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Scientists Uncover the Genome Sequence of the Vampire Squid

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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

Researchers sequence genome of pineapple mint | Sci.News

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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

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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

Scientists sequence the genome of Danjou pears

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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