基于线粒体COI序列片段研究华鳈不同地理群体及其他鳈属鱼类的遗传多样性

doi:10.3969/j.issn.1004-1524.20230874

浙江农业学报 ›› 2024, Vol. 36 ›› Issue (8): 1779-1788.DOI: 10.3969/j.issn.1004-1524.20230874

基于线粒体COI序列片段研究华鳈不同地理群体及其他鳈属鱼类的遗传多样性

黄辉(), 储忝江, 谢楠, 刘凯()

杭州市农业科学研究院水产研究所,浙江杭州 310024

收稿日期:2023-07-24 出版日期:2024-08-25 发布日期:2024-09-06
作者简介:*刘凯,E-mail: xqa9038@dingtalk.com
黄辉(1988—),男,浙江温岭人,学士,工程师,主要从事水产养殖工作。E-mail: 47411354@qq.com
通讯作者: 刘凯
基金资助:
杭州市农业和社会发展一般项目(202203B17);杭州市农科院创新基金项目(2022HNCT-01)

Investigation on the genetic diversity of Sarcocheilichthys sinensis from diverse geographical populations and other species within the Sarcocheilichthys genus through the analysis of mitochondrial COI sequence segments

HUANG Hui(), CHU Tianjiang, XIE Nan, LIU Kai()

Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China

Received:2023-07-24 Online:2024-08-25 Published:2024-09-06
Contact: LIU Kai

摘要/Abstract

摘要：

鳈属(Sarcocheilichthys)鱼类是东亚地区常见小型淡水鱼类,并具有一定的养殖开发潜力。深入了解鳈属鱼类的遗传结构及其地域变异,对科学制定保护计划和可持续利用野生资源具有重要意义。试验采用鳈属鱼类包括小鳈(S. parvus, XQ)20尾,江西鳈(S. kiangsiensis, JXQ)20尾,黑鳍鳈(S. nigripinnis, HQQ)20尾,东北鳈(S. lacustris, DBQ)24尾,华鳈(S. sinensis)淮河群体(HQ_HH)20尾、闽江群体(HQ_MJ)17尾、江西群体(HQ_JX)15尾和建德群体(HQ_JD)17尾,并对每个群体的线粒体细胞色素C氧化酶亚基Ⅰ(cytochrome C oxidase subunit Ⅰ, COI)序列片段进行了测序和分析。试验结果表明,在获得的153个样本序列(668 bp)中,保守位点507个,变异位点154个,简约信息位点150个,碱基缺失或插入位点27个,平均转换与颠换比值为5.2。HQQ群体的单倍型多样性(H_d)最低(0.442),HQ_HH群体的H_d略高于HQQ群体(0.574),DBQ群体的H_d则稍高于HQ_HH群体(0.707),而XQ群体的H_d最高(0.963),HQ_MJ和HQ_JX群体的H_d则略低于XQ群体(0.860、0.848)。核苷酸多样变化趋势则与H_d结果类似。153尾个体定义了56种单倍型,各群体的单倍型网络中均存在各自群体的主要单倍型,如Hap_2、Hap_33和Hap_37等。基于遗传距离构建的UPGMA分子系统发育树、层次聚类树和NeighborNet分子系统发育网络表明,XQ、HQQ、JXQ和其他鳈属鱼类间遗传关系较远,而DBQ与HQ_HH群体间遗传关系较近。该研究利用COI序列片段评估了4个华鳈地理群体及其他4种鳈属鱼类的遗传多样性。研究结果将有助于了解华鳈不同地理群体及其他4种鳈属鱼类野生资源的遗传多样性现状,为今后华鳈以及其他4种鳈属鱼类种质资源保护及利用提供参考。

关键词: 华鳈, 鳈属, 线粒体, COI, 遗传多样性

Abstract:

The genus Sarcocheilichthys, commonly found in East Asia, comprises small freshwater fish species with potential for aquaculture and development. Gaining a thorough understanding of the genetic structure and geographic variation of Sarcocheilichthys fish is of great significance for scientifically formulating conservation plans and ensuring sustainable utilization of wild resources. The experimental subjects included S. parvus(XQ) of 20 individuals, S. kiangsiensis(JXQ) of 20 individuals, S. nigripinnis(HQQ) of 20 individuals, S. lacustris(DBQ) of 24 individuals, and multiple geographic populations of S. sinensis, including Huaihe population (HQ_HH) of 20 individuals, Minjiang population (HQ_MJ) of 17 individuals, Jiangxi population (HQ_JX) of 15 individuals, and Jiande population (HQ_JD) of 17 individuals. The mitochondrial cytochrome C oxidase subunit I (COI) sequence segments of each population were sequenced and analyzed. Among the 153 obtained sequence samples, there were 507 conserved sites, 154 variable sites, 150 parsimony informative sites, and 27 sites with base deletions or insertions, with an average transition/transversion ratio of 5.2. The H_d (haplotype diversity) of the HQQ population was the lowest (0.442), slightly higher in the HQ_HH population (0.574), and further increased in the DBQ population (0.707). The XQ population showed the highest H_d (0.963), while HQ_MJ and HQ_JX populations had slightly lower H_d values than XQ (0.860 and 0.848, respectively). Nucleotide diversity exhibited a similar trend to H_d results. A total of 153 individuals defined 56 haplotypes, and each population exhibited major haplotypes within their respective haplotype networks, such as Hap_2, Hap_33, and Hap_37, among others. The UPGMA molecular phylogenetic tree, hierarchical clustering tree, and NeighborNet molecular phylogenetic network constructed based on genetic distance indicated that the genetic relationships between XQ, HQQ, JXQ, and other Sarcocheilichthys fish were relatively distant. At the same time, DBQ had a closer genetic relationship with the HQ_HH population. This study used COI sequence segments to assess the genetic diversity of four geographic populations of S. sinensis and four other Sarcocheilichthys species. The research results contribute to understanding the current genetic diversity of different geographic populations of S. sinensis and four other Sarcocheilichthys species, providing valuable insights for the conservation and breeding of germplasm resources in S. sinensis and other Sarcocheilichthys fish in the future.

Key words: Sarcocheilichthys sinensis, Sarcocheilichthys genus, mitochondria, COI, genetic diversity

中图分类号:

黄辉, 储忝江, 谢楠, 刘凯. 基于线粒体COI序列片段研究华鳈不同地理群体及其他鳈属鱼类的遗传多样性[J]. 浙江农业学报, 2024, 36(8): 1779-1788.

HUANG Hui, CHU Tianjiang, XIE Nan, LIU Kai. Investigation on the genetic diversity of Sarcocheilichthys sinensis from diverse geographical populations and other species within the Sarcocheilichthys genus through the analysis of mitochondrial COI sequence segments[J]. Acta Agriculturae Zhejiangensis, 2024, 36(8): 1779-1788.

图/表 5

表1 鳈属鱼类不同群体COI序列片段的碱基组成

Table 1 The base composition of COI sequence segments from different populations of Sarcocheilichthys fish species

群体Populations	T/%	C/%	A/%	G/%	A+T/%	C+G/%	TS/TV
华鳈淮河群体, HQ_HH Huaihe population of S. sinensis	27.28	28.90	23.66	20.16	50.94	49.06	2.0
华鳈建德群体HQ_JD Jiande population of S. sinensis	27.79	28.21	24.02	19.98	51.81	48.19	1.7
华鳈江西群体HQ_JX Jiangxi population of S. sinensis	27.88	28.14	24.14	19.84	52.02	47.98	20.7
华鳈闽江群体HQ_MJ Minjiang population of S. sinensis	27.89	28.06	24.60	19.45	52.49	47.51	11.2
东北鳈 DBQ S. lacustris	27.29	28.87	23.69	20.15	50.98	49.02	1.8
黑鳍鳈HQQ S. nigripinnis	29.36	27.66	23.89	19.09	53.25	46.75	1.7
江西鳈JXQ S. kiangsiensis	27.96	29.05	23.53	19.46	51.49	48.51	4.5
小鳈XQ S. parvus	29.45	27.13	24.76	18.66	54.21	45.79	7.6

表2 鳈属鱼类不同群体COI序列片段的遗传多样性参数

Table 2 Genetic diversity parameters of COI sequence segments from different populations of Sarcocheilichthys fish species

群体 Populations	变异位点数 Number of variation sites	单倍型数 Haplotype number	单倍型多样性H_d Haplotype diversity	核苷酸多样性π Nucleotide diversity	Tajima’s D	Fu’s Fs
华鳈淮河群体, HQ_HH	3	4	0.574	0.001 01	-0.526 40	-0.881 90
Huaihe population of S. sinensis
华鳈建德群体HQ_JD	5	6	0.794	0.001 96	-0.892 18	-1.793 11
Jiande population of S. sinensis
华鳈江西群体HQ_JX	18	9	0.848	0.007 90	-0.110 15	-0.130 98
Jiangxi population of S. sinensis
华鳈闽江群体HQ_MJ	26	9	0.860	0.013 80	0.908 58	2.052 88
Minjiang population of S. sinensis
东北鳈 DBQ S. lacustris	7	9	0.707	0.001 70	-1.210 45	-5.311 87^*
黑鳍鳈HQQ S. nigripinnis	4	5	0.442	0.000 98	-1.205 71	-2.218 43^*
江西鳈JXQ S. kiangsiensis	4	5	0.774	0.001 91	0.388 91	-0.487 48
小鳈XQ S. parvus	47	15	0.963	0.024 58	1.020 70	-1.012 20

图1 基于TCS算法的COI序列片段单倍型网络图 DBQ、HQHH、HQJD、HQJX、HQMJ、HQQ、JXQ和XQ分别表示东北鳈、华鳈淮河群体、华鳈建德群体、华鳈江西群体、华鳈闽江群体、黑鳍鳈,江西鳈和小鳈。下同。

Fig.1 The haplotype network of the COI sequence segments based on the TCS algorithm DBQ, HQHH, HQJD, HQJX, HQMJ, HQQ, JXQ and XQ represent S. lacustris, Huaihe population of S. sinensis, Jiande population of S. sinensis, Jiangxi population of S. sinensis, Minjiang population of S. sinensis, S. nigripinnis, S. kiangsiensis, and S. parvus. The same as below.

表3 鳈属鱼类不同群体内(对角线,粗体)及群体间(对角线下)遗传距离

Table 3 Genetic distances within (highlighted in bold along the diagonal) and between different populations (below the diagonal) of Sarcocheilichthys fish species

群体Populations	HQ_HH	HQ_JD	HQ_JX	HQ_MJ	DBQ	HQQ	JXQ	XQ
HQ_HH	0.001 03
HQ_JD	0.017 13	0.001 27
HQ_JX	0.017 19	0.011 93	0.007 80
HQ_MJ	0.028 84	0.024 98	0.025 11	0.013 56
DBQ	0.001 59	0.017 36	0.017 45	0.028 98	0.001 74
HQQ	0.135 76	0.134 12	0.133 94	0.131 88	0.135 99	0.001 00
JXQ	0.128 40	0.137 85	0.132 57	0.131 41	0.129 88	0.065 47	0.001 94
XQ	0.148 29	0.143 67	0.140 44	0.135 06	0.148 53	0.133 86	0.140 44	0.025 27

图2 基于COI序列片段构建的UPGMA系统发育树、分层聚类树和NeighborNet系统发育网络 A,利用UPGMA方法构建的系统发育树,数字代表Bootstrap概率值;B,利用分层聚类方法构建的聚类树,红色数字表示近似无偏P值,绿色数字表示Bootstrap概率值,支长度对应样本相关性的绝对值;C,利用NeighborNet方法构建的系统发育网络。

Fig.2 The UPGMA phylogenetic tree, the hierarchical clustering tree, and the NeighborNet phylogenetic network constructed based on the COI sequence segments A, The phylogenetic tree constructed using the UPGMA method. The numbers represent bootstrap probability values. B, The clustering tree constructed using the hierarchical clustering method. The red numbers indicate approximate unbiased P-values, while the green numbers represent bootstrap probability values. Branch lengths correspond to the absolute values of sample correlations. C, The phylogenetic network constructed using the NeighborNet method.

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基于线粒体COI序列片段研究华鳈不同地理群体及其他鳈属鱼类的遗传多样性

Investigation on the genetic diversity of Sarcocheilichthys sinensis from diverse geographical populations and other species within the Sarcocheilichthys genus through the analysis of mitochondrial COI sequence segments

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