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Wu W, Qiu J, Lin Y, Li X, Li W, Duan Y, Fu Y. Analysis of genetic diversity among three Triplophysa tenuis populations by RAD-seq. Front Mol Biosci 2024; 11:1373754. [PMID: 39119476 PMCID: PMC11308663 DOI: 10.3389/fmolb.2024.1373754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 06/19/2024] [Indexed: 08/10/2024] Open
Abstract
To investigate the genetic diversity of Triplophysa tenuis in the Shule River Basin of Gansu province, three populations were sequenced via RAD-seq technology. Twenty-nine microsatellite (SSR) markers with polymorphisms were finally screened to access the genetic diversity among the populations, of which 15 had high polymorphisms. The quantity of the alleles detected in the three populations of T. tenuis varied from 2 to 24. The locus with the most alleles was SSRC1, which had 24 alleles. Among the 29 SSRs, the range of effective allele number, observed heterozygosity, expected heterozygosity, and polymorphic information content were 1.246-16.615, 0.222-1, 0.198-0.940, and 0.178-0.937, respectively. Most of the identified loci were in the Hardy-Weinberg equilibrium. Analysis of the population structure revealed that the Yumen and Changma populations shared the same origin, while the Qiaowan population was different from them. The developed SSR markers discovered in this study will contribute to the conservation research on T. tenuis and the conservation of the fishery resources of the Shule River, providing scientific guidance for the development and utilization of T. tenuis resources and environmental protection.
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Affiliation(s)
- Wenqiong Wu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Junqiang Qiu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Yue Lin
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Xike Li
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Wenjuan Li
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Yuanliang Duan
- Fisheries Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Yuanshuai Fu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
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Liu K, Xie N, Wang Y, Liu X. Extensive mitogenomic heteroplasmy and its implications in the phylogeny of the fish genus Megalobrama. 3 Biotech 2023; 13:115. [PMID: 36915286 PMCID: PMC10006376 DOI: 10.1007/s13205-023-03523-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 02/13/2023] [Indexed: 03/12/2023] Open
Abstract
Megalobrama is China's most economically valuable fish genera. Four species make up this genus: M. amblycephala (MA), M. terminalis (MT), M. pellegrini (MP), and M. hoffmanni (MH). Many researchers have investigated the genetic relationship of Megalobrama based on mitochondrial DNA (mtDNA) and discovered that the branches of the phylogenetic tree for MT and MP are intertwined. We hypothesized that this occurs because mitogenomic heteroplasmy is overlooked when working with mtDNA, which causes MP and MT positions to intersect in phylogenetic trees. To eliminate the influence of nuclear mitochondrial DNA fragments (NUMTs) before analyzing mitogenomic heteroplasmy, we used PLastZ to identify NUMTs, which were then removed from the samples for the subsequent heteroplasmy analysis. Using the heteroplasmy caller icHET, we discovered 126, 339, 135, and 203 heteroplasmic variants in six MA, MT, MP, and MH samples. We reconstructed the Megalobrama fish genus's phylogenetic tree using the RY coding method and rejecting the third position on codons, which improved the performance of the phylogenetic tree by increasing the ratio of treeness to relative component variability from 100.02 ± 1.76 to 688.59 ± 190.56. Despite this, the RY coding method cannot alter the intersection of MP and MT positions in phylogenetic trees. We hypothesize that gene flow between MT and MP leads to intertwining mtDNA-based phylogenetic trees. In conclusion, our findings on the mitogenomic heteroplasmy of Megalobrama provide new insights into mtDNA-based phylogenetic studies. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03523-0.
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Affiliation(s)
- Kai Liu
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Nan Xie
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Yuxi Wang
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Xinyi Liu
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
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Gong D, Wang X, Yang J, Liang J, Tao M, Hu F, Wang S, Liu Z, Tang C, Luo K, Zhang C, Ma M, Wang Y, Liu S. Protection and utilization status of Parabramis and Megalobrama germplasm resources. REPRODUCTION AND BREEDING 2023. [DOI: 10.1016/j.repbre.2023.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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Huo B, Liu X, Chen S, Liu J, Zhou Q, Shen J, Li D, Tang R, Chen J, Zhou X. Population Structure, Genetic Diversity and Differentiation of Triplophysa tenuis in Xinjiang Tarim River. Front Genet 2022; 13:860678. [PMID: 35309126 PMCID: PMC8927061 DOI: 10.3389/fgene.2022.860678] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 02/17/2022] [Indexed: 11/28/2022] Open
Abstract
Triplophysa tenuis is an important indigenous fish in the Xinjiang Tarim River. In this study, we collected 120 T. tenuis individuals from 8 T. tenuis populations in the Tarim River. Through genotyping-by-sequencing (GBS), a total of 582,678,756 clean reads were generated for all the genotypes, and after quality filtering, 595,379 SNPs were obtained for the population genetic analyses. Multiple genetic parameters showed that the 8 T. tenuis populations had high genetic diversity. Phylogenetic tree analysis indicated that all T. tenuis individuals were divided into five branches, the individuals from the north of Tarim River were grouped into cluster 1 (SF and WS) and cluster 3 (DWQ, TKX, and KZE), while the AETS, WLWT and LF individuals from the south of Tarim River were clustered into cluster 2. The result was consistent with the admixture analysis, which supported that the 8 T. tenuis populations were clustered into three subgroups. Furthermore, the pairwise FST values and genetic distance indicated that there was a large genetic differentiation between WS and other T. tenuis populations. Collectively, this study provides valuable genome-wide data for the conservation of natural T. tenuis populations in the Tarim River.
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Affiliation(s)
- Bin Huo
- College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Xuan Liu
- College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Shengao Chen
- College of Animal Science, Tarim University, Alar, China
| | - Jieya Liu
- College of Animal Science, Tarim University, Alar, China
| | - Qiong Zhou
- College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Jianzhong Shen
- College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Dapeng Li
- College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Rong Tang
- College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Jing Chen
- College of Fisheries, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Jing Chen, ; Xiaoyun Zhou,
| | - Xiaoyun Zhou
- College of Fisheries, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Jing Chen, ; Xiaoyun Zhou,
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