Population genetic structure of Pelteobagrus vachelli in the upper Yangtze River based on genome re-sequencing

doi:10.17520/biods.2022391

Abstract

Abstract:

Aims: Pelteobagrus vachelli is an important economic fish in the Yangtze River. Nevertheless, it shows a trend of younger age and miniaturization, and the number of reproductive population above the third age was small, which is not benefit to the long-term maintenance of its resources. Therefore, more attention and conservation measure are needed for this species. The aim of this study is to clarify genetic diversity and genetic structure of P. vachelli.

Methods: We collected 136 samples of eight different river sections (Taipingxi, Banan, Hechuan, Minjiangkou, Yibin, Shaonüping, Huixi, Fengjiaping) from the Three Gorges Dam to Baihetan Dam in the upper Yangtze River. High-throughput SNP (single nucleotide polymorphism) markers through genome re-sequencing method was used to study genetic diversity and genetic differentiation of P. vachellipopulations.

Results: The number of SNP and nucleotide diversity of Taipingxi and Banan populations in the Three Gorges Reservoir region were significantly higher than those in the other populations, and there were three genetic branches and abundant genetic sources in the two populations. However, there was only one genetic branch and single genetic source in Minjiangkou, Yibin, Shaonüping and Fengjiaping populations. The populations could be divided into three distinct genetic groups with great genetic differentiation. All individuals in Fengjiaping and Minjiangkou belonged to group 1, all individuals in Shaonüping and Yibin belonged to group 2, Huixi and Hechuan populations had two genetic branches (group 1 and group 2), and Banan and Taipingxi populations had three genetic branches (group 1, group 2 and group 3). The SNP number and nucleotide diversity were significantly affected by channel slope. The genetic differentiation was not related to geographical distance and isolated time.

Conclusion: The upstream populations with lower genetic diversity are more prone to genetic drift and thus need more attention in the fish protection. There are three distinct genetic structures in the upper Yangtze River, which can be regarded as three different genetic units for management of germplasm resource.

Key words: Pelteobagrus vachelli, the upper Yangtze River, genetic differentiation, genetic diversity, genome re-sequencing

Fei Xiong, Hongyan Liu, Dongdong Zhai, Xinbin Duan, Huiwu Tian, Daqing Chen. Population genetic structure of Pelteobagrus vachelli in the upper Yangtze River based on genome re-sequencing[J]. Biodiv Sci, 2023, 31(4): 22391.

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URL: https://www.biodiversity-science.net/EN/10.17520/biods.2022391

https://www.biodiversity-science.net/EN/Y2023/V31/I4/22391

Figures/Tables 9

References 31

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群体 Population	采样时间 Sampling time	样本数 No. of sample	海拔 Elevation (m)	坡降 Channel slope (m/km)	生境类型 Habitat type
太平溪 TP	2019.8	14	110	0.12	水库 Reservoir
巴南 BN	2019.8	25	160	0.20	回水区 Backwater area
合川 HC	2019.9	4	187	1.85	水库 Reservoir
岷江口 MJ	2019.10	25	257	2.26	河流 River
宜宾 YB	2019.10	6	253	0.70	河流 River
邵女坪 SN	2019.10	12	296	0.90	水库 Reservoir
桧溪 HX	2019.10	25	356	1.40	河流 River
冯家坪 FJ	2019.10	25	578	1.50	河流 River

群体 Population	采样时间 Sampling time	样本数 No. of sample	海拔 Elevation (m)	坡降 Channel slope (m/km)	生境类型 Habitat type
太平溪 TP	2019.8	14	110	0.12	水库 Reservoir
巴南 BN	2019.8	25	160	0.20	回水区 Backwater area
合川 HC	2019.9	4	187	1.85	水库 Reservoir
岷江口 MJ	2019.10	25	257	2.26	河流 River
宜宾 YB	2019.10	6	253	0.70	河流 River
邵女坪 SN	2019.10	12	296	0.90	水库 Reservoir
桧溪 HX	2019.10	25	356	1.40	河流 River
冯家坪 FJ	2019.10	25	578	1.50	河流 River

群体 Population	样本数 No. of sample	Clean data (Gb)	Q30 (%)	测序深度Sequencing depth	序列比对率 Sequence mapped (%)	基因组覆盖度Coverage of genomic reference (%)	SNP数目 Number of SNP	核苷酸多样性指数Nucleotide diversity
太平溪 TP	14	145.22	93.11	9.54	54.31	72.92	4,172,876	2.44 × 10^?3
巴南 BN	25	236.41	92.82	8.71	53.43	71.68	3,543,176	2.81 × 10^?3
合川 HC	4	35.77	92.81	8.38	49.94	66.28	534,504	8.59 × 10^?4
岷江口 MJ	25	217.32	92.73	8.25	50.68	66.39	419,733	5.60 × 10^?4
宜宾 YB	6	50.16	91.87	7.44	48.50	67.36	563,968	6.76 × 10^?4
邵女坪 SN	12	128.29	92.79	9.37	49.09	69.64	457,603	5.75 × 10^?4
桧溪 HX	25	258.76	92.79	9.20	49.22	68.87	597,465	6.60 × 10^?4
冯家坪 FJ	25	273.27	92.78	9.57	49.06	69.73	441,092	5.84 × 10^?4
总体 Total	136	1,345.21	92.78	8.95	50.73	69.43	7,341,959	1.19 × 10^?3

群体 Population	样本数 No. of sample	Clean data (Gb)	Q30 (%)	测序深度Sequencing depth	序列比对率 Sequence mapped (%)	基因组覆盖度Coverage of genomic reference (%)	SNP数目 Number of SNP	核苷酸多样性指数Nucleotide diversity
太平溪 TP	14	145.22	93.11	9.54	54.31	72.92	4,172,876	2.44 × 10^?3
巴南 BN	25	236.41	92.82	8.71	53.43	71.68	3,543,176	2.81 × 10^?3
合川 HC	4	35.77	92.81	8.38	49.94	66.28	534,504	8.59 × 10^?4
岷江口 MJ	25	217.32	92.73	8.25	50.68	66.39	419,733	5.60 × 10^?4
宜宾 YB	6	50.16	91.87	7.44	48.50	67.36	563,968	6.76 × 10^?4
邵女坪 SN	12	128.29	92.79	9.37	49.09	69.64	457,603	5.75 × 10^?4
桧溪 HX	25	258.76	92.79	9.20	49.22	68.87	597,465	6.60 × 10^?4
冯家坪 FJ	25	273.27	92.78	9.57	49.06	69.73	441,092	5.84 × 10^?4
总体 Total	136	1,345.21	92.78	8.95	50.73	69.43	7,341,959	1.19 × 10^?3

群体 Population	太平溪 TP	巴南 BN	合川 HC	岷江口 MJ	宜宾 YB	邵女坪 SN	桧溪 HX
巴南 BN	0.050
合川 HC	?0.109	?0.039
岷江口 MJ	0.112	0.143	0.075
宜宾 YB	?0.020	0.043	0.152	0.233
邵女坪 SN	0.068	0.112	0.192	0.235	0.000
桧溪 HX	0.126	0.154	0.079	0.179	?0.008	0.002
冯家坪 FJ	0.125	0.152	0.092	0.016	0.261	0.257	0.193