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Gao K, He Z, Xiong J, Chen Q, Lai B, Liu F, Chen P, Chen M, Luo W, Huang J, Ding W, Wang H, Pu Y, Zheng L, Jiao Y, Zhang M, Tang Z, Yue Q, Yang D, Yan T. Population structure and adaptability analysis of Schizothorax o'connori based on whole-genome resequencing. BMC Genomics 2024; 25:145. [PMID: 38321406 PMCID: PMC10845765 DOI: 10.1186/s12864-024-09975-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 01/04/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND Schizothorax o'connori is an endemic fish distributed in the upper and lower reaches of the Yarlung Zangbo River in China. It has experienced a fourth round of whole gene replication events and is a good model for exploring the genetic differentiation and environmental adaptability of fish in the Qinghai-Tibet Plateau. The uplift of the Qinghai-Tibet Plateau has led to changes in the river system, thereby affecting gene exchange and population differentiation between fish populations. With the release of fish whole genome data, whole genome resequencing has been widely used in genetic evolutionary analysis and screening of selected genes in fish, which can better elucidate the genetic basis and molecular environmental adaptation mechanisms of fish. Therefore, our purpose of this study was to understand the population structure and adaptive characteristics of S. o'connori using the whole-genome resequencing method. RESULTS The results showed that 23,602,746 SNPs were identified from seven populations, mostly distributed on chromosomes 2 and 23. There was no significant genetic differentiation between the populations, and the genetic diversity was relatively low. However, the Zangga population could be separated from the Bomi, Linzhi, and Milin populations in the cluster analysis. Based on historical dynamics analysis of the population, the size of the ancestral population of S. o'connori was affected by the late accelerated uplift of the Qinghai Tibet Plateau and the Fourth Glacial Age. The selected sites were mostly enriched in pathways related to DNA repair and energy metabolism. CONCLUSION Overall, the whole-genome resequencing analysis provides valuable insights into the population structure and adaptive characteristics of S. o'connori. There was no obvious genetic differentiation at the genome level between the S. o'connori populations upstream and downstream of the Yarlung Zangbo River. The current distribution pattern and genetic diversity are influenced by the late accelerated uplift of the Qinghai Tibet Plateau and the Fourth Ice Age. The selected sites of S. o'connori are enriched in the energy metabolism and DNA repair pathways to adapt to the low temperature and strong ultraviolet radiation environment at high altitude.
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Affiliation(s)
- Kuo Gao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Zhi He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jinxin Xiong
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Qiqi Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Bolin Lai
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Fei Liu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Ping Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Mingqiang Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Wenjie Luo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Junjie Huang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Wenxiang Ding
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Haochen Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yong Pu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Li Zheng
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yuanyuan Jiao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Mingwang Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Ziting Tang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Qingsong Yue
- Huadian Tibet Hydropower Development Co.,Ltd, Dagu Hydropower Station, Sangri, 856200, Shannan, China
| | - Deying Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.
| | - Taiming Yan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.
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Mu W, Li K, Yang Y, Breiman A, Lou S, Yang J, Wu Y, Wu S, Liu J, Nevo E, Catalan P. Scattered differentiation of unlinked loci across the genome underlines ecological divergence of the selfing grass Brachypodium stacei. Proc Natl Acad Sci U S A 2023; 120:e2304848120. [PMID: 37903254 PMCID: PMC10636366 DOI: 10.1073/pnas.2304848120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 09/27/2023] [Indexed: 11/01/2023] Open
Abstract
Ecological divergence without geographic isolation, as an early speciation process that may lead finally to reproductive isolation through natural selection, remains a captivating topic in evolutionary biology. However, the pattern of genetic divergence underlying this process across the genome may vary between species and mating systems. Here, we present evidence that Brachypodium stacei, an annual and highly selfing grass model species, has undergone sympatric ecological divergence without geographic isolation. Genomic, transcriptomic, and metabolomic analyses together with lab experiments mimicking the two opposite environmental conditions suggest that diploid B. stacei populations have diverged sympatrically in two slopes characterized by distinct biomes at Evolution Canyon I (ECI), Mount Carmel, Israel. Despite ongoing gene flow, primarily facilitated by seed dispersal, the level of gene flow has progressively decreased over time. This local adaptation involves the scattered divergence of many unlinked loci across the total genome that include both coding genes and noncoding regions. Additionally, we have identified significant differential expressions of genes related to the ABA signaling pathway and contrasting metabolome composition between the arid- vs. forest-adapted B. stacei populations in ECI. These results suggest that multiple small loci involved in environmental responses act additively to account for ecological adaptations by this selfing species in contrasting environments.
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Affiliation(s)
- Wenjie Mu
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou730000, China
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou730000, China
- Departamento de Agricultura y Medio Ambiente, Escuela Politecnica Superior de Huesca, Universidad de Zaragoza, Huesca22071, Spain
| | - Kexin Li
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Adina Breiman
- Department of Molecular Biology and Ecology of Plants, Faculty of Life Sciences, University of Tel-Aviv, Tel-Aviv6997801, Israel
| | - Shangling Lou
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Jiao Yang
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Ying Wu
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Shuang Wu
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Eviatar Nevo
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Mount Carmel, Haifa3498838, Israel
| | - Pilar Catalan
- Departamento de Agricultura y Medio Ambiente, Escuela Politecnica Superior de Huesca, Universidad de Zaragoza, Huesca22071, Spain
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O’Brien SJ, Luo SJ. Taxonomic species recognition should be consistent. Natl Sci Rev 2022; 9:nwad022. [PMID: 36788967 PMCID: PMC9923365 DOI: 10.1093/nsr/nwad022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/23/2023] [Indexed: 01/26/2023] Open
Affiliation(s)
- Stephen J O’Brien
- Guy Harvey Oceanographic Center, Halmos College of Arts and Sciences, Nova Southeastern University, USA
| | - Shu-Jin Luo
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, China
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