基于线粒体COI和12S rDNA基因构建珠江河口鱼类DNA宏条形码数据库

蒋佩文; 李敏; 张帅; 陈作志; 徐姗楠

doi:10.12131/20210210

基于线粒体COI和12S rDNA基因构建珠江河口鱼类DNA宏条形码数据库

doi: 10.12131/20210210

蒋佩文^{1, 2, 3,},
李敏^{2, 3},
张帅²,
陈作志^{2, 3},
徐姗楠^{2, 3, ,}

1.
上海海洋大学水产与生命学院，上海 201306
2.
中国水产科学研究院南海水产研究所/农业农村部外海渔业可持续利用重点实验室/广东省渔业生态环境重点实验室，广东广州 510300
3.
南方海洋科学与工程广东省实验室 (广州)，广东广州 511458

基金项目: 广东省基础与应用基础研究重大项目 (2019B030302004-05)；广东省科技计划项目 (2019B121201001)；南方海洋科学与工程广东省实验室 (广州) 人才团队引进重大专项 (GML2019ZD0605)；中国水产科学研究院南海水产研究所中央级公益性科研院所基本科研业务费专项资金资助 (2019TS13, 2021SD18)

详细信息

作者简介:
蒋佩文(1997—)，男，硕士研究生，研究方向为水生生物学。E-mail: wdnmd19974529@163.com

通讯作者:
徐姗楠 (1979—)，女，研究员，博士，从事海洋生物学研究。E-mail: xushannan@scsfri.ac.cn

中图分类号: S 917.4
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出版历程
- 收稿日期: 2021-07-28
- 修回日期: 2021-08-16
- 录用日期: 2021-09-03
- 网络出版日期: 2021-10-18
- 刊出日期: 2022-06-05

Construction of DNA meta-barcode database of fish in Pearl River Estuary based on mitochondrial cytochrome COI and 12S rDNA gene

JIANG Peiwen^{1, 2, 3
,},
LI Min^{2, 3},
ZHANG Shuai²,
CHEN Zuozhi^{2, 3},
XU Shannan^{2, 3
, ,}

1.
College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
2.
South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences/Key Laboratory for Sustainable Utilization of Open-Sea Fishery, Ministry of Agriculture and Rural Affairs/Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, Guangzhou 510300, China
3.
Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China

摘要

摘要: 为建立珠江河口鱼类本底DNA条形码数据库，为珠江河口鱼类种类识别和多样性研究提供信息化基础，于2020—2021年在珠江河口采集鱼类样本251尾，测定了6目10科41属99种鱼类的219条线粒体COI基因5'端的652 bp序列和247条线粒体12S rDNA基因5'端的163~185 bp序列。同时，从GenBank数据库下载珠江河口鱼类COI序列165条和12S rDNA序列128条，共获得172种鱼类的384条COI序列与375条12S rDNA序列，初步构建了珠江河口鱼类条形码数据库。研究发现：COI序列种内平均遗传距离为0.20%，种间平均遗传距离为25.54%；12S rDNA序列种内平均遗传距离为0.12%，种间平均遗传距离为34.39%。基于COI基因的DNA条形码可形成明显的条形码间隙；而基于12S rDNA基因的DNA条形码不能形成明显的条形码间隙，11个物种 (占总种类的6.4%) 存在区分困难的情况。珠江河口鱼类DNA条形码数据库的建立，有利于推进该河口鱼类生态系统的环境DNA分析，并为珠江河口鱼类生物多样性的保护和种群动态监测提供可靠的技术支持。
- 鱼类 /
- COI基因 /
- 12S rDNA基因 /
- DNA条形码数据库 /
- 珠江河口
Abstract: In order to establish a DNA barcode background database of fish in the Pearl River Estuary and provide information basis for fish species identification and diversity research, we had collected 251 samples from the Pearl River Estuary from 2020 to 2021, and determined 652 bp fragments of mitochondrial cytochrome oxidase subunit I (COI) of 219 individuals and 163−185 bp fragments of mitochondrial 12s rDNA of 247 individuals of 99 species, 10 families, 41 genera, 6 orders. Besides, we downloaded 165 COI sequences and 128 12S rDNA sequences from GenBank database, and had obtained 384 COI sequences and 375 12S rDNA sequences of 172 species of fish. The results show that the average intraspecific genetic distance of COI sequence was 0.20%, and the average interspecific genetic distance was 25.54%. The average intraspecific genetic distance of 12S rDNA sequence was 0.12%, and the average interspecific genetic distance was 34.39%. The DNA barcode of COI gene could form an obvious barcode gap, but the DNA barcode based on 12s rDNA gene could not, and it was difficult to distinguish the 11 species (6.4% of the total species). The establishment of the DNA barcode database of fish in the Pearl River Estuary is conductive to the environmental DNA analysis of the fish ecosystem in that area, providing reliable technical support for the protection of fish biodiversity and the monitoring of population dynamics in the Pearl River Estuary.
- Fish /
- COI gene /
- 12S rDNA gene /
- DNA barcode database /
- Pearl River Estuary

HTML全文

图 1 珠江河口采样站位

Figure 1. Sampling stations in Pearl River Estuary

下载: 全尺寸图片幻灯片

图 2 珠江河口鱼类种类组成

Figure 2. Fish species composition in Pearl River Estuary

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图 3 基于COI基因 (a) 和12S rDNA基因 (b) 的种内和种间K2P遗传距离的频率分布

Figure 3. Frequency distributions of intraspecific and interspecific pairwise genetic K2P distance based on COI gene (a) and 12S rDNA gene (b)

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图 4 基于COI序列构建的系统发育树

Figure 4. Phylogenetic tree based on COI sequence

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图 5 基于12S rDNA序列构建的系统发育树

Figure 5. Phylogenetic tree based on 12S rDNA sequence

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表 1 基于COI和12S rDNA序列的种内与种间遗传距离

Table 1. Genetic distance of intraspecies and interspecies based on mitochondrial COI and 12S rDNA sequences %

遗传距离 Genetic distance	COI序列 COI sequence			12S rDNA序列 12S rDNA sequence
遗传距离 Genetic distance	最小值 Minmum	最大值 Maxium	平均值 Mean	最小值 Minmum	最大值 Maxium	平均值 Mean
种内 Intraspecies	0	1.66	0.2	0	1.79	0.12
种间 Interspecies	2.16	40.87	25.54	0.59	72.32	34.39

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