Tag

Pangenome

All articles tagged with #pangenome

science2 hours ago•12 min saved

The 8% That Took 19 Years to Read: Completing the Human Genome

The 2003 Human Genome Project declared the genome essentially finished, but about 8% remained unread, concentrated in centromeres, telomeres, and segmental duplications. In 2022 the Telomere-to-Telomere (T2T-CHM13) assembly delivered a gapless genome (except Y) using long-read sequencing, revealing complete centromeres and new sequence, including immune-related gene families. But it's a single reference genome, not the full human variation; the next milestone is a population-scale pangenome.

via Space Daily|

#centromeres #human-genome-project #long-read-sequencing

science2 months ago•85 min saved

Sorghum pangenome reveals hidden diversity to boost trait discovery

A 33-member sorghum pangenome and a 1,984-genotype diversity panel expand beyond the BTx623 reference to capture extensive structural variation and presence–absence variation. The study annotates genes with RNA-seq, identifies large-scale variants, and uses a fast k-mer genotyping approach to map complex alleles at loci like SH1 and the dhurrin biosynthetic cluster. By linking genomic diversity to traits such as drought tolerance, biomass, and leaf chemistry, the work provides a framework to accelerate trait discovery and breeding across global sorghum germplasm.

via Nature|

#breeding #genomics #pangenome

science2 months ago•18 min saved

AI uncovers predictable patterns in bacterial evolution

Researchers analyzed thousands of E. coli genomes and trained a random-forest model to predict whether accessory genes appear based on other genes in the genome. They found reliable predictability for a substantial portion of the accessory genome, with some gene families co‑occurring and others mutually exclusive, suggesting structured evolutionary dynamics beyond random mutation. The work, led by James McInerney, Alan Beavan, and Maria Rosa Domingo-Sananes, has implications for diagnostics, antibiotic resistance surveillance, and the design of genetic constructs, though not all genes are predictable; the full study was published in Proceedings of the National Academy of Sciences (PNAS).

via Earth.com|

#bacteria #evolution #genetics

science7 months ago•86 min saved

Decoding oat genetics for healthier, climate-resistant crops

The article presents a comprehensive study of the oat genome, including the assembly of 33 diverse oat lines, analysis of gene expression, structural variations, and the impact of chromosomal rearrangements on breeding and traits like flowering time and yield, highlighting the importance of pangenomic resources for oat improvement.

via Nature|

#breeding #genomic-diversity #hexaploid-oat

biology7 months ago•68 min saved

Mapping Yeast Genomes to Predict Trait Variations and Mutations

This study assembled near telomere-to-telomere genomes for 1,086 yeast isolates, revealing extensive structural variation and gene content diversity, and demonstrated that structural variants are more frequently associated with phenotypic traits and exhibit greater pleiotropy than SNPs, significantly advancing our understanding of the genetic basis of phenotypic diversity in yeast.

via Nature|

#biology #genotype-to-phenotype #long-read-sequencing

science-and-technology3 years ago•10 min saved

"Revolutionizing Genetics: A New Era of Ethnic Diversity-Informed Healthcare"

The Human Pangenome Reference Consortium has created a more inclusive human reference genome by assembling genomic sequences of 47 individuals from around the world, revealing almost 120 million DNA base pairs previously unseen. By providing a more accurate representation of human genetic diversity, researchers can refine their understanding of the link between genes and diseases, accelerate clinical research, and ultimately help address health disparities. The pangenome is public and can be used by scientists around the world as a new standard human genome reference. The HPRC’s ultimate goal is to produce high-quality, nearly error-free genomes from at least 350 individuals from diverse populations by mid-2024.

via SciTechDaily|

#clinical-research #genetic-diversity #health-disparities

science-and-technology3 years ago•5 min saved

"Human Pangenome Unveiled: Cataloguing Genetic Diversity for Ethnic Diversity-Informed Tests and Treatments"

Researchers have published a draft human ‘pangenome’ that captures more of human diversity than has been previously available. The international project aims to map the entirety of human genetic variation, to create a comprehensive reference against which geneticists will be able to compare other sequences. The draft pangenome represents a collection of sequences from a diverse selection of 47 people from around the globe, including individuals from Africa, the Americas, Asia and Europe. However, ethical considerations surrounding the effort to make genome research more inclusive have been highlighted.

via Nature.com|

#ethical-considerations #genetic-diversity #genome-research

science-and-technology3 years ago•4 min saved

"New Human Pangenome Reveals Greater Diversity in DNA"

Scientists have published a more accurate and inclusive edition of the human genome, called the "pangenome," which incorporates near-complete genetic sequences from 47 men and women of diverse origins, including African Americans, Caribbean Islanders, East Asians, West Africans, and South Americans. The pangenome could greatly expand the reach of personalized medicine and represents a crucial tool for scientists and clinicians hoping to identify genetic variations associated with disease. The architects of the project are continuing to add more population groups, with the goal of including at least 350 high-quality genomes that encompass the bulk of global human diversity.

via The New York Times|

#dna-sequencing #genetic-diversity #human-genome