A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants.

Autor: Rice ES; Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.; Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität, Munich, Germany., Alberdi A; Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen (UCPH), Copenhagen, Denmark., Alfieri J; Department of Ecology & Evolutionary Biology, Texas A&M University, College Station, TX, USA., Athrey G; Department of Poultry Science, Texas A&M University, College Station, TX, USA., Balacco JR; Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA., Bardou P; Sigenae, GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, 31326, France., Blackmon H; Department of Biology, Texas A&M University, College Station, TX, USA., Charles M; University Paris-Saclay, INRAE, AgroParisTech, GABI, Sigenae, Jouy-en-Josas, France., Cheng HH; Avian Disease and Oncology Laboratory, USDA, ARS, USNPRC, East Lansing, MI, USA., Fedrigo O; Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA., Fiddaman SR; Department of Biology, University of Oxford, Oxford, OX1 3SZ, UK., Formenti G; Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA., Frantz LAF; Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität, Munich, Germany.; School of Biological and Behavioural Sciences, Queen Mary University of London, London, E1 4DQ, UK., Gilbert MTP; Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen (UCPH), Copenhagen, Denmark., Hearn CJ; Avian Disease and Oncology Laboratory, USDA, ARS, USNPRC, East Lansing, MI, USA., Jarvis ED; Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA.; The Howard Hughes Medical Institute, Chevy Chase, MD, USA., Klopp C; Sigenae, Genotoul Bioinfo, MIAT UR875, INRAE, Castanet Tolosan, France., Marcos S; Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen (UCPH), Copenhagen, Denmark.; Applied Genomics and Bioinformatics, University of the Basque Country (UPV/EHU), Leioa, Bilbao, Spain., Mason AS; Department of Biology, The University of York, York, UK., Velez-Irizarry D; Avian Disease and Oncology Laboratory, USDA, ARS, USNPRC, East Lansing, MI, USA., Xu L; Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, 400715, China., Warren WC; Department of Animal Sciences, University of Missouri, Columbia, MO, USA. warrenwc@missouri.edu.
Jazyk: angličtina
Zdroj: BMC biology [BMC Biol] 2023 Nov 22; Vol. 21 (1), pp. 267. Date of Electronic Publication: 2023 Nov 22.
DOI: 10.1186/s12915-023-01758-0
Abstrakt: Background: The red junglefowl, the wild outgroup of domestic chickens, has historically served as a reference for genomic studies of domestic chickens. These studies have provided insight into the etiology of traits of commercial importance. However, the use of a single reference genome does not capture diversity present among modern breeds, many of which have accumulated molecular changes due to drift and selection. While reference-based resequencing is well-suited to cataloging simple variants such as single-nucleotide changes and short insertions and deletions, it is mostly inadequate to discover more complex structural variation in the genome.
Methods: We present a pangenome for the domestic chicken consisting of thirty assemblies of chickens from different breeds and research lines.
Results: We demonstrate how this pangenome can be used to catalog structural variants present in modern breeds and untangle complex nested variation. We show that alignment of short reads from 100 diverse wild and domestic chickens to this pangenome reduces reference bias by 38%, which affects downstream genotyping results. This approach also allows for the accurate genotyping of a large and complex pair of structural variants at the K feathering locus using short reads, which would not be possible using a linear reference.
Conclusions: We expect that this new paradigm of genomic reference will allow better pinpointing of exact mutations responsible for specific phenotypes, which will in turn be necessary for breeding chickens that meet new sustainability criteria and are resilient to quickly evolving pathogen threats.
(© 2023. The Author(s).)
Databáze: MEDLINE
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