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

Abstract 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...

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Autores principales:	Tetsuo Kon, Liyi Pei, Ryota Ichikawa, Chunyan Chen, Ping Wang, Ikuyo Takemura, Yingying Ye, Xiaojun Yan, Baoying Guo, Weiye Li, Hagai Nsobi Lauden, Hiromasa Tabata, Hao Pan, Yoshihiro Omori, Atsushi Ogura, Lihua Jiang
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/e82662626b4a4dbc8338145d857a774d
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spelling	oai:doaj.org-article:e82662626b4a4dbc8338145d857a774d2021-12-02T15:00:59ZWhole-genome resequencing of large yellow croaker (Larimichthys crocea) reveals the population structure and signatures of environmental adaptation10.1038/s41598-021-90645-12045-2322https://doaj.org/article/e82662626b4a4dbc8338145d857a774d2021-05-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-90645-1https://doaj.org/toc/2045-2322Abstract 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.Tetsuo KonLiyi PeiRyota IchikawaChunyan ChenPing WangIkuyo TakemuraYingying YeXiaojun YanBaoying GuoWeiye LiHagai Nsobi LaudenHiromasa TabataHao PanYoshihiro OmoriAtsushi OguraLihua JiangNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Tetsuo Kon Liyi Pei Ryota Ichikawa Chunyan Chen Ping Wang Ikuyo Takemura Yingying Ye Xiaojun Yan Baoying Guo Weiye Li Hagai Nsobi Lauden Hiromasa Tabata Hao Pan Yoshihiro Omori Atsushi Ogura Lihua Jiang Whole-genome resequencing of large yellow croaker (Larimichthys crocea) reveals the population structure and signatures of environmental adaptation
description	Abstract 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.
format	article
author	Tetsuo Kon Liyi Pei Ryota Ichikawa Chunyan Chen Ping Wang Ikuyo Takemura Yingying Ye Xiaojun Yan Baoying Guo Weiye Li Hagai Nsobi Lauden Hiromasa Tabata Hao Pan Yoshihiro Omori Atsushi Ogura Lihua Jiang
author_facet	Tetsuo Kon Liyi Pei Ryota Ichikawa Chunyan Chen Ping Wang Ikuyo Takemura Yingying Ye Xiaojun Yan Baoying Guo Weiye Li Hagai Nsobi Lauden Hiromasa Tabata Hao Pan Yoshihiro Omori Atsushi Ogura Lihua Jiang
author_sort	Tetsuo Kon
title	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_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_sort	whole-genome resequencing of large yellow croaker (larimichthys crocea) reveals the population structure and signatures of environmental adaptation
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/e82662626b4a4dbc8338145d857a774d
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Whole-genome resequencing of large yellow croaker (Larimichthys crocea) reveals the population structure and signatures of environmental adaptation

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