Genetic Diversity, Population Structure, and Environmental Adaptation Signatures of Chinese Coastal Hard-Shell Mussel <i>Mytilus coruscus</i> Revealed by Whole-Genome Sequencing
The hard-shell mussel (<i>Mytilus coruscus</i>) is widespread in the temperate coastal areas of the northwest Pacific and holds a significant position in the shellfish aquaculture market in China. However, the natural resources of this species have been declining, and population genetic...
| Main Authors: | , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-09-01
|
| Series: | International Journal of Molecular Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1422-0067/24/17/13641 |
| _version_ | 1797582323126894592 |
|---|---|
| author | Feng Guo Yingying Ye Kecheng Zhu Shuangrui Lin Yuxia Wang Zhenyu Dong Ronghui Yao Hongfei Li Weifeng Wang Zhi Liao Baoying Guo Xiaojun Yan |
| author_facet | Feng Guo Yingying Ye Kecheng Zhu Shuangrui Lin Yuxia Wang Zhenyu Dong Ronghui Yao Hongfei Li Weifeng Wang Zhi Liao Baoying Guo Xiaojun Yan |
| author_sort | Feng Guo |
| collection | DOAJ |
| description | The hard-shell mussel (<i>Mytilus coruscus</i>) is widespread in the temperate coastal areas of the northwest Pacific and holds a significant position in the shellfish aquaculture market in China. However, the natural resources of this species have been declining, and population genetic studies of <i>M. coruscus</i> are also lacking. In this study, we conducted whole-genome resequencing (WGR) of <i>M. coruscus</i> from eight different latitudes along the Chinese coast and identified a total of 25,859,986 single nucleotide polymorphism (SNP) markers. Our findings indicated that the genetic diversity of <i>M. coruscus</i> from the Zhoushan region was lower compared with populations from other regions. Furthermore, we observed that the evolutionary tree clustered into two primary branches, and the Zhangzhou (ZZ) population was in a separate branch. The ZZ population was partly isolated from populations in other regions, but the distribution of branches was not geographically homogeneous, and a nested pattern emerged, consistent with the population differentiation index (<i>F</i><sub>ST</sub>) results. To investigate the selection characteristics, we utilized the northern <i>M. coruscus</i> populations (Dalian and Qingdao) and the central populations (Zhoushan and Xiangshan) as reference populations and the southern ZZ population as the target population. Our selection scan analysis identified several genes associated with thermal responses, including <i>Hsp70</i> and <i>CYP450</i>. These genes may play important roles in the adaptation of <i>M. coruscus</i> to different living environments. Overall, our study provides a comprehensive understanding of the genomic diversity of coastal <i>M. coruscus</i> in China and is a valuable resource for future studies on genetic breeding and the evolutionary adaptation of this species. |
| first_indexed | 2024-03-10T23:20:26Z |
| format | Article |
| id | doaj.art-5df4daa0e8344189b5409da9e36fc2f6 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T23:20:26Z |
| publishDate | 2023-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-5df4daa0e8344189b5409da9e36fc2f62023-11-19T08:20:12ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-09-0124171364110.3390/ijms241713641Genetic Diversity, Population Structure, and Environmental Adaptation Signatures of Chinese Coastal Hard-Shell Mussel <i>Mytilus coruscus</i> Revealed by Whole-Genome SequencingFeng Guo0Yingying Ye1Kecheng Zhu2Shuangrui Lin3Yuxia Wang4Zhenyu Dong5Ronghui Yao6Hongfei Li7Weifeng Wang8Zhi Liao9Baoying Guo10Xiaojun Yan11National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, ChinaNational Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, ChinaKey Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, ChinaNational Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, ChinaMarine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, ChinaMarine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, ChinaMarine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, ChinaNational Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, ChinaMarine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, ChinaMarine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, ChinaNational Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, ChinaNational Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, ChinaThe hard-shell mussel (<i>Mytilus coruscus</i>) is widespread in the temperate coastal areas of the northwest Pacific and holds a significant position in the shellfish aquaculture market in China. However, the natural resources of this species have been declining, and population genetic studies of <i>M. coruscus</i> are also lacking. In this study, we conducted whole-genome resequencing (WGR) of <i>M. coruscus</i> from eight different latitudes along the Chinese coast and identified a total of 25,859,986 single nucleotide polymorphism (SNP) markers. Our findings indicated that the genetic diversity of <i>M. coruscus</i> from the Zhoushan region was lower compared with populations from other regions. Furthermore, we observed that the evolutionary tree clustered into two primary branches, and the Zhangzhou (ZZ) population was in a separate branch. The ZZ population was partly isolated from populations in other regions, but the distribution of branches was not geographically homogeneous, and a nested pattern emerged, consistent with the population differentiation index (<i>F</i><sub>ST</sub>) results. To investigate the selection characteristics, we utilized the northern <i>M. coruscus</i> populations (Dalian and Qingdao) and the central populations (Zhoushan and Xiangshan) as reference populations and the southern ZZ population as the target population. Our selection scan analysis identified several genes associated with thermal responses, including <i>Hsp70</i> and <i>CYP450</i>. These genes may play important roles in the adaptation of <i>M. coruscus</i> to different living environments. Overall, our study provides a comprehensive understanding of the genomic diversity of coastal <i>M. coruscus</i> in China and is a valuable resource for future studies on genetic breeding and the evolutionary adaptation of this species.https://www.mdpi.com/1422-0067/24/17/13641<i>Mytilus coruscus</i>whole-genome resequencingsingle nucleotide polymorphismsgenetic diversityselection signatures |
| spellingShingle | Feng Guo Yingying Ye Kecheng Zhu Shuangrui Lin Yuxia Wang Zhenyu Dong Ronghui Yao Hongfei Li Weifeng Wang Zhi Liao Baoying Guo Xiaojun Yan Genetic Diversity, Population Structure, and Environmental Adaptation Signatures of Chinese Coastal Hard-Shell Mussel <i>Mytilus coruscus</i> Revealed by Whole-Genome Sequencing International Journal of Molecular Sciences <i>Mytilus coruscus</i> whole-genome resequencing single nucleotide polymorphisms genetic diversity selection signatures |
| title | Genetic Diversity, Population Structure, and Environmental Adaptation Signatures of Chinese Coastal Hard-Shell Mussel <i>Mytilus coruscus</i> Revealed by Whole-Genome Sequencing |
| title_full | Genetic Diversity, Population Structure, and Environmental Adaptation Signatures of Chinese Coastal Hard-Shell Mussel <i>Mytilus coruscus</i> Revealed by Whole-Genome Sequencing |
| title_fullStr | Genetic Diversity, Population Structure, and Environmental Adaptation Signatures of Chinese Coastal Hard-Shell Mussel <i>Mytilus coruscus</i> Revealed by Whole-Genome Sequencing |
| title_full_unstemmed | Genetic Diversity, Population Structure, and Environmental Adaptation Signatures of Chinese Coastal Hard-Shell Mussel <i>Mytilus coruscus</i> Revealed by Whole-Genome Sequencing |
| title_short | Genetic Diversity, Population Structure, and Environmental Adaptation Signatures of Chinese Coastal Hard-Shell Mussel <i>Mytilus coruscus</i> Revealed by Whole-Genome Sequencing |
| title_sort | genetic diversity population structure and environmental adaptation signatures of chinese coastal hard shell mussel i mytilus coruscus i revealed by whole genome sequencing |
| topic | <i>Mytilus coruscus</i> whole-genome resequencing single nucleotide polymorphisms genetic diversity selection signatures |
| url | https://www.mdpi.com/1422-0067/24/17/13641 |
| work_keys_str_mv | AT fengguo geneticdiversitypopulationstructureandenvironmentaladaptationsignaturesofchinesecoastalhardshellmusselimytiluscoruscusirevealedbywholegenomesequencing AT yingyingye geneticdiversitypopulationstructureandenvironmentaladaptationsignaturesofchinesecoastalhardshellmusselimytiluscoruscusirevealedbywholegenomesequencing AT kechengzhu geneticdiversitypopulationstructureandenvironmentaladaptationsignaturesofchinesecoastalhardshellmusselimytiluscoruscusirevealedbywholegenomesequencing AT shuangruilin geneticdiversitypopulationstructureandenvironmentaladaptationsignaturesofchinesecoastalhardshellmusselimytiluscoruscusirevealedbywholegenomesequencing AT yuxiawang geneticdiversitypopulationstructureandenvironmentaladaptationsignaturesofchinesecoastalhardshellmusselimytiluscoruscusirevealedbywholegenomesequencing AT zhenyudong geneticdiversitypopulationstructureandenvironmentaladaptationsignaturesofchinesecoastalhardshellmusselimytiluscoruscusirevealedbywholegenomesequencing AT ronghuiyao geneticdiversitypopulationstructureandenvironmentaladaptationsignaturesofchinesecoastalhardshellmusselimytiluscoruscusirevealedbywholegenomesequencing AT hongfeili geneticdiversitypopulationstructureandenvironmentaladaptationsignaturesofchinesecoastalhardshellmusselimytiluscoruscusirevealedbywholegenomesequencing AT weifengwang geneticdiversitypopulationstructureandenvironmentaladaptationsignaturesofchinesecoastalhardshellmusselimytiluscoruscusirevealedbywholegenomesequencing AT zhiliao geneticdiversitypopulationstructureandenvironmentaladaptationsignaturesofchinesecoastalhardshellmusselimytiluscoruscusirevealedbywholegenomesequencing AT baoyingguo geneticdiversitypopulationstructureandenvironmentaladaptationsignaturesofchinesecoastalhardshellmusselimytiluscoruscusirevealedbywholegenomesequencing AT xiaojunyan geneticdiversitypopulationstructureandenvironmentaladaptationsignaturesofchinesecoastalhardshellmusselimytiluscoruscusirevealedbywholegenomesequencing |