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

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 ca...

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Autores principales: Rice, Edward S., Alberdi, Antton, Alfieri, James, Athrey, Giridhar, Balacco, Jennifer R., Bardou, Philippe, Blackmon, Heath, Charles, Mathieu, Cheng, Hans H., Fedrigo, Olivier, Fiddaman, Steven R., Formenti, Giulio, Frantz, Laurent A. F., Gilbert, M. Thomas P., Hearn, Cari J., Jarvis, Erich D., Klopp, Christophe, Marcos, Sofia, Mason, Andrew S., Velez-Irizarry, Deborah, Xu, Luohao, Warren, Wesley C.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10664547/
https://www.ncbi.nlm.nih.gov/pubmed/37993882
http://dx.doi.org/10.1186/s12915-023-01758-0
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author Rice, Edward S.
Alberdi, Antton
Alfieri, James
Athrey, Giridhar
Balacco, Jennifer R.
Bardou, Philippe
Blackmon, Heath
Charles, Mathieu
Cheng, Hans H.
Fedrigo, Olivier
Fiddaman, Steven R.
Formenti, Giulio
Frantz, Laurent A. F.
Gilbert, M. Thomas P.
Hearn, Cari J.
Jarvis, Erich D.
Klopp, Christophe
Marcos, Sofia
Mason, Andrew S.
Velez-Irizarry, Deborah
Xu, Luohao
Warren, Wesley C.
author_facet Rice, Edward S.
Alberdi, Antton
Alfieri, James
Athrey, Giridhar
Balacco, Jennifer R.
Bardou, Philippe
Blackmon, Heath
Charles, Mathieu
Cheng, Hans H.
Fedrigo, Olivier
Fiddaman, Steven R.
Formenti, Giulio
Frantz, Laurent A. F.
Gilbert, M. Thomas P.
Hearn, Cari J.
Jarvis, Erich D.
Klopp, Christophe
Marcos, Sofia
Mason, Andrew S.
Velez-Irizarry, Deborah
Xu, Luohao
Warren, Wesley C.
author_sort Rice, Edward S.
collection PubMed
description 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12915-023-01758-0.
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spelling pubmed-106645472023-11-22 A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants Rice, Edward S. Alberdi, Antton Alfieri, James Athrey, Giridhar Balacco, Jennifer R. Bardou, Philippe Blackmon, Heath Charles, Mathieu Cheng, Hans H. Fedrigo, Olivier Fiddaman, Steven R. Formenti, Giulio Frantz, Laurent A. F. Gilbert, M. Thomas P. Hearn, Cari J. Jarvis, Erich D. Klopp, Christophe Marcos, Sofia Mason, Andrew S. Velez-Irizarry, Deborah Xu, Luohao Warren, Wesley C. BMC Biol Research Article 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12915-023-01758-0. BioMed Central 2023-11-22 /pmc/articles/PMC10664547/ /pubmed/37993882 http://dx.doi.org/10.1186/s12915-023-01758-0 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research Article
Rice, Edward S.
Alberdi, Antton
Alfieri, James
Athrey, Giridhar
Balacco, Jennifer R.
Bardou, Philippe
Blackmon, Heath
Charles, Mathieu
Cheng, Hans H.
Fedrigo, Olivier
Fiddaman, Steven R.
Formenti, Giulio
Frantz, Laurent A. F.
Gilbert, M. Thomas P.
Hearn, Cari J.
Jarvis, Erich D.
Klopp, Christophe
Marcos, Sofia
Mason, Andrew S.
Velez-Irizarry, Deborah
Xu, Luohao
Warren, Wesley C.
A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants
title A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants
title_full A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants
title_fullStr A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants
title_full_unstemmed A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants
title_short A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants
title_sort pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10664547/
https://www.ncbi.nlm.nih.gov/pubmed/37993882
http://dx.doi.org/10.1186/s12915-023-01758-0
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