Revealing genetic diversity, population structure, and selection signatures of the Pacific oyster in Dalian by whole-genome resequencing
Introduction The Pacific oyster ( Crassostrea gigas ), one of the major aquaculture shellfish worldwide, has strong environmental adaptability. However, genetic diversity and population structure of the Pacific oysters in Dalian Sea, the major natural and farming area of the species in China, has no...
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Online Access: | http://dx.doi.org/10.3389/fevo.2023.1337980 https://www.frontiersin.org/articles/10.3389/fevo.2023.1337980/full |
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crfrontiers:10.3389/fevo.2023.1337980 2024-02-11T10:03:14+01:00 Revealing genetic diversity, population structure, and selection signatures of the Pacific oyster in Dalian by whole-genome resequencing Mao, Junxia Tian, Ying Liu, Qian Li, Danyang Ge, Xinfan Wang, Xubo Hao, Zhenlin 2024 http://dx.doi.org/10.3389/fevo.2023.1337980 https://www.frontiersin.org/articles/10.3389/fevo.2023.1337980/full unknown Frontiers Media SA https://creativecommons.org/licenses/by/4.0/ Frontiers in Ecology and Evolution volume 11 ISSN 2296-701X Ecology Ecology, Evolution, Behavior and Systematics journal-article 2024 crfrontiers https://doi.org/10.3389/fevo.2023.1337980 2024-01-26T10:02:13Z Introduction The Pacific oyster ( Crassostrea gigas ), one of the major aquaculture shellfish worldwide, has strong environmental adaptability. However, genetic diversity and population structure of the Pacific oysters in Dalian Sea, the major natural and farming area of the species in China, has not been systematically investigated, especially at genome-wide level, limiting the conservation and management of the species. Methods In this study, whole-genome resequencing of 105 individuals from seven Pacific oyster populations, including five wild and one cultured populations in Dalian and one wild population in Qingdao relatively distant from others, were first performed. Results A total of 2,363,318 single nucleotide polymorphisms (SNPs) were identified. Based on all these SNPs, similar but relatively low genetic diversity (0.2352~0.2527) was found in the seven populations. The principal component analysis (PCA), phylogenetic and population structure analysis consistently revealed weak differentiation among the seven populations. Frequent migration events were detected among the studied populations by TreeMix, which probably led to a high genetic similarity of these populations. Rapid linkage disequilibrium (LD) decay was observed in the genome of the Pacific oyster. Investigation of genome-wide selection signatures of these populations identified many selected genes involved in the biological processes related to DNA metabolism and stability, shell formation, and environmental stress response, which may be critical for oysters to adapt to the stressful environments. Discussion This study laid theoretical basis for the subsequent germplasm conservation, management and genetic breeding of the indigenous Pacific oysters, and provided novel insights for the adaptive evolutionary mechanism of oysters. Article in Journal/Newspaper Crassostrea gigas Pacific oyster Frontiers (Publisher) Pacific Frontiers in Ecology and Evolution 11 |
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Ecology Ecology, Evolution, Behavior and Systematics |
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Ecology Ecology, Evolution, Behavior and Systematics Mao, Junxia Tian, Ying Liu, Qian Li, Danyang Ge, Xinfan Wang, Xubo Hao, Zhenlin Revealing genetic diversity, population structure, and selection signatures of the Pacific oyster in Dalian by whole-genome resequencing |
topic_facet |
Ecology Ecology, Evolution, Behavior and Systematics |
description |
Introduction The Pacific oyster ( Crassostrea gigas ), one of the major aquaculture shellfish worldwide, has strong environmental adaptability. However, genetic diversity and population structure of the Pacific oysters in Dalian Sea, the major natural and farming area of the species in China, has not been systematically investigated, especially at genome-wide level, limiting the conservation and management of the species. Methods In this study, whole-genome resequencing of 105 individuals from seven Pacific oyster populations, including five wild and one cultured populations in Dalian and one wild population in Qingdao relatively distant from others, were first performed. Results A total of 2,363,318 single nucleotide polymorphisms (SNPs) were identified. Based on all these SNPs, similar but relatively low genetic diversity (0.2352~0.2527) was found in the seven populations. The principal component analysis (PCA), phylogenetic and population structure analysis consistently revealed weak differentiation among the seven populations. Frequent migration events were detected among the studied populations by TreeMix, which probably led to a high genetic similarity of these populations. Rapid linkage disequilibrium (LD) decay was observed in the genome of the Pacific oyster. Investigation of genome-wide selection signatures of these populations identified many selected genes involved in the biological processes related to DNA metabolism and stability, shell formation, and environmental stress response, which may be critical for oysters to adapt to the stressful environments. Discussion This study laid theoretical basis for the subsequent germplasm conservation, management and genetic breeding of the indigenous Pacific oysters, and provided novel insights for the adaptive evolutionary mechanism of oysters. |
format |
Article in Journal/Newspaper |
author |
Mao, Junxia Tian, Ying Liu, Qian Li, Danyang Ge, Xinfan Wang, Xubo Hao, Zhenlin |
author_facet |
Mao, Junxia Tian, Ying Liu, Qian Li, Danyang Ge, Xinfan Wang, Xubo Hao, Zhenlin |
author_sort |
Mao, Junxia |
title |
Revealing genetic diversity, population structure, and selection signatures of the Pacific oyster in Dalian by whole-genome resequencing |
title_short |
Revealing genetic diversity, population structure, and selection signatures of the Pacific oyster in Dalian by whole-genome resequencing |
title_full |
Revealing genetic diversity, population structure, and selection signatures of the Pacific oyster in Dalian by whole-genome resequencing |
title_fullStr |
Revealing genetic diversity, population structure, and selection signatures of the Pacific oyster in Dalian by whole-genome resequencing |
title_full_unstemmed |
Revealing genetic diversity, population structure, and selection signatures of the Pacific oyster in Dalian by whole-genome resequencing |
title_sort |
revealing genetic diversity, population structure, and selection signatures of the pacific oyster in dalian by whole-genome resequencing |
publisher |
Frontiers Media SA |
publishDate |
2024 |
url |
http://dx.doi.org/10.3389/fevo.2023.1337980 https://www.frontiersin.org/articles/10.3389/fevo.2023.1337980/full |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_source |
Frontiers in Ecology and Evolution volume 11 ISSN 2296-701X |
op_rights |
https://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.3389/fevo.2023.1337980 |
container_title |
Frontiers in Ecology and Evolution |
container_volume |
11 |
_version_ |
1790599418374782976 |