Results 11 to 20 of about 1,282 (176)
Personalized Pangenome References [PDF]
Nature Methods, 2023 Abstract Pangenomes, by including genetic diversity, should reduce reference bias by better representing new samples compared to them. Yet when comparing a new sample to a pangenome, variants in the pangenome that are not part of the sample can be misleading, for example, causing false read mappings.
Jouni Sirén +11 more
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Challenges in Bringing Pangenome Research Into Breeding: A Case Study in Rice. [PDF]
Plant Biotechnol JABSTRACT Crop breeding has entered the pangenomics era, unlocking a far more comprehensive view of genetic diversity than a single reference genome can capture. In rice (Oryza sativa), a staple crop critical to global food security, the construction of pangenome resources has uncovered extensive structural variations (SVs), presence/absence variations (
Nie S +7 more
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Vavilov Journal of Genetics and Breeding, 2021 Progress in genome sequencing, assembly and analysis allows for a deeper study of agricultural plants’ chromosome structures, gene identif ication and annotation. The published genomes of agricultural plants proved to be a valuable tool for studing gene functions and for marker-assisted and genomic selection.
A. Yu. Pronozin +2 more
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mSystems, 2023 Microbiomes are intricately intertwined with human health, geochemical cycles, and food production. While many microbiomes of interest are highly complex and experimentally intractable, cheese rind microbiomes have proven to be powerful model systems for
Christina C. Saak +6 more
doaj +1 more source
Unbiased pangenome graphs [PDF]
Bioinformatics, 2022 Abstract Motivation Pangenome variation graphs model the mutual alignment of collections of DNA sequences. A set of pairwise alignments implies a variation graph, but there are no scalable methods to generate such a graph from these alignments.
Erik Garrison, Andrea Guarracino
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Using Nanopore Sequencing to Obtain Complete Bacterial Genomes from Saliva Samples
mSystems, 2022 Obtaining complete, high-quality reference genomes is essential to the study of any organism. Recent advances in nanopore sequencing, as well as genome assembly and analysis methods, have made it possible to obtain complete bacterial genomes from ...
Jonathon L. Baker
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Site Specialization of Human Oral Veillonella Species
Microbiology Spectrum, 2023 Veillonella species are abundant members of the human oral microbiome with multiple interspecies commensal relationships. Examining the distribution patterns of Veillonella species across the oral cavity is fundamental to understanding their oral ecology.
Jonathan J. Giacomini +4 more
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Annual Review of Genomics and Human Genetics, 2020 Low-cost whole-genome assembly has enabled the collection of haplotype-resolved pangenomes for numerous organisms. In turn, this technological change is encouraging the development of methods that can precisely address the sequence and variation described in large collections of related genomes.
Eizenga, Jordan M +15 more
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The Ecology and Evolution of Pangenomes [PDF]
Current Biology, 2019 Since the first genome-scale comparisons, it has been evident that the genomes of many species are unbound by strict vertical descent: Large differences in gene content can occur among genomes belonging to the same prokaryotic species, with only a fraction of genes being universal to all genomes. These insights gave rise to the pangenome concept.
Brockhurst, M.A. +5 more
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Challenges in prokaryote pangenomics
Microbial Genomics, 2023 Horizontal gene transfer (HGT) and the resulting patterns of gene gain and loss are a fundamental part of bacterial evolution. Investigating these patterns can help us to understand the role of selection in the evolution of bacterial pangenomes and how bacteria adapt to a new niche.
Gerry Tonkin-Hill +2 more
openaire +5 more sources