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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...
Autores principales: | , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Nature Publishing Group UK
2021
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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. |
format | Online Article Text |
id | pubmed-8159941 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
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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