment in ancient Egypt, with his skeleton excavated in 1902 and subsequently donated to the World Museum in Liverpool.”

“We are beginning to uncover this individual’s story, revealing ancestral connections to the fertile crescent and illustrating the intermingling of diverse groups during this time.”

“The skeletal markings provide significant clues about his personal life and lifestyle. His pelvic bones are enlarged, showing extensive activity, and his arms exhibit signs of repetitive motion, while his right foot displays notable arthritis.”

“These findings suggest a connection to ceramics, possibly involving the use of ceramic wheels in ancient Egypt.”

“Nonetheless, the elevated burial status associated with his remains is not typically expected for potters, indicating he may have achieved a higher social standing.”

study published in the journal Nature.

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A. Mores Jacobs et al. The genomes of the ancestors of the Old Kingdom Egyptians. Nature, published on July 2, 2025. doi:10.1038/s41586-025-09195-5

Source: www.sci.news

The Entire Genome of Ancient Egypt Has Been Deciphered

Posted on July 2, 2025 by Igor Mitreski

Fresco from the Theban Necropolis showcasing an ancient Egyptian potter

DeAgostini/Getty Images

In a groundbreaking discovery, researchers sequenced the complete genome of an ancient Egyptian individual for the first time. The DNA was sourced from the remains of an elderly man, possibly a potter, who lived over 4,500 years ago.

The analysis revealed that this ancient Egyptian had inherited roughly 20% of his DNA from ancestors residing in the fertile crescent, situated more than 1,000 kilometers east of Egypt. This indicates a connection between Egyptian and Mesopotamian cultures, despite the considerable distance.

The remains were unearthed in the early 1900s from Nuweyrat, a necropolis located near Beni Hasan, Egypt. They were discovered within a ceramic vessel placed in the tomb of Iwage. Currently, these remains are housed at the World Museum in Liverpool, England.

“We successfully dated this individual’s remains using radiocarbon analysis,” states Adeline Morez Jacobs from Liverpool John Moore University. He lived between 2855 and 2570 BC, making him one of the earliest individuals from ancient Egypt, whose history spans from 3150 to 30 BC.

Both the skeleton and DNA confirm that the individual was male. Signs of arthritis and other physical indicators suggest he was between 44 and 64 years old. “He was likely in his 60s at the time of death, which is quite advanced for that period,” says Joel Eilish at Liverpool John Moore University.

The man’s social status remains uncertain. “He might have been buried in a manner associated with the upper class,” observes Ireland. However, his skeletal structure indicates a struggle with physical activity. Evidence suggests he frequently looked down or leaned forward, and that he sat on hard surfaces for extended periods. Researchers speculate that his probable profession was as a potter, based on preserved representations of various ancient Egyptian occupations.

Using samples collected from his tooth roots, the team was able to sequence the entire male genome. Previously, only partial genomes from three ancient Egyptians who lived in the region over 1,000 years ago had been achieved.

“There are few genetic sequences available from ancient Egypt,” remarks Shirly Ben-Dor Evian from Haifa University, Israel.

This scarcity is largely attributed to the warm climate, which accelerates DNA degradation. “The conditions are simply too hot,” avers team member Pontus Skoglund from the Francis Crick Institute in London, referring to the sequence as a ‘long shot.’

“We speculated that pot burials would create a stable environment, complementing the rock-cut tombs where these burials occurred,” explains Linus Girdland-Flink from the University of Aberdeen, UK.

As expected, around 80% of the genetic lineage of this male individual corresponds to North African ancestry. However, the remaining 20% aligns with populations from the fertile crescent covering parts of modern-day Iraq, western Iran, Syria, and Turkey.

There are multiple theories regarding this finding, according to Ben-Dor Evian. “Explorers often speculate about these connections,” she comments. Even after agriculture became prevalent, “there always existed a segment of the population that remained nomadic or semi-nomadic,” which may account for DNA migration between the fertile crescent and Egypt.

Archaeological evidence has previously indicated a link between ancient Egypt and Mesopotamia. “A significant cultural connection existed between the two, sharing artistic motifs,” states Ireland, noting that items like Lapis Lazuli were traded between the regions.

This connection might also have influenced the inception of writing systems. “Initial writing appeared almost simultaneously in both areas,” he explains, “with the development of Mesopotamian and Egyptian hieroglyphics taking place just 300 years apart.”

“Was it a local invention originating in both regions? [or] Did they influence each other in some manner?” queries Ben-Dor Evian. “This theory could suggest interaction through the movement of individuals.”

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Source: www.newscientist.com

A Silent Virus Rapidly Alters Our Genome and Enhances Its Growth

Posted on June 19, 2025 by Igor Mitreski

Human DNA within cells in its natural state (left) contrasted with its state eight hours after cold sore virus infection (right)

Esther Gonzalez Almera and Alvaro Castells Garcia

Viruses that typically cause herpes can reform their genome within an hour following infection, potentially allowing scientists to address severe cases more effectively.

Billions globally are infected by Herpes Simplex Virus Type 1 (HSV-1), often without their knowledge. Transmission occurs via contact with infected saliva or skin around the mouth.

Upon invading a host cell, the virus replicates within the nucleus, where genetic material is preserved among the strands of DNA. These strands surround proteins, with some sections tightly coiling to deactivate genes while others form looser loops where genes remain active. In these less dense areas, proteins can transcribe DNA into messenger RNA, encoding for a protein essential for cellular function.

Prior research has indicated that the human genome becomes more tightly coiled following HSV-1 infection, possibly disrupting cellular functions, although the cause of this coiling was previously uncertain.

For further details, consult Alvaro Castells-Garcia at the genome regulatory center in Barcelona, Spain, whose team employs advanced microscopy to investigate HSV-1, infecting human lung cells and observing structures that are 3,500 times thinner than a hair. “This offers a higher resolution than most prior studies,” notes Castells-Garcia.

They discovered that within an hour post-infection, transcription factors were already pilfered from the human genome, corroborating previous findings.

Moreover, this thievery is what appears to cause the host’s DNA to coil more tightly, compressing it to 30% of its volume within 8 hours of infection.

The virus also interacts with specific areas of the host genome that encode the stolen transcription factors, inhibiting activity in those regions and enhancing the expression of genes that facilitate its own growth.

“Previously, I thought the virus made random contacts with the genome,” comments team member Esther Gonzalez Almera at the genome regulation center. “However, it’s clear that viruses specifically target certain regions of their genome, which often contain genes critical to sustaining the infection and producing viral RNA and proteins.”

In another segment of the study, researchers found that utilizing experimental cancer treatments to obstruct one of the transcription factors taken by HSV-1 inhibited its replication in human lung cells in the laboratory. This suggests that such medications could assist in treating HSV-1 in individuals suffering from severe herpes outbreaks and those at higher risk for complications, as González-Almela explains. Mild cases typically resolve without intervention.

This treatment may also be effective against other pathogens, such as adenoviruses that lead to colds, and noroviruses associated with gastroenteritis. “Other viruses similar to HSV-1 may employ analogous strategies,” states Benjamin Krishna from Cambridge University. “These could represent [potential types of experimental drugs] for addressing such cases as well,” he adds.

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Source: www.newscientist.com

Genome Sequencing by BlackBerry Researchers

Posted on April 30, 2025 by Igor Mitreski

Researchers at the University of Florida have successfully generated a chromosomal-scale genomic assembly for the spinless tetraploid blackberry BL1, which is primocanfluting. Their findings are expected to serve as crucial resources for accelerating genetic analysis in blackberries and fostering the development of new, enhanced varieties that improve horticultural and nutritional attributes.

blackberries. Image credit: Lin Animalart.

Blackberries belong to the genus Rubus, subgenus Rubus (formerly subgenus Eubatus) within the Rose family.

These fruits are noted for their rich dark purple to deep black colors, complex fruit structures, and a delightful balance of tartness and sweetness.

Blackberry fruits are a significant source of anthocyanins, antioxidants, and dietary fiber, offering numerous health benefits to consumers.

In the last two decades, a surge in consumer interest has greatly expanded the market for fresh and processed blackberries in the United States and internationally.

As the fourth most economically significant berry crop in the U.S., the nation produced 16,850 metric tons of processed blackberries and 1,360 tons of fresh blackberries in 2017.

In 2021, the U.S. imported 122,873 metric tons of fresh blackberries and 16,738 tons of frozen blackberries, valued at $519 million and $43 million, respectively.

Global blackberry production is estimated to exceed 900,000 metric tons, playing a crucial role in the international berry market.

The ongoing development and introduction of improved varieties continue to drive consumer demand and enhance blackberry production worldwide.

“This new research not only deepens our understanding of blackberry genetics but also lays the groundwork for significant advancements in blackberry breeding techniques,” says Dr. Zhanao Deng, PhD, in the journal Horticulture Research.

“The ultimate goal is to create a superior, more resilient blackberry variety that benefits both growers and consumers globally.”

Utilizing a comprehensive collection of DNA sequences from the experimental BlackBerry BL1, Dr. Deng and his team meticulously calculated and reconstructed the original sequences across the blackberry genome.

It begins with recognizing that BL1 is a tetraploid fruit, which derives from a plant possessing four copies of each chromosome within its cells.

This characteristic results in twice as many chromosomes compared to typical diploid plants such as raspberries.

“Working with tetraploids is more complex than with diploids,” Dr. Deng remarked.

“The release of the tetraploid blackberry genome can facilitate more efficient and targeted breeding, ultimately enhancing fruit quality and leading to the creation of new varieties resilient to critical diseases.”

“The reference genome derived from this study will serve as a powerful tool for researchers working with blackberries.”

The genome assembly also unlocks insights into key traits such as the cultivation of spinless blackberry plants and the processes behind anthocyanin production, which influences the color and health benefits of the fruit.

“This discovery helps us understand why blackberries attain their distinctive deep purple/black hues over time and how we might potentially improve this process for more nutritious berries,” Dr. Deng added.

The team’s research is published in the journal Horticultural Research.

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Dev Paudel et al. 2025. Chromosomal scale and haplotype-resolved genome assembly of tetraploid blackberries (Rubus L. subgenus Rubus Watson). Horticultural Research 12 (6): UHAF052; doi: 10.1093/hr/uhaf052

Source: www.sci.news

New Genome Study Unveils the Evolution and Diversity of the Apple Genus

Posted on April 26, 2025 by Igor Mitreski

Malus is a genus comprising over 35 species that thrive in the temperate Northern Hemisphere, spanning regions from East Asia to Europe and North America. This genus includes the cultivated apple, Malus domestica, along with its wild relatives. Recent research has unveiled the evolutionary connections among Malus species and traced their genetic development over the past 60 million years.

Malus evolutionary landscape informed by phylogenetics. Image credits: Li et al., doi: 10.1038/s41588-025-02166-6.

“There are around 35 species within the Malus genus; however, despite the significance of apples as a fruit crop, comprehensive research on the evolution of this group’s genome has been lacking.”

“This study provided insights into the Malus genome, established the apple family tree, documented genomic events including whole-genome overlap and hybridization among species, and identified genomic regions linked to specific traits, such as resistance to apple scab disease.”

Professor Ma and his team compiled the genomes of 30 species by sequencing their DNA, focusing on the Malus genus known for its delicious golden apple varieties.

Among the 30 species, 20 are diploid, meaning they possess two chromosome copies per set, similar to humans, while 10 are polyploid, indicating they have three or four chromosome copies, likely resulting from recent hybridization with diploid relatives of Malus.

By scrutinizing nearly 1,000 gene sequences across these species, researchers constructed a phylogenetic tree for the genus and employed biogeographical analysis to trace its origins back to Asia approximately 56 million years ago.

“The evolutionary narrative of the genus is intricate, showcasing numerous instances of hybridization among species and shared whole-genome events that complicate comparisons,” stated Professor Ma.

“Access to high-quality genomes for a large number of species within the genus has enabled us to explore how Malus evolved and the interrelationships among these species.”

Further research into the evolutionary history of Malus genomes utilized analytical techniques called pan-genomics.

This methodology encompasses a thorough comparison of conserved genes and so-called ‘jumping genes’ that can move within the genome across the 30 species, along with genes found only in a subset of the genomes.

The analysis of pan-gene dynamics benefited greatly from the use of a pangenome graph tool, which amalgamates genomic data from closely related groups to elucidate evolutionary conservation and divergence.

“Utilizing 30 pangenomes significantly aided in identifying structural variations, gene duplications, and rearrangements among species that could have been missed with fewer genome comparisons,” remarked Professor Ma.

“Notably, one structural variant uncovered allowed us to pinpoint genomic segments related to apple scab resistance, a fungal disease impacting apples globally.”

The researchers also developed a pangenome analysis tool designed to detect evidence of selective sweeps, a process whereby advantageous traits rapidly increase in frequency within a population.

With this approach, they pinpointed genomic regions linked to cold and disease resistance in wild Malus species, which might also correlate with undesirable fruit taste.

“Attempts to cultivate the best flavor in fruit may have inadvertently diminished the hardiness of cultivated apple varieties,” noted Professor Ma.

Understanding structural variations in Malus, including hybridization histories, interspecies relationships, and pangenomic insights can inform future breeding strategies aimed at retaining both flavor and disease-resistant traits in apples.

Research findings published in the journal Nature Genetics.

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W. Li et al. Pangenome analysis reveals evolution and diversity in Malus. Nat Genet. Published online on April 16th, 2025. doi:10.1038/s41588-025-02166-6

Source: www.sci.news

Pistachio Genome Sequenced by Scientists

Posted on March 23, 2025 by Igor Mitreski

Researcher of University of California, Davis We generated the chromosomal scale reference genome of the most widely grown pistachio variety, “Kerman.”

pistachio(Pistasia Bella) A sustainable nut crop with exceptional climate resilience and nutritional value. Image credit: NONAME_13.

pistachio(Pistasia Bella)) Along with cashews and mangoes, it belongs to the family of the Anacardia family and is the only species of the genus. Pistasia It is grown for edible fruits.

Although commonly known as nuts, pistachio fruit is a plant-based heat-deficient collision consisting of leathery exomesocarps, inner stone inner membrane (shell), and edible seeds (kanel).

Pistachios are rich in unsaturated fatty acids, antioxidants and vitamins.

Given the highly resilient resilience to abiotic stress, particularly drought and salt, pistachio trees are predicted to be an important source of sustainable nutrition in the face of next-generation climate change, with global production of pistachios more than doubled in the past 20 years.

“Scientists have previously sequenced pistachio DNA, but the new genetic maps are very detailed and accurate,” says Dr. J. Greymonroe, a researcher at the University of California, Davis.

“Improved accuracy of the new reference genome is like moving from hand-drawn maps of the landscape to satellite images from Google Earth.”

The authors also identified four important stages of nut growth from flower to harvest, providing a complete physiological assessment, including shell hardening and kernel growth.

“Knowing how nuts change through development will help farmers make better decisions, such as when to water the trees, leading to more sustainable pistachio production,” said Dr. Bárbara Blanco-lute, University of California, Davis.

“A more accurate assessment of its development will also provide growers with a better strategy for harvesting and help avoid problems such as insect damage and fungal infections.

“It was important to detail not only the physical changes in pistachios, but also the genetic and molecular drivers of those properties.”

“Genome sequencing contains precedent configuration information on how different genes behave in nuts over the growing season.”

Researchers also identified genes and pathways that affect the nutritional value of pistachios.

This includes insight into how proteins and unsaturated fatty acids accumulate. This is important for both shelf life and dietary benefits.

“We get information on how all of these nutritional properties can be obtained with pistachios and how they can be improved from a management perspective,” Dr. Blanco Raul said.

Survey results Published in the journal New Botanist.

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Jaclyn A. Adaskaveg et al. In short, the development of the pistachio genome and kernel. New BotanistPublished online on March 19, 2025. doi: 10.1111/nph.70060

Source: www.sci.news

Sequencing the Genome of White Oak Trees: Latest Scientific Discovery

Posted on February 26, 2025 by Igor Mitreski

The scientist is White Oak (Quercus alba), a rich forest tree species in eastern North America of ecological, cultural and economic importance.

Quercus alba Individual sequences of genome assemblies growing at Star Hill Farm in Loretto, Kentucky, USA. Image credit: D. Larson.

“The Oaks are an important member of many ecosystems around the world,” said a researcher at the University of Tennessee. Meg Staton And a colleague.

“In eastern North America, white oak is a keystone species and is one of the most abundant forest trees across its range.”

“In addition to its ecological and cultural importance, white oak has a very economic importance, including many high value material applications and the main species used in barrel styles for the aging of distilled spirits. It's there.”

“However, few studies have addressed the diversity of white oak genomes. The lack of available genetic and genomic resources now creates barriers to fostering understanding of white oak biology and evolutionary history. It's presenting it.”

In their study, the authors sequenced individual genomes of white oak from a forest near Loretto, Kentucky, USA.

They found that this oak species has a high genetic diversity, many of which preceded divergence from other oaks, and likely could affect divergence time estimates .

“The White Oak genome represents a major new resource for studying genome diversity and evolution. Quercus” said Dr. Staton.

“Also, unbiased gene annotations are key to accurately assessing the evolution of R (disease-resistant) genes. Quercus. ”

“Our paper addresses the degree of genetic diversity and population differentiation in white oaks and how gene content and disease resistance genes evolved. Quercus Related species. ”

The authors say that the amount of standing genetic variation and the degree to which the population is regionally adapted will affect the response of white oaks and other oak species to increasingly common heat and drought stress. It points out.

“The details are interesting for those who are invested in the sustainability of White Oak, across economic, ecological and cultural boundaries,” they said.

study Published in the journal New Botanist.

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Drew A. Larson et al. Haplotype-degradated reference genomes Quercus alba It sheds light on the history of orc evolution. New BotanistPublished online on February 11th, 2025. doi: 10.1111/nph.20463

Source: www.sci.news

Ancient modern human genome successfully sequenced

Posted on December 13, 2024 by Igor Mitreski

Scientists sequenced and analyzed the genomes of seven people who lived between 42,000 and 49,000 years ago in Ranis, Germany, and Zlatiks, Czech Republic. As a result, the Ranis and Zlati Kush were linked by distant kinship ties, and that they were part of the same small, isolated group, representing the deepest known split from lineages outside Africa. was shown. The Ranis genome contains a Neanderthal component derived from a single admixture event common to all non-Africans, which the authors date back 45,000 to 49,000 years ago. This means that all non-African ancestors sequenced so far existed in a common population during this time, and further The human remains suggest that they represent a distinct non-African population.

Illustration of the Zlati Kush, who belonged to the same group as the Ranis and had close relationships with two of them. Image credit: Tom Björklund / Max Planck Institute for Evolutionary Anthropology.

Dr. Alev Schumer of the Max Planck Institute for Evolution said, “After modern humans left Africa, they met and interbred with Neanderthals, and as a result, approximately 2 to 3 percent of Neanderthal DNA is present in all areas outside Africa.'' It's in people's genomes.” Anthropology and its colleagues.

“However, little is known about the genetics of Europe's first settlers or the timing of interbreeding between Neanderthals and non-Africans.”

“An important site in Europe is Zlaty Kush in the Czech Republic, where the complete skull of a single individual who lived about 45,000 years ago was discovered and previously genetically analyzed.”

“However, due to the lack of archaeological context, we were unable to link this person to an archaeologically defined group.”

“Ilsenhöhle, located in Ranis, Germany, about 230 km from the nearby site Zlatiks, is known for a particular type of archeology, Rincombi-Ranissian-Jersmanovičian (LRJ), dating back about 45,000 years. ”

“It has long been debated whether the LRJ culture was created by Neanderthals or early modern humans.”

“Although most small bone fragments have been preserved at Ranis, previous research was able to analyze mitochondrial DNA from 13 of these remains, indicating that they belong to modern humans rather than Neanderthals. It turns out.”

“However, because mitochondrial sequences represent only a small portion of genetic information, their relationship to other modern humans has remained a mystery.”

In the new study, the authors analyzed the nuclear genomes of 13 specimens taken from Ranis and found that they represented at least six individuals.

Based on the size of the bones, it was determined that two of the children were infants, and that three were genetically male and three were female.

Interestingly, these individuals included mothers and daughters as well as more distant biological relatives.

The researchers also sequenced more DNA from the female skull found in Zlati Kush, producing a high-quality genome for this individual.

“To our surprise, we discovered that there is a fifth or sixth degree genetic relationship between the two people from Zlati Kush and Ranis,” Dr. Schumer said.

“This means that Zlati Kush is genetically part of an extended family of Ranis and likely created LRJ-type tools as well.”

Of the six Ranis bones, one bone is particularly well preserved, in fact, it is the best preserved modern human bone from the Pleistocene for DNA searches.

This allowed the research team to obtain a high-quality genome from this male individual, called Ranis13.

Together, the Ranis13 and Zlatý kůň genomes represent the oldest high-quality living human genome sequenced to date.

Analyzing genetic variation associated with phenotypic traits, scientists found that Ranis and Zlati Kush individuals carried mutations associated with dark skin and hair color, as well as brown eyes. I did. This reflects the recent African origins of this early European population.

By analyzing parts of the genomes of Ranis and Zlati Kush inherited from the same ancestor, the authors found that their populations consisted of at most a few hundred individuals and were spread over a larger area. We estimate that there is a possibility.

They found no evidence that this small early modern human population contributed to later European or other world populations.

The Zlati Kush/Ranis people coexisted with Neanderthals in Europe, raising the possibility that Neanderthals were among their recent ancestors after they migrated to Europe.

Previous studies of modern humans dating back more than 40,000 years have found evidence of recent admixture between modern humans and Neanderthals.

However, no such evidence for recent Neanderthal admixture was detected in the genomes of Zlati-Kush/Ranis individuals.

Illustration by Zlatý kůň/Ranis group. Image credit: Tom Björklund / Max Planck Institute for Evolutionary Anthropology.

“The fact that no such Neanderthal ancestry remains in Ranis and Zlati Kush, while modern human populations that may have later arrived in Europe inherited such Neanderthal ancestry. is an older Zlati Kush/Ranis lineage This could mean that they entered Europe by a different route or may not have overlapped with the areas inhabited by Neanderthals.''Also Max Planck. said Dr. Kay Pruefer of the Institute for Evolutionary Anthropology.

The Zlati Kush/Ranis population represents the earliest divergence from modern human groups that migrated from Africa and later dispersed across Eurasia.

Despite this early separation, the Neanderthal ancestry of Zlatikush and Ranis derives from the same ancient admixture event that can be detected in all peoples outside Africa today.

By analyzing the length of Neanderthal-contributed segments in the high-coverage Ranis13 genome and using direct radiocarbon dating of this individual, researchers found that this common Neanderthal admixture dates back to 45,000 years ago. It was estimated to be 49,000 years old.

Since all modern non-African populations share this Neanderthal ancestry with the Zlati Kush and Ranis, this means that approximately 45,000 to 49,000 years ago, non-African populations of consistent ancestry still existed. It means you must have done it.

Dr Johannes Kraus, a researcher at the Max Planck Institute for Evolutionary Anthropology, said: “These results provide a deeper understanding of the early pioneers who settled in Europe.”

“They also suggest that the remains of modern humans more than 50,000 years old found outside Africa have interbred with Neanderthals and are part of the general non-African population now found in many parts of the world. This indicates that it may not have been the case.”

of findings Published in today's magazine nature.

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AP Sumer others. The genomes of the earliest modern humans constrain the timing of admixture with Neanderthals. naturepublished online on December 12, 2024. doi: 10.1038/s41586-024-08420-x

This article is adapted from the original release by the Max Planck Institute for Evolutionary Anthropology.

Source: www.sci.news

Shared DNA Mutations Impacting the Genome in Cancer Cells

Posted on December 2, 2024 by Igor Mitreski

The human genome consists of approximately 3 billion DNA base pairs. If these base pairs were letters grouped together on a single line, they would fill more than 6,000 novels, too large to fit in a cell. Instead, some proteins organize and reform DNA into a more functional 3D structure called DNA. chromatin. These proteins regulate how different parts of the genome interact, controlling which genes are activated and which remain silent within each cell. One such protein is CCCTC binding factor or CTCF.

For CTCF to work, it must first bind to a specific spot on the DNA called CTCF. binding site. Scientists report that these CTCF binding sites behave differently in each scenario. Some lose their binding ability due to chemical interactions within the DNA, while others remain stable. Scientists call something stable Persistent CTCF binding site.

Scientists have previously reported that mutations in CTCF binding sites are common in cancer cells and disrupt the normal 3D structure of the genome. However, it was unclear whether these mutations were concentrated at persistence sites or what role they played. Australian researchers sought to understand mutations in persistent CTCF binding sites and how they affect different cancers.

To address these questions, the research team developed a computational tool based on machine learning models. CTCF-INSITE. Their tool uses genetic data and the interactions of organic compounds such as methyl in the genome to predict which CTCF binding sites are likely to persist even as CTCF protein levels decline. Researchers will use this tool to determine which persistent CTCF binding sites across the genome may be particularly vulnerable to mutations and whether these mutations are associated with cancer growth. I mapped it.

Using data from several human cell culture samples, including prostate cancer cells, breast cancer cells, and lung cancer cells, researchers developed a tool that allows them to distinguish between stable and unstable CTCF binding sites. trained. They exploited characteristics such as protein binding strength, the relative location of binding sites within the genome, and how distant regions of DNA interact to produce proteins.

The researchers then looked at mutation data from 12 types of cancer. International Cancer Genome Consortium. To avoid imbalance, we filtered out data entries with too few or too many mutations. Next, we applied CTCF-INSITE. A tool to test whether persistent CTCF binding sites are more likely to mutate in cancer cells than other CTCF binding sites.

They found significantly more mutations in persistent CTCF binding sites in all cancer types examined. This means that there were more mutations at these sites than would be expected by random chance. The researchers noted that the mutations were specific to the CTCF binding site, rather than in parts of the DNA close to it. They also reported that these mutations were more prominent in breast and prostate cancer cells than in other types of cancer.

The researchers also sought to understand whether these mutations alter the 3D structure of the genome. Using experimental techniques such as fluorescence imaging, they examined some of these cancer-specific mutations and found that many of them alter the genome structure and reduce the strength and effectiveness of CTCF binding. It turned out that. They explained that this reduction could affect gene expression in a way that promotes cancer growth.

The researchers emphasized that their findings were not limited to one or two types of cancer, as similar results were found for stomach, lung, prostate, breast and skin cancers. Although the exact mutation patterns vary between cancers, persistent CTCF binding sites were reported to have consistently higher mutations overall.

The researchers concluded that their findings may help other cancer researchers understand similarities in the onset and progression of multiple cancer types. They also proposed that their machine learning tools could provide future researchers with CTCF binding site candidates relevant to experiments investigating undocumented causes of cancer.

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Source: sciworthy.com

Scientists release complete pea genome at chromosomal level

Posted on November 2, 2024 by Igor Mitreski

A research team led by scientists at the John Innes Center sequenced and annotated the chromosome-scale genome assembly. Grass peas (Latilus sativus)is a promising legume crop that is tolerant to a wide range of stress factors and has potential for climate resilient agriculture.

Grass peas (Latilus sativus). Image credit: William Curtis / The Botanical Magazine.

Grass peas are legume crops valued for their resilience in the face of environmental stresses such as drought, flooding, and salinity.

This crop has been cultivated for at least 8,000 years. widely distributed It is cultivated in parts of Europe, Asia, and Africa, but most current cultivation occurs in southern Asia and the highlands of Ethiopia and Eritrea.

Widespread cultivation of peas has been hampered by toxins in the seeds and shoots. The toxin can cause a disease called neurolatyrism, which causes irreversible paralysis in malnourished people.

Another major barrier to improved crop breeding has been the lack of genomic references for the crop.

The availability of new genome sequences means researchers can use gene editing and modern breeding methods to develop grass pea varieties with improved agronomic properties and low or no toxin content. means.

This means that grass peas may be poised to make an important contribution to a more diverse and climate-resilient food system in the future.

“We hope to establish this new genome sequence as a reference genome for grass pea communities, and we are pleased to share this valuable resource for other scientists to use and learn about grass pea.” says researcher Dr. Peter Emrich. Norwich Institute for Sustainable Development and the John Innes Centre.

“As climate shocks increase, this genome allows us to unlock the secrets of grass pea's resilience, further improve this crop for farmers, and inform the development of other crops such as pea. ”

The sugar bean genome sequence, which is nearly twice the size of the human genome, was assembled from scratch and is an improvement on an earlier draft assembly of the active sugar bean line LS007.

Dr Ann Edwards, a researcher at the John Innes Center, said: “As we prepare for a future with even more climate change, we will need crops that can cope with drought, flooding and saltwater inundation.”

“This new genome sequence means we are even closer to adding grass beans to the list of future climate-smart crops.”

“This is a very exciting time to be joining the grass pea research community.”

of findings Published in a magazine scientific data.

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M. Vigroux others. 2024. Chromosome-scale reference genome of Poaceae (Latilus sativus). scientific data 11, 1035; doi: 10.1038/s41597-024-03868-y

Source: www.sci.news

Colossal, the company blamed for endangering species, announces nearly complete possum genome

Posted on October 17, 2024 by Igor Mitreski

The possum, or Tasmanian tiger, became extinct in 1936

huge life science

The genome of the extinct possum has been almost completely sequenced, the company that brought it back from extinction, Colossal, has announced. The group says the genome is more than 99.9 percent complete and that just 45 gaps will soon be filled, but it has not provided any evidence to support that claim.

“It's quite difficult to obtain the complete genome of almost any organism,” says Emilio Marmol Sánchez of the University of Copenhagen, Denmark, whose team first extracted RNA from preserved quolls. For example, the last few holdouts of the human genome have only been fully sequenced in the past few years.

Quosos, also known as Tasmanian tigers, were once carnivorous marsupials found throughout Australia, but by the time European explorers arrived they were restricted to Tasmania. The last known possum died in a zoo in 1936.

The conserved quoll genome is First sequenced in 2017 The tissue used was from a 108-year-old bag of quolls that had been preserved in alcohol. However, this genome was far from complete and had many gaps. Colossal, which is also currently aiming to recreate the woolly mammoth, says it has nearly completed the genome with the help of additional DNA from a 120-year-old tooth.

“While our genome is not as complete as the most complete human genome, we were able to take advantage of some of the same technologies,” said Andrew of the University of Melbourne in Australia, a member of Colossal's scientific advisory board. Pask said.

Completely deciphering the genomes of plants and animals is difficult because they contain large sections of the same sequence that repeat over and over again. Standard techniques for sequencing small segments of DNA at a time do not work for these parts. This is like trying to reconstruct a book from a list of words in the book.

New, long-read techniques can sequence much larger segments of DNA, equivalent to entire pages of a book. However, these methods are not very useful because old DNA is usually split into many small pieces.

“Most ancient samples preserve DNA fragments that are a few dozen or, if we're lucky, a few hundred bases long,” Pask says. “The samples we had access to were so well preserved that we were able to recover DNA fragments several thousand bases long.”

There is no direct way to know how complete it is, given that there are no other possum genomes to compare it to. Instead, Pask says Colossal uses other closely related species in the same family to make this estimate.

But even if the genome were as complete as Colossal thinks and could indeed fill in the remaining gaps, there is currently no feasible way to generate living cells containing this genome. Instead, Colossal plans to genetically modify a living marsupial called a fat-tailed dunnart to resemble a possum.

“This is rather a reproduction of some characteristics,” says Marmol Sánchez. “It would not be an extinct animal, but a very strange and modified version of a modern animal, similar to our image of an extinct animal.”

Colossal announces record 300 gene edits It affects the genome of Dunnart cells growing in culture. So far, the changes have been small, but Pask says the team plans to swap out tens of thousands of base pairs of thylacine DNA in the near future. He says it's not yet clear how much editing will be needed to achieve the company's goal of recreating the sugar glider.

When asked why Colossal did not provide any evidence to support its claims, the company's CEO, Ben Lamb, said that the company's sole focus was eradicating extinction and that the scientific literature He said it was not writing. “We are not an academic lab whose primary focus is papers,” Lamb said. “We will continue to make progress much faster than the process of writing a scientific paper.”

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Source: www.newscientist.com

Spotted Handfish Genome Decoded | Latest Scientific Findings

Posted on October 9, 2024 by Igor Mitreski

team of researchers CSIRO We decoded the genome of Spotted handfish (Brachyonychthys hirsutus)an endangered species of marine fish endemic to Tasmania.

Spotted handfish (Brachyonychthys hirsutus). Image credit: CSIRO.

Brachyonychthys hirsutus It is a rare benthic fish of the handfish family. Brachionidae.

This rare fish is found only in Tasmania's Derwent River estuary and nearby areas. It is usually found at depths of 5 to 10 meters (16 to 33 feet).

It was first officially described in 1804. Brachyonychthys hirsutus have Their highly adapted pectoral fins look like hands and allow them to walk on the ocean floor.

This species' diet includes small shellfish, shrimp, and polychaetes.

Brachyonychthys hirsutus teeth classified as endangered species Listed on the IUCN Red List 2020. Scientists estimate that fewer than 2,000 individuals remain in the wild.

Its rapid decline is thought to be due to historical fishing practices, coastal development, climate change, and the arrival of invasive species.

“Genome sequencing will aid ongoing efforts to increase population numbers and monitor genetic diversity,” said CSIRO researcher Gunjan Pandey.

“Genomes help us understand how organisms work.”

This provides a basis for understanding gene expression in everyday life and provides insight into its evolutionary history.”

“With the genome, we can help detect species, monitor populations, and even estimate the lifespan of fish.”

“This rich genetic information will help inform long-term conservation strategies,” added CSIRO researcher Carly Devine.

“Recognizing that a multidisciplinary approach alongside ecological research is essential for effective conservation of endangered species, conservation measures are being expanded to include genetics.”

“Marine creatures like the spotted handfish are notoriously difficult to handle.”

“DNA is rapidly degraded and contaminated by microorganisms.”

“This makes it very difficult to assemble a pure genome.”

Using a so-called low-input protocol, the research team was able to sequence the complete genome from a small amount of low-quality DNA.

“We are one of only three teams in the world using this protocol,” Dr. Pandey said.

“We customized the entire process, from the lab setup to the bioinformatics software, to sequence high-quality genomes from low-quality DNA.”

“Work that previously took six to 12 months can now be completed in a matter of days. This technology holds great promise for the understanding and conservation of threatened species across Australia and around the world.”

Source: www.sci.news

Neanderthal fossil genome uncovers ancient tribe isolated for centuries

Posted on September 11, 2024 by Igor Mitreski

The jawbone of a Neanderthal known as Thorin, thought to have belonged to an isolated group

Xavier Mus

Genetic analysis of Neanderthal fossils found in France has revealed that they are the remnants of a previously unknown lineage of ancient people that remained extremely isolated for more than 50,000 years, shedding new light on the final stages of the species' existence.

The fossil has been named Thorin, after a character from J.R.R. Tolkien's novels. The HobbitIt was discovered in 2015 in the Mandolin Cave in the Rhône Valley in southern France. Ludovic Slimak Researchers from the Centre for Human Biology and Genomics in Toulouse discovered a few teeth in the soil of the cave, and after nine years of painstaking excavation, they uncovered 31 teeth, a jawbone, part of a skull, and thousands of other bone fragments.

The discovery of so many fossils of Neanderthals, who lived in Eurasia from about 400,000 to 40,000 years ago and are now extinct, is extremely rare and a surprising find in itself.

Even more surprising, even though DNA doesn't normally preserve in warm climates, a fragment of Thorin's tooth yielded his genome, revealing that the fossil was male but solving a mystery that will take years to unravel.

Srimak and his colleagues compared Thorin's genome with those of other Neanderthals and estimated that he lived about 105,000 years ago, but archaeological evidence and isotope analysis of his bones clearly show that Thorin lived no more than 50,000 years ago, making him a “late Neanderthal” from the final stage of Neanderthal existence.

“We have been together for a long time [geneticists] “We were confident that Thorin was indeed an early Neanderthal precisely because his genetic lineage is very distantly related to modern Neanderthals from the same region,” the team said. Tarshika Vimala “On the one hand, archaeologists were convinced he was a late Neanderthal. It took years of work on both sides to arrive at the answer,” said a researcher from the University of Copenhagen.

Eventually, the researchers realized they must have discovered a previously unknown Neanderthal lineage: Thorin was part of a small group that lived between 42,000 and 50,000 years ago. This group was likely a remnant of a much older Neanderthal population that split off from the main Neanderthal population about 105,000 years ago and remained genetically isolated for more than 50,000 years afterwards.

Thorin's bones unearthed in the Mandolin Cave in France

Ludovic Slimak

Thorin's DNA showed no evidence of interbreeding between his lineage and the main Neanderthal population, despite their close proximity. “Thorin was completely different from other Neanderthals,” Slimak says.

This isolation may have made this population particularly vulnerable: “Prolonged isolation and inbreeding can reduce genetic diversity over time, which is detrimental to a population's survival, which in turn can negatively affect its ability to adapt to a changing environment,” Vimala says.

Srimak, Vimala and their colleagues then reanalyzed the genome of another Neanderthal who lived about 43,000 years ago at Les Côtés in France, and found traces in its DNA of a “ghost population” that interbred with another, previously unknown, Neanderthal group about 15,000 to 20,000 years ago.

“This means that there weren't just two populations among late Neanderthals, but possibly three,” says Slimak. Previously, it was thought that all Neanderthals before their extinction were part of a single genetically similar population.

“The evidence from Mandrin Cave is very exciting because it gives us fascinating insights into late Neanderthal populations and their movements.” Emma Pomeroy At Cambridge University.

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Source: www.newscientist.com

New study uncovers common, mysterious I motif structure in human genome DNA

Posted on September 3, 2024 by Igor Mitreski

The so-called i-motif is a knot-like DNA structure that forms in the nuclei of human cells and is thought to provide important genome control. Garvan Institute of Medical Research Other studies have used immunoprecipitation and next-generation sequencing to identify i-motif structures in human DNA.

Peña Martinez othersIn total, we observed 53,000 i-motifs across three human cell lines (MCF7, U2OS, and HEK293T). Image courtesy of Peña Martínez. others., doi: 10.1038/s44318-024-00210-5.

The I motif is a DNA structure that differs from the iconic double helix shape.

These form when runs of cytosine letters on the same DNA strand pair up with each other to form a four-stranded twisted structure that juts out from the double helix.

In 2018, scientists at the Garvan Institute of Medical Research were the first to successfully directly visualize i-motifs inside living human cells, using new antibody tools they developed to recognise and bind to the i-motifs.

The new study expands on these findings by using the antibody to identify the location of i-motifs throughout the genome.

“In this study, we have mapped more than 50,000 i-motif sites in the human genome that are found in all three cell types we looked at,” said Professor Daniel Crist from the Garvan Institute of Medical Research, lead author of the study.

“This is a surprisingly high number for a DNA structure whose presence in cells was once a matter of debate.”

“Our findings confirm that the i-motif is not just an object of laboratory study, but is widespread and likely plays an important role in genome function.”

The researchers found that i-motifs are not scattered randomly, but are concentrated in important functional regions of the genome, including those that control gene activity.

“We found that the i-motif is associated with genes that are highly active at specific times in the cell cycle,” said lead author Cristian David Peña Martinez, PhD, also of the Garvan Medical Institute.

“This suggests that it plays a dynamic role in regulating gene activity.”

“We also discovered that i-motifs are formed in the promoter regions of cancer genes. For example, MYC Oncogenes encode one of cancer’s most notoriously ‘untreatable’ targets.”

“This opens up exciting opportunities to target disease-related genes through i-motif structures.”

“The widespread presence of the i-motif near these 'holy grail' sequences implicated in hard-to-treat cancers opens up new possibilities for novel diagnostic and therapeutic approaches,” said study co-author Sarah Kummerfeld, PhD, a researcher at the Garvan Medical Institute.

“It may be possible to design drugs that target the i-motif to affect gene expression, potentially expanding current treatment options.”

Team result Published in EMBO Journal.

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Christian David Peña Martinez othersi-motif structures are widely distributed in human genomic DNA. Embo JPublished online August 29, 2024, doi: 10.1038/s44318-024-00210-5

Source: www.sci.news

The South American lungfish has the largest genome ever sequenced to date.

Posted on August 20, 2024 by Igor Mitreski

Researchers from the University of Konstanz and other institutions Africa(Protopterus annectens) and South American lungfish (Lepidosiren paradoxa)The genome of the South American lungfish (approximately 91 gigabases, about 30 times the size of the human genome) is the largest animal genome sequenced to date. Australia(Neoceratodus forsteri) African lungfish.

South American lungfish (Lepidosiren paradoxaImage courtesy of Katherine Seghers, Louisiana State University.

Lungfish are freshwater vertebrates belonging to the order Dipnoi (Pulmonaceae) and have existed for 400 million years, from the Devonian to the present day.

Some people consider lungfish to be “living fossils” because their morphology has changed very little over the years.

They, like all terrestrial vertebrates, have the ability to breathe air through lungs similar to our own.

Only six species of lungfish remain today: four live in Africa, one in South America, and one in Australia.

“These ancient 'living fossils' still resemble their ancestors so closely that they seem to have been forgotten during evolution,” said biologist Axel Meyer of the University of Konstanz and his colleagues.

“Since our genetic material, DNA, is made up of nucleobases and the sequence of these nucleobases contains the actual genetic information, a comparative analysis of the lungfish genome will only be possible if we know its complete sequence.”

“We already knew that the lungfish genome was large, but until now it was unclear how large it really was and what we could learn from it,” the researchers added.

“Sequencing the lungfish genome has therefore been very labor-intensive and complex, both from a technical and bioinformatics point of view.”

In a new study, scientists have sequenced the genome of African and South American lungfish.

“The South American species' DNA is 91 gigabases (or 91 billion bases), the largest of any animal genome and more than twice the size of the genome of the previous record holder, the Australian lungfish,” Dr Meyer said.

“Eighteen of the South American lungfish's 19 chromosomes are each larger than the entire human genome, about 3 billion base pairs in length.”

The largest genome sequence to date, that of the Australian lungfish, was also sequenced by the same team.

“Autonomous transposons are responsible for the large size of the lungfish genome over time,” the authors write.

“These are DNA sequences that are 'replicated' and change position in the genome, which causes the genome to grow.”

“Although similar phenomena have occurred in other organisms, our analysis shows that the South American lungfish has by far the fastest rate of genome expansion ever recorded; every 10 million years, its genome has expanded to a size equivalent to the entire human genome.”

“And it continues to grow. We now have evidence that the transposon responsible is still active.”

“We have identified a mechanism for this enormous genome growth. This extreme expansion is due, at least in part, to the very low presence of piRNAs.”

“This type of RNA is normally part of the molecular mechanism that silences transposons.”

Team paper Published in the journal Nature.

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M. Chartres othersAll lungfish genomes provide information on genome expansion and tetrapod evolution. NaturePublished online August 14, 2024, doi: 10.1038/s41586-024-07830-1

Source: www.sci.news

The largest sequenced genome is 30 times larger than the human genome

Posted on August 14, 2024 by Igor Mitreski

South American lungfish probably has a lot of 'junk' DNA

Katherine Segers/Louisiana State University

The largest sequenced genome on record, containing 90 billion DNA letters, belongs to a South American lungfish.

“Obviously, making this happen was a technical challenge,” he said. Axel Meyer “This is the largest animal genome ever found,” said researchers from the University of Konstanz in Germany.

South American lungfish (Lepidosiren paradoxaThere are two copies of the human genome, with a total of 180 gigabases (Gb) of DNA, which would stretch to 55 metres if laid out in a line – 30 times the amount of DNA found in a single human cell (6 Gb).

The South American lungfish has 19 chromosomes, 18 of which are larger than a single copy of the human genome, Meyer said.

His team also sequenced a single copy of the 40 Gb African lungfish genome (Protopterus annectens), the researchers have now sequenced all six species of lungfish found around the world, all of which have unusually large genomes.

“It's really puzzling how these fish can tolerate such large genomes,” Meyer says. The nucleus in each cell must be very large to accommodate so much DNA, meaning each cell is larger than normal, he says. Replicating that much DNA also requires a lot of energy with each cell division.

There's no evidence that this extra DNA does anything useful. Rather, it appears to be the result of a “genetic parasite” replicating itself endlessly. It's probably mostly junk, Meyer says.

His team found that mechanisms that other organisms use to limit the spread of genetic parasites appear to be damaged or missing in all lungfish species, resulting in the South American lungfish genome growing by 3.7 Gb every 10 million years – more than one copy of the human genome.

The reason for sequencing all lungfish species is to get a better understanding of what their common ancestor was like, a close relative of the lungfish that evolved into the first tetrapod land animal.

“Of all fish, lungfish are our closest relatives,” Meyer says. As their name suggests, lungfish breathe air and would drown without it.

They can also live for more than 100 years and regrow fins and tails, Meyer said, and his team hopes to figure out how they do this.

Some plant genomes are even larger than that of the South American lungfish: a small fern found on several Pacific islands is thought to have 321 Gb of DNA per cell, but there are no plans to sequence it.

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Source: www.newscientist.com

Scientists decipher the ginseng genome

Posted on July 18, 2024 by Igor Mitreski

A team of Chinese scientists has assembled a reference genome from telomere to telomere. Korean ginseng (Korean ginseng)A representative of traditional Chinese medicine.

Overview of morphological characteristics of Korean ginseng (Korean ginseng). Image credit: Song others., doi: 10.1093/hr/uhae107.

Ginseng is one of the most important medicinal plants and is cultivated in Northeast Asia, including China, Korea, Siberia, and Japan, and in smaller quantities in North America.

As recorded in the ancient Chinese text Shennong Benmatao Jing, the perennial root of ginseng has been used for thousands of years in traditional medicine and as a functional food and beverage with bodily and immune-boosting properties.

Ginseng has a very long history of being collected from the wild in fields, and cultivation began about 500 years ago. Since then, selective breeding has begun and cultivated varieties have become common.

“Like other herbs, medicinal ginseng has complex metabolites that are believed to be active compounds, of which triterpene saponins (ginsenosides) are the most important class,” said Wei Li, PhD, of the Shenzhen Institute of Agricultural Genomics, Chinese Academy of Agricultural Sciences, and colleagues.

“Ginseng probably contains more than 100 types of ginsenosides, but the synthesis pathways of most of the ginsenosides remain unknown.”

In the new study, Dr. Lee and his co-authors assembled a ginseng reference genome from telomere to telomere.

“We used this intertelomeric reference genome to study the phylogeny and evolution of ginseng and to explore the asymmetric loss and biased expression of genes among its subgenomes,” they explained.

The authors identified 77,266 protein-coding genes in the 3.45 Gb ginseng genome.

The team also identified asymmetric gene loss and biased gene expression across the subgenomes, tracing the divergence back approximately 6.07 million years.

Their analysis revealed extensive expansion of gene families related to saponin biosynthesis and highlighted the importance of specific gene duplications in enriching these pathways.

Comparative genomic analysis with related species will provide further insight into the evolutionary strategies employed by ginseng to maximize its medicinal properties.

“The complete sequencing of the ginseng genome is a monumental achievement in plant research,” Dr Lee said.

“Not only will it broaden our understanding of the genetic complexity of medicinal plants, but it will also introduce sophisticated methods for cultivating ginseng varieties with superior health properties.”

“Comprehensive sequencing of the ginseng genome has laid the foundation for precision breeding techniques aimed at enhancing its medicinal properties.”

“This research not only has immediate applications in the intensification of ginseng cultivation, but also serves as a model for studying other medicinal plants, potentially revolutionizing pharmacology and crop intensification strategies with natural products.”

of result Published in the journal Horticultural Research.

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Song Yi-ting others2024. Telomere-to-telomere reference genome Korean ginseng Our focus is on the evolution of saponin biosynthesis. Horticultural Research 11 (6): uhae107; doi: 10.1093/hr/uhae107

Source: www.sci.news

Biologists find ancient giant virus inserted into genome of a single-celled parasite

Posted on July 17, 2024 by Igor Mitreski

Amoebidium appalachenseViruses in protists closely related to animals weave remnants of ancient giant viruses into their genetic code, according to a new study led by Queen Mary, University of London. The discovery sheds light on how complex organisms acquire parts of their genes and highlights the dynamic interplay between viruses and their hosts.

Amoebidium appalachense A unique model for understanding the hybrid origin of eukaryotic DNA. Image courtesy of Alex de Mendoza.

In this study, Dr. Alex de Mendoza Soler and his colleagues Amoebidium appalachense A unicellular parasite first isolated from the epidermis of a freshwater arthropod.

They found a surprising amount of genetic material from giant viruses, some of the largest known to science.

The sequences of these viruses are highly methylated, a chemical tag that often silences genes.

“It's like a hidden Trojan horse. Amoebidium appalachense It’s the DNA of,” says Dr. de Mendoza Soler.

“These viral insertions are potentially harmful, but Amoebidium appalachense It seems like we are suppressing them by chemically silencing them.”

The researchers then investigated how widespread this phenomenon may be.

They are some Amoebidium appalachense Examination of the isolates revealed wide variation in viral content.

This suggests that the processes of viral integration and silencing are continuous and dynamic.

“These findings call into question our understanding of viruses and the relationship between them and their hosts,” said Dr de Mendoza Soler.

“Traditionally, viruses are thought of as invaders, but this study suggests a more complex story.”

“Viral insertions may have played a role in the evolution of complex organisms by contributing new genes.”

“And this can be done by chemically controlling the invader's DNA.”

moreover, Amoebidium appalachense It shows intriguing parallels to how our own genomes interact with viruses.

It's similar to Amoebidium appalachense Humans and other mammals carry remnants of ancient viruses called endogenous retroviruses built into their DNA.

These remnants were previously thought to be inactive junk DNA, but now it appears some may be beneficial.

but, Amoebidium appalachense Endogenous retroviruses are much smaller, while the human genome is significantly larger.

Future studies can explore these similarities and differences to understand the intricate interactions between viruses and complex life forms.

Team Investigation result Published in today's journal Scientific advances.

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Luke A. Saleh others 2024. DNA methylation enables recurrent internalization of giant viruses in animal relatives. Scientific advances 10(28); Source: 10.1126/sciadv.ado6406

This article has been edited from an original release from Queen Mary, University of London.

Source: www.sci.news

Study finds ancient genome structure preserved in 52,000-year-old mammoth skin

Posted on July 12, 2024 by Igor Mitreski

Scientists from Baylor College of Medicine and other institutions have announced the discovery of ancient chromosome subfossils in a female mammoth fossil.Mammutus primigeniusThe mammoth, a species of mammoth known as the pygmy mammoth, died 52,000 years ago in what is now Siberia. The fossil preserves the structure of its ancient chromosomes down to the nanometer (billionth of a meter) scale. Researchers hypothesize that the cold of Siberia naturally freeze-dried the mammoth's skin, causing a glass transition that preserved the fossil.

Sandoval Velasco othersAssembled the genome and 3D chromosome structure of a 52,000-year-old woolly mammoth. Image courtesy of Sandoval Velasco. others., doi: 10.1016/j.cell.2024.06.002.

“This is a new type of fossil, one whose scale far exceeds that of individual ancient DNA fragments, with sequences a million times larger,” said Dr. Erez Lieberman Aiden, director of the Center for Genome Architecture at Baylor College of Medicine.

“This is also the first time that an ancient sample has been karyotyped.”

Knowing the three-dimensional structure of a genome gives us a lot of additional information beyond its sequence, but most ancient DNA specimens are made up of very small, jumbled up pieces of DNA.

Building on their work mapping the 3D structure of the human genome, Dr Aiden and his colleagues reasoned that the same strategy could be used to assemble ancient genomes, provided suitable ancient DNA samples were found.

The researchers tested dozens of samples over a five-year period, eventually locating an unusually well-preserved woolly mammoth that was unearthed in September 2018 near Belaya Gora, in the Sakha Republic in northeastern Siberia.

“We believe that the freeze-drying occurred naturally shortly after death, and the nuclear structures in the dried samples can remain viable for an incredibly long period of time,” said Dr. Olga Dudchenko of the Center for Genome Structure at Baylor College of Medicine.

To reconstruct the mammoth's genome structure, the authors extracted DNA from skin samples taken from behind the mammoth's ears.

They are, High C This allows them to detect which parts of DNA are in spatial proximity and likely to interact in their natural state within the nucleus.

“Imagine having a puzzle with 3 billion pieces, but not having the final puzzle picture at hand,” said Professor Marc-Marty-Renom, a structural genomicist at the National Center for Genome Analysis and Genomic Regulation.

“Hi-C allows me to get a rough idea of what the picture looks like before I start putting the puzzle pieces together.”

They then combined the physical information from the Hi-C analysis with DNA sequences to identify interacting DNA sections and produced a neat map of the mammoth genome using the modern elephant genome as a template.

The analysis revealed that mammoths had 28 chromosomes, the same number as modern Asian and African elephants.

Remarkably, the fossilized mammoth chromosomes retained a great deal of physical integrity and detail, including the nanoscale loops that contact transcription factors with the genes they control.

By examining the compartmentalization of genes within the nucleus, the scientists were able to identify active and inactive genes in the mammoth skin cells, a proxy for epigenetics and transcriptomics.

Compared with skin cells from the mammoth's closest relative, the Asian elephant, the mammoth's skin cells showed different gene activation patterns, including genes that may be related to fur and cold tolerance.

“For the first time we have mammoth tissue where we can roughly tell which genes are on and which are off,” said Professor Martti Renom.

“This is a surprising new type of data, the first time we've measured cell-specific genetic activity of genes in ancient DNA samples.”

Team result Published in today's journal cell.

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Marcela Sandoval Velasco others2024. A 52,000-year-old mammoth skin sample contains 3D genome structure. cell 187(14):3541-3562; doi:10.1016/j.cell.2024.06.002

Source: www.sci.news

Unraveling the Secrets of Dark DNA: Scientists on the Verge of Decoding Your Genome

Posted on June 30, 2024 by Igor Mitreski

Back in the spring of 2003, the Human Genome Project completed the monumental task of sequencing the human genome.

Even now, The Book of Life remains a captivating and complex subject for the world’s top geneticists, as they work to unravel its mysteries.

This achievement was not only a major milestone for science but for life on our planet, marking the first time any organism had documented its fundamental genetic makeup. This event sparked the ongoing genetic revolution but also presented profound questions.

Questions like, “Why is there so much genetic material?”

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One intriguing aspect of the human genome is that the majority of it seems to serve no apparent function. With around 3 billion nucleotide pairs (A, C, G, T), fewer than 2% (approximately 20,000) of these are genes responsible for coding proteins that direct cellular activity in the body. So, what purpose do the remaining genes serve?

Some have referred to these as junk DNA: seemingly meaningless genetic remnants accumulated over the course of evolution or like a convoluted word puzzle with little coherence.

However, ongoing research indicates that at least some of these regions are not simply genetic debris but have crucial regulatory and corrective roles in the human genome’s protein-coding genes. These DNA sequences are likened to the controls for gene expression.

For instance, enhancer sequences boost gene transcription from DNA to RNA, while silencers have the opposite effect.

The dark genome largely consists of lengthy repeat DNA sequences called Transposons, which play vital roles in gene expression, evolutionary processes, and environmental adaptation.

These “jumping genes” can relocate within the genome, potentially causing significant genetic mutations or inversions. Scientists posit that transposons are linked to evolutionary developments such as opposable thumbs in humans and the loss of tails in humans and apes.

In certain scenarios, transposons may contribute to the onset of tumors and genetic disorders like hemophilia and Duchenne muscular dystrophy, stemming from repetitive DNA sequences associated with transposons.

As a result, the dark genome has become a focal point of medical research, with hopes that increased understanding over the next two decades will lead to revolutionary therapies for genetic diseases.

This content addresses the query of “What makes up the other 98% of DNA?” posed by Asa Mcintyre via email.

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Source: www.sciencefocus.com

The genome of a new fern species from New Caledonia is the largest among all organisms

Posted on June 3, 2024 by Igor Mitreski

Tumecipteris oblancorata is a rare fern species known as the wolf lark, found in New Caledonia, a French overseas territory in the southwest Pacific Ocean. It has recently broken the world record with its genome size of 160.45 billion base pairs (Gbp), challenging current understanding and paving the way for further exploration of genome gigantism.

Tumecipteris oblancorata. Image courtesy of Pol Fernández.

Tomesypteris is a small and relatively understudied genus consisting of 15 species, mostly found in Oceania and some Pacific islands.

Scientists have previously estimated the genome sizes of two Tomesypteris species – Tumecipteris tannensis and Tomesypteris obliqua – with large genomes of 73.19 Gbp and 147.29 Gbp, respectively.

In 2023, Dr. Jaume Pellicer and his colleagues from the Royal Botanic Gardens, Kew, traveled to New Caledonia to analyze the genome size of Tumecipteris oblancorata.

The analysis revealed a record-breaking genome size of 160.45 Gbp for Tumecipteris oblancorata, also known as Tumecipteris truncata, surpassing the genome size of the Japanese flower plant species Paris Japonica (148.89 Gbp). For comparison, the human genome contains approximately 3.1 Gbp across 23 chromosomes.

Tomesypteris is a unique fern genus whose ancestors date back around 350 million years, characterized by primarily being epiphytes with a distribution limited to Oceania and a few Pacific islands.

Dr. Ilia Reich of the Royal Botanic Gardens, Kew, expressed surprise at the world record held by the inconspicuous Tumecipteris oblancorata, highlighting the diversity of plants at the DNA level and their importance in Earth’s biodiversity.

The team’s findings were published in the journal iScience.

Genome size diversity in eukaryotes: (A) Current distribution of genome sizes in the major lineages of plants, animals, and fungi. (B) Top 10 largest genome sizes recorded in eukaryotes. Image courtesy of Pol Fernández et al., doi: 10.1016/j.isci.2024.109889.

This remarkable discovery raises questions about the biological limits and complexities of plant genomes, inspiring further exploration into the mysteries of genome gigantism.

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Pol Fernandez othersThe 160 Gbp fork fern genome breaks eukaryotic size record. iSciencePublished online May 31, 2024, doi: 10.1016/j.isci.2024.109889

Source: www.sci.news

Researchers sequence genome of pineapple mint | Sci.News

Posted on May 28, 2024 by Igor Mitreski

The researchers: Pineapple Mint (Mint)This herb is highly valued for its unique aroma and medicinal properties.

Pineapple Mint (Mint) is cultivated worldwide for its unique aroma and commercial value. Image credit: Yang others., doi: 10.1093/hr/uhae022.

Genus MintThis plant, known as mint, is a type of herb with a strong scent. Lamiaceae.

This versatile plant contains a variety of components, including essential oils and non-essential compounds, making it suitable for a wide range of uses.

Mint Essential oils have a long history of medicinal use as digestive aids and pain relievers. Essential oils have a wide range of biological activities, including antioxidant, antibacterial, antiradiation, anticancer, and antihypertensive properties.

Pineapple mint is a cultivated variegated variety of apple mint.

It grows as a wild plant all over the world and is widely used in the medical field due to its many therapeutic properties.

“Despite their importance, understanding the genetic basis of these traits remains Mint “This gene is very unique, characterized by high heterozygosity and numerous structural mutations,” said Qi Song, PhD, of Chengdu University of Traditional Chinese Medicine, and his colleagues.

“Comprehensive research Mint “Sequencing the genome was essential to uncover the genetic factors that influence its unique characteristics.”

In this study, the researchers succeeded in generating the first high-quality, haplotyped genome assembly of pineapple mint, with a genome size of 414.3 Mb and 31,251 coding genes.

By integrating data from different sequencing platforms, we resolved two complete haplotype assemblies with nearly complete annotated telomeres and centromeres.

Remarkably, they uncovered 41,135 structural variations, including deletions, insertions, duplications, and translocations, many of which affect genes involved in terpenoid biosynthesis.

One important finding is that piperitenone oxide dominates among the volatile compounds produced by pineapple mint, in contrast to menthol, which is more common in other plants. Mint seed.

The authors identified three genes. Isopiperitenone reductase We identified ISPR, a key enzyme in menthol biosynthesis, but found that its low transcription level likely led to the accumulation of piperitenone oxide instead.

“The completion of the gap-free genome Mint “This is an important milestone in plant genomics,” Dr. Song said.

“This comprehensive genetic map provides a basis for investigating the molecular mechanisms underlying pineapple mint's unique properties, which may lead to innovative applications in medicine and agriculture.”

of result Published in the journal Horticultural Research.

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Hanting Yang others2024. Haplotyped gap-free genome assembly provides new insights into monoterpenoid diversification. Mint “Variegata”. Horticultural Research 11(3):uhae022; doi:10.1093/hr/uhae022

Source: www.sci.news

Scientists Successfully Sequence Genome of Extinct Little Bushmower

Posted on May 28, 2024 by Igor Mitreski

Scientists at Harvard University and elsewhere have used ancient DNA recovered from fossil bones on New Zealand’s South Island to identify the tiny bushmower.Anomalopteryx didiformisIt is one of nine species of flightless birds that once roamed the forested islands of New Zealand.

Moas fed on trees and shrubs in the forest understory. Image by Heinrich Harder.

There are currently nine recognized species of extinct New Zealand moas, which belong to the infraclass Aves. PaleognathomorphaThese include flightless ratites (ostriches, emus, cassowaries, kiwis, rheas, moas and elephant birds) and flying shorebirds and skylarks.

The extinction of all moa species is thought to have occurred shortly after Polynesian migration to New Zealand in the 13th century, and is the result of direct human exploitation combined with anthropogenic land-use change and impacts associated with invasive species.

“New Zealand’s extinct moa is our Taonga “It’s a species that has fascinated generations of New Zealand children,” said Dr Nick Lawrence, a palaeontologist at the University of Otago who was not involved in the study.

“Since the advent of ancient DNA, we’ve learned a lot more about the nine moa species that call Aotearoa home, but there are still many questions that remain unanswered.”

“Having the nuclear genome of the male little bush moa is the first step in exploring more deeply what makes moas so special. Even though it’s still in draft form, it’s about 85% complete.”

In the new study, Harvard researcher Scott Edwards and his colleagues assembled the complete mitochondrial and nuclear genomes of a male moa by sequencing ancient DNA and comparing it with the high-quality genome of the closely related emu.

They first calculated that the size of the moa nuclear genome was approximately 1.07 to 1.12 billion bases.

By analyzing the genetic diversity of the mitochondrial genome, the researchers estimated the bushmore’s long-term population to be approximately 237,000 individuals.

“Reconstructing the genome of a species like the tiny bushmore is difficult because there is only so much degraded ancient DNA to recover,” said Dr Gillian Gibb, a researcher at Massey University who was not involved in the study.

“In the case of moas, an additional challenge exists because the closest extant species with high-quality genomes to compare with diverged about 70 million years ago.”

“Despite these challenges, we have been able to recover a large portion of the genome, providing insight into moa evolution.”

The authors also investigated genes involved in the moa’s sensory biology and concluded that the bird probably has an extensive sense of smell and ultraviolet (UV) receptors in its eyes.

“This new study uses the genome to estimate the little bushmouse population at around 240,000 individuals, a number that is probably too high and the authors acknowledge it is a rough estimate,” Dr Lawrence said.

“Ecological estimates of moa are Motu “The (country) has a bird population of between 2 and 10 birds per square kilometre, with a total population of between 500,000 and 2.5 million birds.”

“The genome also shows that the little bush moa had a complex olfactory repertoire, which is consistent with what is seen in the moa skull.”

“Moas could also see in the ultraviolet spectrum, which may have helped them to find food, such as brightly colored truffle-like fungi, that they may have dispersed.”

“Moas, like other birds, are sensitive to bitter foods.”

“Moas are the only birds that have completely lost their wings,” added Prof Paul Schofield from the Canterbury Museum, who was not involved in the study.

“In this new paper, we also take a closer look at the big mystery of how this happened, concluding that it is not due to the loss of genes responsible for wing development, as previously suggested.”

“The paper also found that despite having an abnormal arrangement of the olfactory cortex in the brain, moas had normal avian olfactory abilities.”

of study Published in the journal Scientific advances.

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Scott V. Edwards others2024. Nuclear genome assembly of the extinct flightless bird, Little Bushmoore. Scientific advances 10(21); doi: 10.1126/sciadv.adj6823

Source: www.sci.news

Sugarcane genome successfully sequenced by scientists

Posted on March 29, 2024 by Igor Mitreski

Sugarcane is the world's most harvested crop by tonnage and has shaped world history, trade, and geopolitics, now responsible for 80% of the world's sugar production. Traditional sugarcane breeding methods have been effective in producing varieties adapted to new environments and pathogens, but sugar yield improvements have recently plateaued. The cessation of yield increase may be due to limited genetic diversity within the breeding population, long breeding cycles, and the complexity of its genome. Now, an international research team has created a polyploid reference genome for R570, a typical modern sugarcane variety.

Saccharum officinarum. Image credit: Ton Rulkens / CC BY-SA 2.0 Certificate.

Domestication of sugarcane began about 10,000 years ago. The first “sweet” varieties (Saccharum officinarum) derived from robustum sugar.

However, all modern varieties are derived from several interspecific crosses made by breeders a century ago between “sweet varieties” and “sweet varieties.” Saccharum officinarum And that 'wild' natural sugar.

Sugarcane hybridization has led to major advances in disease resistance and adaptation to stressful environmental conditions. However, early generation hybrids also had much lower sugar yields due to the greater contribution of the wild genome.

The complexity of the hybrid sugarcane genome and phylogeny is R570 varietyproduced by a breeder on Reunion Island in 1980.

“The sugarcane genome is very complex because it is large and contains more copies of chromosomes than a typical plant, a feature called polyploidy,” said researchers at the Hudson Alpha Institute for Bioengineering. said Dr. Jeremy Schmutz and colleagues.

“Sugar cane has about 10 billion base pairs, the building blocks of DNA. By comparison, the human genome has about 3 billion genes.”

“Many parts of sugarcane DNA are identical within and between different chromosomes, which makes it difficult to correctly reconstruct all the small segments of DNA while reconstructing the complete genetic blueprint. Masu.”

“We solved the puzzle by combining multiple gene sequencing technologies, including a newly developed method known as PacBio HiFi sequencing that can precisely sequence longer sections of DNA.”

“This was the most complex genome sequence we have ever completed,” Dr. Schmutz added.

“It shows how far we have come. This is something that seemed impossible 10 years ago. We are now reaching goals that we thought were impossible with plant genomics. We have been able to achieve this.”

CSIRO researcher Dr Karen Aitken said: “This groundbreaking result addresses the critical challenge of stagnant sugar yields by harnessing previously inaccessible genetic information from the sugarcane genome. ” he said.

“This is a major step forward for sugarcane research and will improve our understanding of complex traits such as yield, adaptation to diverse environmental conditions, and disease resistance.”

“We are working to understand how specific genes in plants are related to the quality of the biomass obtained downstream, which can then be turned into biofuels and bioproducts.” said Dr. Blake Simmons, a researcher at the Joint BioEnergy Institute.

“A deeper understanding of sugarcane genetics will help us better understand the plant genotypes required for the production of sugar and bagasse-derived intermediates needed for sustainable sugarcane conversion technologies at scales relevant to the bioeconomy.” and be in control.”

of result appear in the diary Nature.

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Al Healy other. Complex polyploid genome structure of sugarcane. Nature, published online March 27, 2024. doi: 10.1038/s41586-024-07231-4

Source: www.sci.news

Scientists use genome sequencing to reconstruct the face of China’s Emperor Wu.

Posted on March 29, 2024 by Igor Mitreski

A team of researchers from Fudan University and others has successfully generated the genome. Emperor Wu of China led by Xianbei (Emperor Wu) Northern Zhou Dynasty. The authors determined that Emperor Wu had a typical East Asian or Northeast Asian appearance and was susceptible to certain illnesses, such as stroke.

Reconstruction of the face (left) and portrait (right) of Emperor Wu of China's Northern Zhou Dynasty. Image credit: Du other., doi: 10.1016/j.cub.2024.02.059.

For more than 2,000 years, Chinese emperors have been accorded symbolic importance and are considered “sons of heaven” endowed with a “heavenly mission” and enjoy what is seen as divinely ordained rule over the nation. was doing.

The title “emperor” first appeared in 221 BC. In Gencalls himself “First Emperor.''

This position continued until the last emperor of the Qing Dynasty abdicated. Aisin Geolo Puyirecorded a total of 2,132 years and 83 feudal dynasties.

Emperor Wu, known as Yuwenyong (543-578 CE), was a highly influential emperor who overthrew the Northern Qi dynasty, reformed the local military system, pacified the Turks, and unified northern China. was.

He was ethnically Xianbei, an ancient nomadic group that lived in what is today Mongolia and northern and northeastern China.

“Some scholars have said that the Xianbei people have an 'exotic' appearance, with thick beards, high noses, and yellow hair,” said Dr. Xiaoqing Wen, a researcher at Fudan University.

“Our analysis shows that Emperor Wu had typical East Asian or Northeast Asian facial features.”

In 1996, archaeologists discovered Emperor Wu's tomb in northwestern China and discovered his bones, including a nearly complete skull.

Thanks to recent advances in ancient DNA research, Dr. Wen and his colleagues have successfully recovered more than 1 million single nucleotide polymorphisms (SNPs) from his DNA, some of which are associated with Emperor Wu's skin and hair color. information was included.

Researchers also succeeded in reconstructing the emperor's face in 3D.

They found that Emperor Wu had brown eyes, black hair, dark to medium skin, and facial features similar to those of modern North Asians and East Asians.

“Our work brought historical figures to life,” said Dr. Pianpian Wei, also from Fudan University.

“Previously, we had to rely on historical records and wall paintings to imagine what ancient peoples looked like.”

“We were able to directly reveal the true nature of the North Korean people.”

“Emperor Wu died at the age of 36, and his son also died young for no apparent reason,” the scientists said.

“Some archaeologists claim that Emperor Wu died of illness, while others claim that he was poisoned by his rivals.”

Analysis of Emperor Wu's DNA revealed that he was at increased risk of stroke.

This finding is consistent with historical records that describe the emperor as having aphasia, droopy eyelids, and an abnormal gait – potential symptoms of a stroke.

Genetic analysis shows that the Xianbei people intermarried with the Han Chinese when they migrated south to northern China.

“This is important information for understanding how ancient humans spread across Eurasia and how they integrated with local peoples,” Dr. Wen said.

of result Published in this week's magazine current biology.

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Panshin Du other. The ancient genome of Emperor Wu of northern China. current biology, published online March 28, 2024. doi: 10.1016/j.cub.2024.02.059

Source: www.sci.news

The blue whale genome is sequenced by researchers

Posted on March 20, 2024 by Igor Mitreski

An international team of scientists has created a reference-quality, long-read-based genome assembly. blue whale (glans muscle).

blue whale (glans muscle). Image credit: NOAA.

The blue whale is one of the largest animals to have ever existed, with adults reaching up to 33 meters (110 feet) and weighing up to 150 tons.

Megaanimal genome research is of interest to several subfields of biomedicine.

Understanding the developmental mechanisms that control body size may have applications in regenerative medicine and animal husbandry.

Although large mammals tend to live longer and have orders of magnitude more cells, meaning they divide more, they develop mechanisms that increase their resistance to cancer. I am.This mysterious phenomenon is known as Peto's paradox.

“The genome is the blueprint of an organism,” he said. Dr. Yuri Bukmana computational biologist at the Morgridge Institute.

“You need to know the genome of that species in order to manipulate cell cultures and measure things like gene expression. That allows you to do more research.”

“It is generally understood that larger organisms take longer to develop from fertilized egg to adult than smaller organisms, but we do not yet understand why.”

“From that perspective, just the basic biological knowledge is important: How do you make an animal that big? How do you make it work?”

“The practical application of this knowledge lies in the emerging field of stem cell-based therapy,” he said.

“Healing the injury requires stem cells to differentiate into specialized cell types in the relevant organ or tissue.”

“The rate of this process is controlled by some of the same molecular mechanisms underlying the developmental clock.”

In the study, the authors analyzed segmental duplications, large regions of duplicated sequences that often contain genes, which can provide insight into evolutionary processes when compared to other closely or distantly related species. can.

They found that blue whales have had extensive segmental duplication in the recent past, with more copies than bottlenose dolphins (Tursiops truncatus) and that Vorpoise (Phocoena Cave)the world's smallest Cetacea.

Most of the copies of genes created in this way are probably non-functional or their functions are still unknown, but several known genes were identified.

One encodes a protein called metallothionein, which is known to bind to heavy metals and sequester their toxicity, a mechanism useful for large animals that accumulate heavy metals while living in the ocean. be.

Reference genomes also help preserve species. Blue whales were hunted to near extinction in the first half of the 20th century. It is now protected by international treaties and its population is recovering.

“In the world's oceans, blue whales are basically everywhere except in the high Arctic,” Dr. Buchman said.

“So having a reference genome will allow us to make comparisons and better understand the population structure of different groups of blue whales in different parts of the globe.”

“The blue whale genome is highly heterozygous and there is still a lot of genetic diversity, which has important implications for conservation.”

of result appear in the diary molecular biology and evolution.

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Yuri V. Buchman other. 2024. High-quality blue whale genomes, partial duplications, and historical demography. molecular biology and evolution 41 (3): msae036; doi: 10.1093/molbev/msae036

Source: www.sci.news

Scientists sequence the genome of Danjou pears

Posted on March 18, 2024 by Igor Mitreski

Researchers at Hudson Alpha Bioengineering Institute and elsewhere Danjou pearA short-necked variety. Pear (Pyrus Communis).

green anjou fruit. Image credit: USA Pears.

Pears belong to the following Pyrusfamily genus Rosaceae Consists of cultivated and wild pears.

The genus is divided into two broad categories: European pear and Asian pear, whose divergence is estimated to be approximately 3 to 6 million years ago.

at least 26 Pyrus Currently, 10 naturally occurring interspecific hybrids of these species have been found in West Asia, East Asia, Europe, North Africa, and the Middle East.

In 2021, the value of utilized pear production in the United States reached $353 million. This makes the pear one of the most cultivated pear fruits around the world.

One of the most important pear varieties in North America, Anjou, also known as Beurre d'Anjou or simply Anjou, is believed to have originated in Belgium and was named after the Anjou region of France.

“Pears are big business in the Pacific Northwest,” said lead author Dr. Alex Harkes, a researcher at the Hudson Alpha Institute for Bioengineering, and colleagues.

“But did you know that traditional pear breeding has changed little over the centuries?”

“This slow process is difficult and expensive, requiring long-term inputs of labor, materials, and land and spatial resources.”

“But thanks to a unique collaboration between students, scientists, and the pear industry fostered through an initiative called American Campus Tree Genomes (ACTG), traditional pear breeding is getting a helping hand from genomics. There is a possibility.”

“ACTG is leveraging iconic and economically valuable trees to bridge the gap between students and cutting-edge genomics.”

“Students work together to collect and analyze tree genomes, publish in prestigious academic journals, and gain valuable experience.”

The meticulous work of ACTG students has resulted in a complete chromosome-scale step-by-step assembly of the D'Anjou pear. This is a significant improvement over previous efforts.

This assembly revealed thousands of genomic variations that are of great importance to pear breeding efforts.

This high-quality resource unlocks a treasure trove of information for pear breeders.

This assembly is also an important tool for studies of pear evolution, domestication, and molecular breeding.

“The ACTG program not only built a high-quality genomic resource for a valuable pear variety that will ultimately benefit growers and consumers alike, but also trained nearly 20 students on the needs of the apple and pear industry. and educated scientists,” said Dr. Inez Hanrahan. , executive director of the Washington Tree and Fruit Research Committee.

team's paper It was published in the magazine G3: Genes, genomes, genetics.

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Alan Yocca other. 2024. Chromosome-scale assembly of pear 'Danjou'. G3: Genes, genomes, genetics 14(3):jkae003; doi: 10.1093/g3journal/jkae003

Source: www.sci.news

Researchers successfully decode the genome of the elusive night parrot

Posted on February 16, 2024 by Igor Mitreski

CSIRO researchers first genome of night parrot (Pezoporus occidentalis)one of the rarest and most elusive birds in the world.

night parrot (Pezoporus occidentalis). Image credit: Arianna Urso / Western Australian Museum.

The night parrot is a relatively small, short-tailed parrot species endemic to Australia.

This species is also known as the porcupine parrot, nocturnal ground parakeet, midnight parrot, solitaire, spinifex parrot, and nocturnal parakeet. first explained It was published in 1861 by British ornithologist John Gould.

The night parrot is one of the most elusive and mysterious birds in the world, with no confirmed sightings from 1912 to 1979.

They were once widespread in the arid regions of Australia, but their numbers have declined due to environmental changes such as predation by cats and foxes.

It is now known only from localized areas in south-west Queensland and Western Australia.

“Dozens of scientific specimens were collected in the 19th century, with one specimen collected in 1912. A specimen was then discovered in south-west Queensland in 1990,” says the CSIRO Australian National Wildlife Collection. said Dr. Leo Joseph, Director.

“A live bird was reported from the same area in 2013, and a live parrot was finally captured and tagged in 2015.”

“This genome will allow us to explore the genetic basis of why parrots are nocturnal, a trait that is very rare in parrots,” he added.

“We investigate functions such as navigation, sense of smell, beak shape, and suboptimal night vision.”

“Researchers will also be able to perform statistical analysis of this individual's genome to estimate the historical population size of Australia's night parrot.”

“We can now compare this annotated genome with other closely related parrot species, revealing the reasons behind its rarity and limited distribution compared to many closely related species. You can.”

Dr Joseph and his colleagues sequenced the armyworm genome using tissue obtained from specimens found in the Pilbara region.

“Access to high-throughput sequencing technology through CSIRO's Applied Genomics Initiative is accelerating genomics research in Australia,” said Dr Gunjun Pandey, CSIRO Environment Directorate Night Parrot Genomics Project Leader.

“We can now generate very high-quality genomes from very small tissue samples, as small as an ant's head or a single mosquito.”

“This level of quality and detail was not possible even five years ago.”

“Genetic data can be used to maximize diversity in conservation programs, so species are resilient and have the best chance of long-term survival.”

The night parrot genome is an exciting scientific resource for understanding more about this bird, but protecting this species from cats, foxes, fire, and habitat loss is also important for its conservation.

“The night parrot genome will open up many opportunities for further research that will help protect this species,” Dr. Pandey said.

“This will allow scientists to develop a plan to save the night parrot, with the ultimate goal of sequencing and publishing the genome.”

Source: www.sci.news

Arabica Coffee Genome Sequenced at Chromosome Scale by Scientists

Posted on January 24, 2024 by Igor Mitreski

researchers Genomica Application Laboratory and elsewhere are releasing improved genome assemblies. Arabica coffee (arabica coffee tree)a hybrid of coffee tree and robusta coffee (Coffea genus) contributes to approximately 60% of the world's coffee production.

arabica coffee tree. Image credit: Fadil Askar.

arabica coffee tree derived from interbreeding between modern ancestors Coffea genus and another closely related coffee species, coffee tree.

As a result of this hybridization, arabica coffee treeflavor and its large and complex genome pose challenges to breeding and genetic research.

Some partial genome assemblies arabica coffee tree is currently available, but the mechanisms that generate its genetic diversity are unknown.

Researchers Michele Morgante and Gabriele Di Gaspero and their colleagues at the Istituto di Genomica Appplicata used the latest sequencing technology to generate a more complete genome assembly. arabica coffee treeallowing detailed analysis of its chromosomal structure.

Analysis of the genome, including previously inaccessible regions such as around centromeres, revealed differences in genome structure, function, and evolution contributed by the two ancestral species, particularly in genes involved in caffeine biosynthesis. found.

For this study, they also analyzed the genomes of 174 samples collected from different species within Earth. coffee genus and found a very low level of genetic diversity within it. arabica coffee tree.

Diversity found to be increasing in some regions arabica coffee tree Varieties of specific genomic regions due to two different sources of variation: chromosomal abnormalities and gene segments provided by so-called Timor hybrids. Arabica coffee x Canephora coffee tree A hybrid from East Timor.

This hybrid is the parent line for many modern varieties that combine disease resistance traits. Coffea genus And its unique flavor is arabica coffee tree.

The authors argue that genetic diversity arabica coffee tree Essential for commercial success, this discovery could help develop new coffee varieties with desirable traits, such as disease resistance or different flavor profiles.

“Resequence data from large accession sets reveal low intraspecific diversity at the center of species origin. arabica coffee tree” the authors write in their paper.

“Across a limited number of genomic regions, the diversity of some cultivated genotypes has increased to levels similar to that observed in one of the ancestral species. Coffea genusThis is probably the result of introgression derived from Timor hybrids. ”

“We also found that in addition to very few early exchanges between homologous chromosomes, there are many recent chromosomal abnormalities such as aneuploidies, deletions, duplications, and exchanges.”

“These phenomena are still polymorphic in the germplasm and may be the root cause of genetic variation in such low-variability species.”

of paper Published in this week's magazine nature communications.

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S. Scalabrine other. 2024.Chromosome-scale assembly reveals chromosomal abnormalities and exchanges that generate genetic diversity arabica coffee tree germ plasm. Nat Commune 15,463; doi: 10.1038/s41467-023-44449-8

Source: www.sci.news

Ancient migration revealed in Balkan genome

Posted on December 23, 2023 by Igor Mitreski

An international research team has unraveled the complex genomic history of the Balkans since Roman times, revealing a mix of Anatolian and Slavic influences. The study combines ancient DNA analysis with historical and archaeological data to show how migration and Roman imperial policies have shaped the genetic makeup of the modern-day Balkan population.

Credit: SciTechDaily.com

Interdisciplinary research reveals the genomic history of the Balkans, highlighting the significant impact of Anatolian and Slavic migrations during and after the Roman Empire. This study highlights a shared demographic history across the Balkans.

An interdisciplinary study led by Spain’s Institute of Evolutionary Biology (a joint center between Spain’s National Research Council and Pompeu Fabra University), the University of Belgrade in Serbia, the University of Western Ontario in Canada, and Harvard University in the United States. We reconstruct the genomic history of the Balkans during the first millennium of the Common Era, a time and place of major demographic, cultural, and linguistic changes.

The research team recovered and analyzed whole-genome data from 146 ancient humans excavated primarily in Serbia and Croatia. More than a third of these came from the Roman border area at the huge ruins of Viminacium in Serbia. The data were jointly analyzed. the rest of the Balkans and neighboring areas.

Works published in magazines cellhighlights the cosmopolitanism of the Roman frontier and the long-term effects of migration that accompanied the collapse of Roman rule, including the arrival of Slavic-speaking peoples.archaeological DNA It has become clear that, despite being divided by nation-state boundaries, the populations of the Balkans have been shaped by common demographic processes.

Reconstruction of the amphitheater at the ruins of Viminacium. Credit: Boris Hammer

During the Roman Empire, there was a large influx of people from the east into the Balkans, much of it from the Eastern Mediterranean and even from East Africa.

After Rome occupied the Balkans, this border area became a crossroads that would eventually lead to 26 Roman emperors. Among them was Constantine the Great, who founded the city of Constantinople and moved the capital of his empire to the eastern Balkans.

The researchers’ analysis of ancient DNA shows that people of Anatolian descent made a significant demographic contribution during Roman rule, leaving a long-term genetic imprint on the Balkans. This ancestral migration is very similar to what happened in the megacity of Rome itself, the original core of the empire, in previous studies, but it is noteworthy that this also happened on the periphery of the Roman Empire. .

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Source: scitechdaily.com