Tag Archives: genome

Arabica Coffee Genome Sequenced at Chromosome Scale by Scientists

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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

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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. .

and so on…

Source: scitechdaily.com

Chia Genome Sequenced by Researchers, New Study Finds

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Cheer (salvia hispanica) It is one of the most popular nutrient-dense foods and pseudocereals of the Lamiaceae family Lamiaceae. Chia seeds are rich in protein, polyunsaturated fatty acids, dietary fiber, and antioxidants. A team of scientists at Oregon State University has sequenced the chia genome, providing a blueprint for future research to exploit the nutritional and human health benefits of the chia plant.

chia seeds. Image credit: Valeria Lu.

Chia is an annual herbaceous plant in the Lamiaceae family, which also includes popular culinary herbs.

It is grown in southern Mexico and Central America for its nutrient-rich seeds containing protein, polyunsaturated fatty acids, dietary fiber, antioxidants, and minerals.

Compared to dietary fiber sources such as soy, wheat, and corn, chia seeds contain approximately 54g of dietary fiber per 100g, of which 93% is insoluble fiber.

Similarly, 60% of the total fatty acids are composed of polyunsaturated fatty acids, and proteins constitute 18–24% of the seed mass.

Additionally, the health-beneficial effects of chia seeds on improving muscle lipid content, cardiovascular health, total cholesterol ratio, triglyceride content, and anti-carcinogenic properties have been demonstrated in humans and animals.

The high fiber content in chia seeds also helps to reduce hypoglycemic effects and stabilize blood sugar levels in people with type 2 diabetes.

Professor Pankaj Jaiwal from Oregon State University said, “Our study opens up the possibility for scientists to study chia seeds with a view to improving human health, while also expanding knowledge of chia’s full range of nutritional benefits.” We will continue to deepen our understanding.”

“Long-term food and nutritional security currently requires diversifying human diets through breeding and genetic improvement of nutrient-rich so-called minor crops like chia,” said Dr. Sushma Naisani of Oregon State University. We have reached a stage where this is necessary.”

In the study, the authors assembled a haploid chia genome with an estimated genome size of 356 Mb.

They identified genes and genetic markers in chia that could help agricultural researchers breed plants to amplify plant traits valuable to human health.

They discovered 29 genes involved in the biosynthesis of polyunsaturated fatty acids and 93 genes that aid chia seeds’ gel-forming properties.

They also found 2,707 genes highly expressed in the seeds that are likely to produce small biologically active peptides (biopeptides) derived from proteins.

When seed proteins are digested in the intestinal tract, these small biopeptides are released and absorbed into the body, with potential properties that may help alleviate human health conditions such as type 2 diabetes and high blood pressure. Masu.

“This is the first report in silico “Annotation of plant genomes for protein-derived small biopeptides associated with improved human health,” the researchers said.

of findings It was published in the magazine Frontiers of plant science.

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parul gupta other. 2023. Reference genome of the nutrient-rich orphan crop chia (salvia hispanica) and implications for future breeding. front.plant science 14; doi: 10.3389/fps.2023.1272966

Source: www.sci.news

The merger of quantum biology and AI fueled genome editing advancements

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Scientists at Oak Ridge National Laboratory have utilized quantum biology and explainable artificial intelligence to advance CRISPR Cas9 technology for genome editing in microorganisms. This breakthrough has enabled more precise genetic modification of microorganisms, opening up possibilities for the production of renewable fuels and chemicals. The research at Oak Ridge National Laboratory has significantly improved the efficiency of CRISPR Cas9 genome editing in microorganisms and contributed to renewable energy development.

CRISPR is a powerful tool for bioengineering, used to modify the genetic code to improve the performance of organisms or correct mutations. ORNL scientists developed a method to improve the accuracy of the CRISPR Cas9 gene editing tool used to modify microorganisms for the production of renewable fuels and chemicals. They have leveraged their expertise in quantum biology, artificial intelligence, and synthetic biology to achieve this.

To improve the modeling and design of guide RNAs, ORNL scientists sought to better understand what is happening at the most fundamental level in the cell nucleus, where genetic material is stored. They turned to quantum biology to study how electronic structure affects the chemical properties and interactions of nucleotides, such as DNA and RNA.

Furthermore, scientists at ORNL have built an explainable artificial intelligence model called iterated random forest, which has been used to train the model on a dataset of about 50,000 guide RNAs targeting the genome of Escherichia coli. This model has provided important features regarding the nucleotides that allow for better selection of guide RNAs.

Improving the CRISPR Cas9 model provides scientists with a high-throughput pipeline for linking genotype to phenotype in functional genomics. This research will impact efforts at the ORNL-led Center for Bioenergy Innovation (CBI), such as improving bioenergy feedstock plants and bacterial fermentation of biomass.

The results of this research significantly improve the prediction of guide RNAs. This represents an exciting advance toward understanding how avoid ‘mistakes’ and improving the ability to use CRISPR tools to predictively modify the DNA of more organisms. The study was funded by SEED SFA and CBI, part of the DOE Office of Science’s Biological and Environmental Research Program, ORNL’s Laboratory-Directed Research and Development Program, and OLCF and Compute’s High Performance Computing Resources and Data Environment for Science, both supported by the Office of Science.

Source: scitechdaily.com