基于3种线粒体标记探讨中日沿海角木叶鲽遗传多样性差异

doi:10.17520/biods.2021485

生物多样性 ›› 2022, Vol. 30 ›› Issue (5): 21485. DOI: 10.17520/biods.2021485

• 研究报告: 遗传多样性 • 上一篇下一篇

基于3种线粒体标记探讨中日沿海角木叶鲽遗传多样性差异

崔静¹, 徐明芳¹, 章群¹^,^*(), 李瑶¹, 曾晓舒¹, 李莎²^,³

1.暨南大学生命科学技术学院, 广州 510632
2.三峡工程鱼类资源保护湖北省重点实验室, 湖北宜昌 443100
3.中国长江三峡集团有限公司中华鲟研究所, 湖北宜昌 443100

收稿日期:2021-11-27 接受日期:2022-01-18 出版日期:2022-05-20 发布日期:2022-03-13
通讯作者: 章群
作者简介:* E-mail: zhangqunjnu@gmail.com
基金资助:
国家重点研发计划(2018YFD0900802);三峡工程鱼类资源保护湖北省重点实验室开放课题(0704157)

Differences in genetic diversity of Pleuronichthys cornutus in the coastal water of China and Japan based on three mitochondrial markers

Jing Cui¹, Mingfang Xu¹, Qun Zhang¹^,^*(), Yao Li¹, Xiaoshu Zeng¹, Sha Li²^,³

1 College of Life Science and Technology, Jinan University, Guangzhou 510632
2 Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang, Hubei 443100
3 Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, Hubei 443100

Received:2021-11-27 Accepted:2022-01-18 Online:2022-05-20 Published:2022-03-13
Contact: Qun Zhang

摘要/Abstract

摘要：

角木叶鲽(Pleuronichthys cornutus)是东亚沿海重要的鲽形目经济鱼类, 为更好地保护和开发利用其种质资源, 有必要全面了解其遗传背景。本研究测定了中国和日本沿海7个群体200尾角木叶鲽线粒体控制区(CR) 5'端、细胞色素b (Cytb)和NADH脱氢酶第二亚基(ND2)基因序列, 比较不同标记在解析遗传多样性和种群结构上的可行性与有效性, 阐明中日沿海角木叶鲽群体间出现遗传分化的分子机制。CR序列分析发现中日沿海7个角木叶鲽群体遗传多样性表现出较高的单倍型多样性(H_d= 0.9699)和较低的核苷酸多样性(π = 0.0061); 各群体间无显著的遗传分化(F_ST = -0.0197-0.0184, P > 0.05); 单倍型网络未显示出明显的地理聚群和谱系结构; 分子方差分析(AMOVA)表明变异主要发生在群体内部(> 99.17%)。进一步通过Cytb和ND2基因分别与CR序列对比分析, 结果表明群体遗传多样性均表现为高H_d(0.9683-0.9829)低π (0.0050-0.0063)模式, 仅有ND2基因分析F_ST值(F_ST= 0.0302, P < 0.05)显示了中国碣石(GDJS)和日本明石(JAP)群体间显著的低水平遗传分化现象。CR、Cytb和ND2的单倍型网络图均无明显的地理聚类和谱系结构, AMOVA分析也显示变异主要来源于群体内(> 98.39%)。种群历史动态分析结果显示, 角木叶鲽可能在第四纪中更新世晚期经历了群体扩张事件, 扩张时间分别为31.93-9.58万年前(CR)、27.53-22.02万年前(Cytb)和26.99-18.75万年前(ND2)。综上所述, 中日沿海的角木叶鲽具有较高遗传多样性, GDJS和JAP群体间存在低度分化; ND2基因比CR和Cytb序列更适于分析角木叶鲽种群遗传结构, 选择多个遗传标记可有效弥补单一标记分析遗传多样性的局限性; 推测冰期两大独立避难所的形成及GDJS和JAP群体距离相隔较远是其发生遗传分化的主要原因。研究结果为中日沿海角木叶鲽渔业资源的种质保护与可持续利用提供了理论依据。

关键词: 角木叶鲽, 遗传多样性, 控制区, 细胞色素b, NADH脱氢酶第二亚基

Abstract

Aims: Understanding genetic diversity and population structure of Pleuronichthys cornutus is essential for the sustainable conservation of threatened fishery resources. This study aims to compare the feasibility and effectiveness of different markers in analyzing genetic diversity and population structure of P. cornutus, and to elucidate the molecular mechanism of genetic differentiation between the populations of P. cornutusin the coastal water of China and Japan.

Methods: A total of 200 individuals of P. cornutus from seven localities in coastal waters of China and Japan were sequenced to assess the genetic diversity and population structure based on three markers of control region (CR, 549 bp), cytochrome b (Cytb, 1,008 bp), and NADH subunit 2 (ND2, 1,044 bp).

Results: CR analysis showed seven populations of P. cornutus in the coastal water of China and Japan had a high haplotype diversity (H_d= 0.9699) and low nucleotide diversity (π = 0.0061), a low and not significant F_ST values (-0.0197-0.0184, P> 0.05), and a high variation within populations (99.17%), indicating that there was no genetic differentiation between the populations, and the haplotype network did not show a clear geographic clustering and genealogical structure among populations. Further analysis of five populations of P. cornutus was done by comparing the Cytb and ND2 genes with CR sequences, respectively. The analysis of genetic diversity (H_d= 0.9683-0.9829, π= 0.0050-0.0063), haplotype distribution, and AMOVA (> 98.39%) by Cytband ND2 genes were consistent with the results of the above analysis of CR sequence. Only the F_STvalue (F_ST= 0.0302, P< 0.05) among populations based on the analysis of the ND2 gene revealed a significant differentiation between the Jieshi population in China and the Akashi population in Japan. The neutrality tests and mismatch analyses based on CR, Cytb, and ND2 sequences, respectively, estimated that P. cornutus may have experienced a recent demographic population expansion event. The expansion was occurred in the late Middle Pleistocene of the Quaternary, which dated from about 319,300 to 95,800 years ago (CR), 275,300 to 220,200 years ago (Cytb), and 269,900 to 187,500 years ago (ND2), respectively.

Conclusion: In summary, high genetic diversity and insignificant genetic differentiation were found in P. cornutusby investigating CRsequences and Cytb and ND2genes, except for a low but significant differentiation between the Jieshi and the Akashi populations in ND2. Hence, ND2 was more suitable than CR and Cytb for the study of population structure of P. cornutus.The presence of two separate refuges during the ice age and the geographical distance were likely to be the main causes of the genetic divergence. The combination of multiple genetic markers in future studies can effectively compensate for the limitations of a single genetic marker for the analysis of population genetic diversity. It provided a theoretical basis for the conservation and sustainable use of the germplasm resources of P. cornutus in the coastal water of China and Japan.

Key words: Pleuronichthys cornutus, genetic diversity, control region, cytochrome b genes, NADH dehydrogenase subunit 2 genes

崔静, 徐明芳, 章群, 李瑶, 曾晓舒, 李莎 (2022) 基于3种线粒体标记探讨中日沿海角木叶鲽遗传多样性差异. 生物多样性, 30, 21485. DOI: 10.17520/biods.2021485.

Jing Cui, Mingfang Xu, Qun Zhang, Yao Li, Xiaoshu Zeng, Sha Li (2022) Differences in genetic diversity of Pleuronichthys cornutus in the coastal water of China and Japan based on three mitochondrial markers. Biodiversity Science, 30, 21485. DOI: 10.17520/biods.2021485.

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链接本文: https://www.biodiversity-science.net/CN/10.17520/biods.2021485

https://www.biodiversity-science.net/CN/Y2022/V30/I5/21485

图/表 12

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海域 Sea region	采样地点 Sample site	样本数量 Sample size	样本编号 Sample no.	经纬度 Coordinates	采样时间 Sampling date	样本来源 Sample source
中国黄海 Yellow Sea, China	辽宁丹东 LNDD	30	LNDD 01-14	39.86° N, 124.16° E	2008.10	朱叶等, 2012
	辽宁丹东 LNDD	30	LNDD 15-30	39.86° N, 124.16° E	2021.04	本研究 This study
	山东青岛 SDQD	36	SDLSh 01-14	36.07° N, 120.42° E	2008.10	朱叶等, 2012
	山东青岛 SDQD	36	SDQD 01-22	36.07° N, 120.38° E	2018.04	本研究 This study
中国东海 East China Sea	浙江舟山 ZJZS	42	ZJDSh 01-13	30.19° N, 122.17° E	2008.11	朱叶等, 2012
	浙江舟山 ZJZS	42	ZJZS 01-29	29.99° N, 122.20° E	2021.05	本研究 This study
	浙江温州 ZJWZ	14	ZJWZ 01-14	28.02° N, 120.79° E	2011.11	本研究 This study
中国南海 South China Sea	广东饶平 GDRP	23	GDRP 01-16	23.62° N, 116.94° E	2008.12	朱叶等, 2012
	广东饶平 GDRP	23	GDNA 01-07	23.42° N, 117.02° E	2021.04	本研究 This study
	广东碣石 GDJS	20	GDJS 01-20	22.81° N, 115.82° E	2014.08	本研究 This study
日本濑户内海 Seto inland sea, Japan	日本明石 JAP	35	JAP 01-35	34.64° N, 134.98° E	2019.07	本研究 This study
合计 Total	-	200	-	-	-	-

海域 Sea region	采样地点 Sample site	样本数量 Sample size	样本编号 Sample no.	经纬度 Coordinates	采样时间 Sampling date	样本来源 Sample source
中国黄海 Yellow Sea, China	辽宁丹东 LNDD	30	LNDD 01-14	39.86° N, 124.16° E	2008.10	朱叶等, 2012
	辽宁丹东 LNDD	30	LNDD 15-30	39.86° N, 124.16° E	2021.04	本研究 This study
	山东青岛 SDQD	36	SDLSh 01-14	36.07° N, 120.42° E	2008.10	朱叶等, 2012
	山东青岛 SDQD	36	SDQD 01-22	36.07° N, 120.38° E	2018.04	本研究 This study
中国东海 East China Sea	浙江舟山 ZJZS	42	ZJDSh 01-13	30.19° N, 122.17° E	2008.11	朱叶等, 2012
	浙江舟山 ZJZS	42	ZJZS 01-29	29.99° N, 122.20° E	2021.05	本研究 This study
	浙江温州 ZJWZ	14	ZJWZ 01-14	28.02° N, 120.79° E	2011.11	本研究 This study
中国南海 South China Sea	广东饶平 GDRP	23	GDRP 01-16	23.62° N, 116.94° E	2008.12	朱叶等, 2012
	广东饶平 GDRP	23	GDNA 01-07	23.42° N, 117.02° E	2021.04	本研究 This study
	广东碣石 GDJS	20	GDJS 01-20	22.81° N, 115.82° E	2014.08	本研究 This study
日本濑户内海 Seto inland sea, Japan	日本明石 JAP	35	JAP 01-35	34.64° N, 134.98° E	2019.07	本研究 This study
合计 Total	-	200	-	-	-	-

地点 Sites	JAP	LNDD	SDQD	ZJZS	ZJWZ	GDRP	GDJS
JAP	-	44.6264	∞	∞	∞	∞	29.9692
LNDD	0.0111	-	109.1491	51.9659	26.7628	34.0782	∞
SDQD	-0.0070	0.0046	-	∞	238.7344	229.9147	198.7032
ZJZS	-0.0046	0.0095	-0.0082	-	∞	∞	56.3828
ZJWZ	-0.0197	0.0184	0.0021	-0.0062	-	∞	31.4081
GDRP	-0.0130	0.0145	0.0022	-0.0188	-0.0071	-	30.4981
GDJS	0.0164	-0.0046	0.0025	0.0088	0.0157	0.0161	-

地点 Sites	JAP	LNDD	SDQD	ZJZS	ZJWZ	GDRP	GDJS
JAP	-	44.6264	∞	∞	∞	∞	29.9692
LNDD	0.0111	-	109.1491	51.9659	26.7628	34.0782	∞
SDQD	-0.0070	0.0046	-	∞	238.7344	229.9147	198.7032
ZJZS	-0.0046	0.0095	-0.0082	-	∞	∞	56.3828
ZJWZ	-0.0197	0.0184	0.0021	-0.0062	-	∞	31.4081
GDRP	-0.0130	0.0145	0.0022	-0.0188	-0.0071	-	30.4981
GDJS	0.0164	-0.0046	0.0025	0.0088	0.0157	0.0161	-

分组方式 Method of grouping	变异比例 Percentage of variation (%)			F_ST 统计值 F_ST statistics (P-value)
分组方式 Method of grouping	组群间 Among groups	组群内群体间 Among populations within groups	群体内 Within populations	F_ST 统计值 F_ST statistics (P-value)
7个群体 Seven populations	0.050	-	99.950	0.00054 (P > 0.05)
中国6个群体和日本1个群体 Six populations from China and one population from Japan	-0.260	0.140	100.120	-0.00118 (P > 0.05)
濑户内海、中国黄海、东海和南海 Seto inland sea, Yellow Sea, East China Sea, and South China Sea	-0.410	0.410	100.000	0.00003 (P > 0.05)
台湾海峡以南和台湾海峡以北 North of Taiwan Strait and south of Taiwan Strait	0.990	-0.160	99.170	-0.00168 (P > 0.05)

基于3种线粒体标记探讨中日沿海角木叶鲽遗传多样性差异

Differences in genetic diversity of Pleuronichthys cornutus in the coastal water of China and Japan based on three mitochondrial markers

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海域 Sea	群体 Population	数量 Sample size	变异位点数 Variable sites	单倍型数 N_h Number of haplotypes	单倍型多样性 H_d Haplotype diversity	核苷酸多样性 π Nucleotide diversity
中国 China	LNDD	29	23	20	0.9606	0.0064
	SDQD	36	21	27	0.9682	0.0063
	ZJZS	42	17	31	0.9826	0.0059
	ZJWZ	14	13	12	0.9780	0.0057
	GDRP	23	10	15	0.9486	0.0055
	GDJS	20	18	16	0.9632	0.0061
日本 Japan	JAP	35	20	23	0.9647	0.0064
总计 Total	-	199	43	90	0.9699	0.0061

群体 Population		数量 Sample size	CR/Cytb/ND2遗传多样性 CR/Cytb/ND2 genetic diversity
群体 Population		数量 Sample size	变异位点 Variable sites	单倍型数 N_h Number of haplotypes	单倍型多样性 H_d Haplotype diversity	核苷酸多样性 π Nucleotide diversity
中国 China	LNDD	30	20/41/36	20/23/22	0.9563/0.9494/0.9678	0.0067/0.0048/0.0048
	SDQD	30	19/44/47	23/27/26	0.9494/0.9908/0.9908	0.0063/0.0058/0.0053
	ZJZS	26	13/27/45	22/22/23	0.9877/0.9846/0.9815	0.0061/0.0039/0.0055
	GDJS	20	18/46/45	16/18/20	0.9632/0.9842/1.0000	0.0061/0.0063/0.0059
日本 Japan	JAP	34	20/40/32	22/25/20	0.9626/0.9768/0.9412	0.0063/0.0050/0.0041
合计 Total		140	35/103/112	74/95/94	0.9683/0.9829/0.9811	0.0063/0.0051/0.0050

序列 Sequences	地点 Sites	JAP	LNDD	SDQD	ZJZS	GDJS
CR	JAP	-	∞	∞	∞	29.3686
	LNDD	-0.0051	-	77.9929	79.3722	∞
	SDQD	-0.0060	0.0064	-	∞	∞
	ZJZS	-0.0302	0.0063	-0.0064	-	19.3728
	GDJS	0.0167	-0.0036	-0.0063	0.0252	-
Cytb	JAP	-	∞	∞	133.9086	49.7008
	LNDD	-0.0059	-	∞	∞	53.3793
	SDQD	-0.0001	-0.0013	-	133.1898	111.8596
	ZJZS	0.0037	-0.0091	0.0037	-	16.1058
	GDJS	0.0100	0.0093	0.0045	0.0301	-
ND2	JAP	-	164.5165	57.1701	369.8704	16.0618
	LNDD	0.0030	-	∞	34.3918	26.5856
	SDQD	0.0087	-0.0037	-	123.8781	∞
	ZJZS	0.0014	0.0143	0.0040	-	27.6373
	GDJS	0.0302*	0.0185	-0.0103	0.0178	-

群体 Population	CR/Cytb/ND2中性检验 CR/Cytb/ND2 neutrality statistics		CR/Cytb/ND2错配分析 CR/Cytb/ND2 mismatch analysis
群体 Population	Tajima’s D	Fu’s F_S	SSD	r	τ
JAP	-1.025/-1.751/-1.624	-15.980/-16.752/-9.805*	0.011*/0.003/0.003	0.044*/0.010/0.019	3.3/4.9/5.0
LNDD	-0.961/-1.943/-1.632	13.064/-15.607/13.174*	0.002/0.002/0.014	0.017/0.006/0.037	3.9/2.4/4.0
SDQD	-0.975/-1.753/-1.983	20.467/-22.938/-21.070*	0.001/0.008/0.006	0.019/0.022/0.016	3.7/4.0/4.0
ZJZS	-0.105/-1.610/-1.966	-21.947/-19.343/-17.299*	0.015*/0.003/0.009	0.052*/0.025/0.017	3.0/3.1/4.0
GDJS	-1.292/-2.044/-2.071	-11.773/-10.660/-17.156*	0.004/0.004/0.016	0.032/0.010/0.030	3.5/4.0/5.0
总体 Overall	-0.872/-1.821/-1.855	-16.646/-17.060/-15.701*	0.006/0.004/0.010	0.033/0.015/0.024	3.5/3.7/4.4

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