Population genomics provides insights into the population structure and temperature-driven adaptation of Collichthys lucidus
Abstract Background Understanding the genetic structure and local adaptive evolutionary mechanisms of marine organisms is crucial for the management of biological resources. As the ecologically and commercially important small-sized shallow-sea fish, Collichthys lucidus plays a vital role in the str...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2021-10-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-021-08045-8 |
| _version_ | 1819026884796612608 |
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| author | Linlin Zhao Fangyuan Qu Na Song Zhiqiang Han Tianxiang Gao Zhaohui Zhang |
| author_facet | Linlin Zhao Fangyuan Qu Na Song Zhiqiang Han Tianxiang Gao Zhaohui Zhang |
| author_sort | Linlin Zhao |
| collection | DOAJ |
| description | Abstract Background Understanding the genetic structure and local adaptive evolutionary mechanisms of marine organisms is crucial for the management of biological resources. As the ecologically and commercially important small-sized shallow-sea fish, Collichthys lucidus plays a vital role in the structure and functioning of marine ecosystem processes. C. lucidus has been shown to have an obvious population structure. Therefore, it is an ideal candidate for investigating population differentiation and local adaptation under heterogeneous environmental pressure. Results A total of 184,708 high-quality single nucleotide polymorphisms (SNPs) were identified and applied to elucidate the fine-scale genetic structure and local thermal adaptation of 8 C. lucidus populations. Population structure analysis based on all SNPs indicated that the northern group and southern group of C. lucidus have a strong differentiation. Moreover, 314 SNPs were found to be significantly associated with temperature variation, and annotations of genes containing temperature-related SNPs suggested that genes were involved in material (protein, lipid, and carbohydrate) metabolism and immune responses. Conclusion The high genetic differentiation of 8 C. lucidus populations may have been caused by long-term geographic isolation during the glacial period. Moreover, we suspected that variation in these genes associated with material (protein, lipid, and carbohydrate) metabolism and immune responses was critical for adaptation to spatially heterogeneous temperatures in natural C. lucidus populations. In conclusion, this study could help us determine how C. lucidus populations will respond to future ocean temperature rising. |
| first_indexed | 2024-12-21T05:33:40Z |
| format | Article |
| id | doaj.art-7c9bd70769d1434492e93c294ea3a933 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-21T05:33:40Z |
| publishDate | 2021-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-7c9bd70769d1434492e93c294ea3a9332022-12-21T19:14:28ZengBMCBMC Genomics1471-21642021-10-0122111010.1186/s12864-021-08045-8Population genomics provides insights into the population structure and temperature-driven adaptation of Collichthys lucidusLinlin Zhao0Fangyuan Qu1Na Song2Zhiqiang Han3Tianxiang Gao4Zhaohui Zhang5First Institute of Oceanography, Ministry of Natural ResourcesFirst Institute of Oceanography, Ministry of Natural ResourcesFisheries College, Ocean University of ChinaSchool of Fishery, Zhejiang Ocean UniversitySchool of Fishery, Zhejiang Ocean UniversityFirst Institute of Oceanography, Ministry of Natural ResourcesAbstract Background Understanding the genetic structure and local adaptive evolutionary mechanisms of marine organisms is crucial for the management of biological resources. As the ecologically and commercially important small-sized shallow-sea fish, Collichthys lucidus plays a vital role in the structure and functioning of marine ecosystem processes. C. lucidus has been shown to have an obvious population structure. Therefore, it is an ideal candidate for investigating population differentiation and local adaptation under heterogeneous environmental pressure. Results A total of 184,708 high-quality single nucleotide polymorphisms (SNPs) were identified and applied to elucidate the fine-scale genetic structure and local thermal adaptation of 8 C. lucidus populations. Population structure analysis based on all SNPs indicated that the northern group and southern group of C. lucidus have a strong differentiation. Moreover, 314 SNPs were found to be significantly associated with temperature variation, and annotations of genes containing temperature-related SNPs suggested that genes were involved in material (protein, lipid, and carbohydrate) metabolism and immune responses. Conclusion The high genetic differentiation of 8 C. lucidus populations may have been caused by long-term geographic isolation during the glacial period. Moreover, we suspected that variation in these genes associated with material (protein, lipid, and carbohydrate) metabolism and immune responses was critical for adaptation to spatially heterogeneous temperatures in natural C. lucidus populations. In conclusion, this study could help us determine how C. lucidus populations will respond to future ocean temperature rising.https://doi.org/10.1186/s12864-021-08045-8Collichthys lucidusGenetic diversityPopulation structureLocal adaptivePopulation genomics |
| spellingShingle | Linlin Zhao Fangyuan Qu Na Song Zhiqiang Han Tianxiang Gao Zhaohui Zhang Population genomics provides insights into the population structure and temperature-driven adaptation of Collichthys lucidus BMC Genomics Collichthys lucidus Genetic diversity Population structure Local adaptive Population genomics |
| title | Population genomics provides insights into the population structure and temperature-driven adaptation of Collichthys lucidus |
| title_full | Population genomics provides insights into the population structure and temperature-driven adaptation of Collichthys lucidus |
| title_fullStr | Population genomics provides insights into the population structure and temperature-driven adaptation of Collichthys lucidus |
| title_full_unstemmed | Population genomics provides insights into the population structure and temperature-driven adaptation of Collichthys lucidus |
| title_short | Population genomics provides insights into the population structure and temperature-driven adaptation of Collichthys lucidus |
| title_sort | population genomics provides insights into the population structure and temperature driven adaptation of collichthys lucidus |
| topic | Collichthys lucidus Genetic diversity Population structure Local adaptive Population genomics |
| url | https://doi.org/10.1186/s12864-021-08045-8 |
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