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Whole-genome resequencing of large yellow croaker (Larimichthys crocea) reveals the population structure and signatures of environmental adaptation

Large yellow croaker is an economically important fish in China and East Asia. Despite its economic importance, genome-wide adaptions of domesticated large yellow croaker are largely unknown. Here, we performed whole-genome resequencing of 198 individuals of large yellow croaker obtained in the sea...

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Autores principales: Kon, Tetsuo, Pei, Liyi, Ichikawa, Ryota, Chen, Chunyan, Wang, Ping, Takemura, Ikuyo, Ye, Yingying, Yan, Xiaojun, Guo, Baoying, Li, Weiye, Lauden, Hagai Nsobi, Tabata, Hiromasa, Pan, Hao, Omori, Yoshihiro, Ogura, Atsushi, Jiang, Lihua
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8159941/
https://www.ncbi.nlm.nih.gov/pubmed/34045615
http://dx.doi.org/10.1038/s41598-021-90645-1
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author Kon, Tetsuo
Pei, Liyi
Ichikawa, Ryota
Chen, Chunyan
Wang, Ping
Takemura, Ikuyo
Ye, Yingying
Yan, Xiaojun
Guo, Baoying
Li, Weiye
Lauden, Hagai Nsobi
Tabata, Hiromasa
Pan, Hao
Omori, Yoshihiro
Ogura, Atsushi
Jiang, Lihua
author_facet Kon, Tetsuo
Pei, Liyi
Ichikawa, Ryota
Chen, Chunyan
Wang, Ping
Takemura, Ikuyo
Ye, Yingying
Yan, Xiaojun
Guo, Baoying
Li, Weiye
Lauden, Hagai Nsobi
Tabata, Hiromasa
Pan, Hao
Omori, Yoshihiro
Ogura, Atsushi
Jiang, Lihua
author_sort Kon, Tetsuo
collection PubMed
description Large yellow croaker is an economically important fish in China and East Asia. Despite its economic importance, genome-wide adaptions of domesticated large yellow croaker are largely unknown. Here, we performed whole-genome resequencing of 198 individuals of large yellow croaker obtained in the sea or from farmers in Zhoushan or Ningde. Population genomics analyses revealed the genetic population structure of our samples, reflecting the living environment. Each effective population size is estimated to be declining over generations. Moreover, we identified genetically differentiated genomic regions between the sea-captured population in the Zhoushan Sea area and that of the Ningde Sea area or between the sea-captured population and the farmed population in either area. Gene ontology analyses revealed the gene groups under selective sweep for the adaptation to the domesticated environment. All these results suggest that individuals of the large yellow croaker populations show genomic signatures of adaptation to different living environments.
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spelling pubmed-81599412021-05-28 Whole-genome resequencing of large yellow croaker (Larimichthys crocea) reveals the population structure and signatures of environmental adaptation Kon, Tetsuo Pei, Liyi Ichikawa, Ryota Chen, Chunyan Wang, Ping Takemura, Ikuyo Ye, Yingying Yan, Xiaojun Guo, Baoying Li, Weiye Lauden, Hagai Nsobi Tabata, Hiromasa Pan, Hao Omori, Yoshihiro Ogura, Atsushi Jiang, Lihua Sci Rep Article Large yellow croaker is an economically important fish in China and East Asia. Despite its economic importance, genome-wide adaptions of domesticated large yellow croaker are largely unknown. Here, we performed whole-genome resequencing of 198 individuals of large yellow croaker obtained in the sea or from farmers in Zhoushan or Ningde. Population genomics analyses revealed the genetic population structure of our samples, reflecting the living environment. Each effective population size is estimated to be declining over generations. Moreover, we identified genetically differentiated genomic regions between the sea-captured population in the Zhoushan Sea area and that of the Ningde Sea area or between the sea-captured population and the farmed population in either area. Gene ontology analyses revealed the gene groups under selective sweep for the adaptation to the domesticated environment. All these results suggest that individuals of the large yellow croaker populations show genomic signatures of adaptation to different living environments. Nature Publishing Group UK 2021-05-27 /pmc/articles/PMC8159941/ /pubmed/34045615 http://dx.doi.org/10.1038/s41598-021-90645-1 Text en © The Author(s) 2021 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/) .
spellingShingle Article
Kon, Tetsuo
Pei, Liyi
Ichikawa, Ryota
Chen, Chunyan
Wang, Ping
Takemura, Ikuyo
Ye, Yingying
Yan, Xiaojun
Guo, Baoying
Li, Weiye
Lauden, Hagai Nsobi
Tabata, Hiromasa
Pan, Hao
Omori, Yoshihiro
Ogura, Atsushi
Jiang, Lihua
Whole-genome resequencing of large yellow croaker (Larimichthys crocea) reveals the population structure and signatures of environmental adaptation
title Whole-genome resequencing of large yellow croaker (Larimichthys crocea) reveals the population structure and signatures of environmental adaptation
title_full Whole-genome resequencing of large yellow croaker (Larimichthys crocea) reveals the population structure and signatures of environmental adaptation
title_fullStr Whole-genome resequencing of large yellow croaker (Larimichthys crocea) reveals the population structure and signatures of environmental adaptation
title_full_unstemmed Whole-genome resequencing of large yellow croaker (Larimichthys crocea) reveals the population structure and signatures of environmental adaptation
title_short Whole-genome resequencing of large yellow croaker (Larimichthys crocea) reveals the population structure and signatures of environmental adaptation
title_sort whole-genome resequencing of large yellow croaker (larimichthys crocea) reveals the population structure and signatures of environmental adaptation
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8159941/
https://www.ncbi.nlm.nih.gov/pubmed/34045615
http://dx.doi.org/10.1038/s41598-021-90645-1
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