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Cotton pan-genome retrieves the lost sequences and genes during domestication and selection

BACKGROUND: Millennia of directional human selection has reshaped the genomic architecture of cultivated cotton relative to wild counterparts, but we have limited understanding of the selective retention and fractionation of genomic components. RESULTS: We construct a comprehensive genomic variome b...

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Autores principales: Li, Jianying, Yuan, Daojun, Wang, Pengcheng, Wang, Qiongqiong, Sun, Mengling, Liu, Zhenping, Si, Huan, Xu, Zhongping, Ma, Yizan, Zhang, Boyang, Pei, Liuling, Tu, Lili, Zhu, Longfu, Chen, Ling-Ling, Lindsey, Keith, Zhang, Xianlong, Jin, Shuangxia, Wang, Maojun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8063427/
https://www.ncbi.nlm.nih.gov/pubmed/33892774
http://dx.doi.org/10.1186/s13059-021-02351-w
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author Li, Jianying
Yuan, Daojun
Wang, Pengcheng
Wang, Qiongqiong
Sun, Mengling
Liu, Zhenping
Si, Huan
Xu, Zhongping
Ma, Yizan
Zhang, Boyang
Pei, Liuling
Tu, Lili
Zhu, Longfu
Chen, Ling-Ling
Lindsey, Keith
Zhang, Xianlong
Jin, Shuangxia
Wang, Maojun
author_facet Li, Jianying
Yuan, Daojun
Wang, Pengcheng
Wang, Qiongqiong
Sun, Mengling
Liu, Zhenping
Si, Huan
Xu, Zhongping
Ma, Yizan
Zhang, Boyang
Pei, Liuling
Tu, Lili
Zhu, Longfu
Chen, Ling-Ling
Lindsey, Keith
Zhang, Xianlong
Jin, Shuangxia
Wang, Maojun
author_sort Li, Jianying
collection PubMed
description BACKGROUND: Millennia of directional human selection has reshaped the genomic architecture of cultivated cotton relative to wild counterparts, but we have limited understanding of the selective retention and fractionation of genomic components. RESULTS: We construct a comprehensive genomic variome based on 1961 cottons and identify 456 Mb and 357 Mb of sequence with domestication and improvement selection signals and 162 loci, 84 of which are novel, including 47 loci associated with 16 agronomic traits. Using pan-genome analyses, we identify 32,569 and 8851 non-reference genes lost from Gossypium hirsutum and Gossypium barbadense reference genomes respectively, of which 38.2% (39,278) and 14.2% (11,359) of genes exhibit presence/absence variation (PAV). We document the landscape of PAV selection accompanied by asymmetric gene gain and loss and identify 124 PAVs linked to favorable fiber quality and yield loci. CONCLUSIONS: This variation repertoire points to genomic divergence during cotton domestication and improvement, which informs the characterization of favorable gene alleles for improved breeding practice using a pan-genome-based approach.
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spelling pubmed-80634272021-04-23 Cotton pan-genome retrieves the lost sequences and genes during domestication and selection Li, Jianying Yuan, Daojun Wang, Pengcheng Wang, Qiongqiong Sun, Mengling Liu, Zhenping Si, Huan Xu, Zhongping Ma, Yizan Zhang, Boyang Pei, Liuling Tu, Lili Zhu, Longfu Chen, Ling-Ling Lindsey, Keith Zhang, Xianlong Jin, Shuangxia Wang, Maojun Genome Biol Research BACKGROUND: Millennia of directional human selection has reshaped the genomic architecture of cultivated cotton relative to wild counterparts, but we have limited understanding of the selective retention and fractionation of genomic components. RESULTS: We construct a comprehensive genomic variome based on 1961 cottons and identify 456 Mb and 357 Mb of sequence with domestication and improvement selection signals and 162 loci, 84 of which are novel, including 47 loci associated with 16 agronomic traits. Using pan-genome analyses, we identify 32,569 and 8851 non-reference genes lost from Gossypium hirsutum and Gossypium barbadense reference genomes respectively, of which 38.2% (39,278) and 14.2% (11,359) of genes exhibit presence/absence variation (PAV). We document the landscape of PAV selection accompanied by asymmetric gene gain and loss and identify 124 PAVs linked to favorable fiber quality and yield loci. CONCLUSIONS: This variation repertoire points to genomic divergence during cotton domestication and improvement, which informs the characterization of favorable gene alleles for improved breeding practice using a pan-genome-based approach. BioMed Central 2021-04-23 /pmc/articles/PMC8063427/ /pubmed/33892774 http://dx.doi.org/10.1186/s13059-021-02351-w Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis 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
Li, Jianying
Yuan, Daojun
Wang, Pengcheng
Wang, Qiongqiong
Sun, Mengling
Liu, Zhenping
Si, Huan
Xu, Zhongping
Ma, Yizan
Zhang, Boyang
Pei, Liuling
Tu, Lili
Zhu, Longfu
Chen, Ling-Ling
Lindsey, Keith
Zhang, Xianlong
Jin, Shuangxia
Wang, Maojun
Cotton pan-genome retrieves the lost sequences and genes during domestication and selection
title Cotton pan-genome retrieves the lost sequences and genes during domestication and selection
title_full Cotton pan-genome retrieves the lost sequences and genes during domestication and selection
title_fullStr Cotton pan-genome retrieves the lost sequences and genes during domestication and selection
title_full_unstemmed Cotton pan-genome retrieves the lost sequences and genes during domestication and selection
title_short Cotton pan-genome retrieves the lost sequences and genes during domestication and selection
title_sort cotton pan-genome retrieves the lost sequences and genes during domestication and selection
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8063427/
https://www.ncbi.nlm.nih.gov/pubmed/33892774
http://dx.doi.org/10.1186/s13059-021-02351-w
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