基于基因组Survey数据的深海尾鳗微卫星特征及系统发育关系分析

doi:10.11924/j.issn.1000-6850.casb2025-0057

中国农学通报 ›› 2025, Vol. 41 ›› Issue (25): 153-164.doi: 10.11924/j.issn.1000-6850.casb2025-0057

• 水产·渔业 • 上一篇

基于基因组Survey数据的深海尾鳗微卫星特征及系统发育关系分析

郑昀凯(), 刘鹏辉, 牛世洋, 杨天燕()

浙江海洋大学水产学院，浙江舟山 316022

收稿日期:2025-01-16 修回日期:2025-06-03 出版日期:2025-09-05 发布日期:2025-09-16
通讯作者:
杨天燕，女，1982年出生，湖北武汉人，副教授，博士，研究方向：渔业资源学。通信地址：316022 浙江省舟山市定海区临城街道海大南路1号，E-mail：hellojelly1130@163.com。
作者简介:
郑昀凯，男，2003年出生，浙江衢州人，研究方向：海洋资源与环境。通信地址：316022 浙江省舟山市定海区临城街道海大南路1号，E-mail：1257263225@qq.com。
基金资助:
浙江省自然科学基金项目“东海蛇鳗科鱼类线粒体基因组重排模式与分类系统演化研究”(LMS25D060002); 舟山市科技计划项目“东海重要海洋鱼类种质资源保护技术研究”(2022C41022); 国家级大学生创新创业训练计划项目“两种深海鳗鲡目鱼类基因组Survey及微卫星分布特征分析”(202410340014)

Analysis of Microsatellites Characterization and Phylogenetic Relationship for Bathyuroconger vicinus Based on Genomic Survey Data

ZHENG Yunkai(), LIU Penghui, NIU Shiyang, YANG Tianyan()

Fishery College of Zhejiang Ocean University, Zhoushan, Zheijiang 316022

Received:2025-01-16 Revised:2025-06-03 Published:2025-09-05 Online:2025-09-16

摘要/Abstract

摘要： 为探究深海尾鳗对极端环境的基因组适应机制及系统演化地位，本研究首次对其开展全基因组Survey测序与系统分析。采用Illumina NovaSeq 6000平台进行基因组测序，结合SOAPdenovo2组装基因组草图，利用MISA筛选微卫星位点，基于线粒体蛋白质编码基因串联序列构建系统发育树。结果显示，深海尾鳗基因组大小约为1414 Mb，杂合率、重复序列比例分别为0.66%、54.93%。筛选得到总长度为10936848 bp的微卫星位点共计1221434个，分布在698950条序列上，发生频率、出现频率和相对丰度分别为19.18%、33.53%和857.57个/Mb。在6种完整型微卫星中，二碱基重复类型占比最大（804493个，65.86%）、出现频率最高(22.08%)且相对丰度最大（564.84个/Mb）。在1484种微卫星重复基元中，种类最多的为六碱基重复基元（668种），其次为五碱基重复（583种）、四碱基重复（231种）、三碱基重复（60种）、二碱基重复（12种）和单碱基重复（4种）。其优势碱基类别分别为A(128843，43.40%)、CA(239966，29.83%)、AAT(9533，12.30%)、AAAT(2663，8.16%)、CATTA(316，5.40%)和CACACT(268，6.56%)。基于线粒体蛋白质编码基因串联序列构建的最大似然树显示，深海尾鳗与尖尾鳗属鱼类的亲缘关系较近。本研究揭示了深海尾鳗基因组的复杂特征及丰富的多态性微卫星位点，为其深海适应机制研究提供了分子基础；筛选的微卫星位点可用于种群遗传学分析；系统发育结果支持其与尖尾鳗属鱼类的近缘关系，明确了其在康吉鳗亚科中的演化地位，并提示康吉鳗科可能为多系群。

关键词: 深海尾鳗, 基因组测序, 微卫星标记, 系统发育, 鳗鲡目

Abstract:

In order to explore the genomic adaptation mechanism and phylogenetic status of Bathyuroconger vicinus to extreme environments, this study carried out whole genome Survey sequencing and systematic analysis for the first time. The Illumina NovaSeq 6000 platform was used for genome sequencing, combined with the SOAPdenovo2 assembly genome sketch, MISA was used to screen microsatellite loci, and a phylogenetic tree was constructed based on the mitochondrial protein-coding gene tandem sequence. K-mer analysis revealed that the genome size of B. vicinus was approximately 1414 Mb, with the heterozygosity rate and repeat sequence proportion of 0.66% and 54.93%, respectively. A total of 1221434 microsatellite loci were identified, with an overall length of 10936848 bp. These microsatellites were randomly distributed across 698950 sequences, with the occurrence frequency, appearance frequency and relative abundance of 19.18%, 33.53%, and 857.57 loci/Mb, respectively. Among the six perfect microsatellite types, the dinucleotide repeat was the most prevalent (804493, 65.86%), with the highest appearance frequency (22.08%) and the greatest relative abundance (564.84 loci/Mb). There were 1484 repeat motifs in all, of which hexanucleotide repeat was the most diverse (668), followed by pentanucleotide repeat (583), tetranucleotide repeat (231), trinucleotide repeat (60), dinucleotide repeat (12), and mononucleotide repeat (4). The dominant repeat motifs were A (128843, 43.40%), CA (239966, 29.83%), AAT (9533, 12.30%), AAAT (2663, 8.16%), CATTA (316, 5.40%), and CACACT (268, 6.56%). The phylogenetic tree based on the concatenated sequences of mitochondrial protein-coding genes was constructed by using the maximum likelihood (ML) method. The topology indicated a close relationship between B. vicinus and the species from genus Uroconger. This study revealed the complex characteristics of B. vicinusis genome and numerous highly polymorphic microsatellite loci, which provided a molecular basis for the study of its deep-sea adaptation mechanism. The selected microsatellite loci can be used for population genetics analysis. The phylogenetic results supported its close relationship with the fish of the genus Uroconger, clarified its evolutionary status in the subfamily Congrinae, and suggested that Congridae may be a polyphyletic group.

Key words: Bathyuroconger vicinus, genome sequencing, microsatellite loci, phylogenetic, Anguilliformes

郑昀凯, 刘鹏辉, 牛世洋, 杨天燕. 基于基因组Survey数据的深海尾鳗微卫星特征及系统发育关系分析[J]. 中国农学通报, 2025, 41(25): 153-164.

ZHENG Yunkai, LIU Penghui, NIU Shiyang, YANG Tianyan. Analysis of Microsatellites Characterization and Phylogenetic Relationship for Bathyuroconger vicinus Based on Genomic Survey Data[J]. Chinese Agricultural Science Bulletin, 2025, 41(25): 153-164.

图/表 12

参考文献 51

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亚科	属	种	GenBank序列号
深海康吉鳗亚科Bathymyrinae	美体鳗属Ariosoma	梅氏美体鳗Ariosoma meeki	OK585090
	美体鳗属Ariosoma	细美体鳗Ariosoma shiroanago	AP010861
	副康吉鳗属Paraconger	几内亚副康吉鳗Paraconger notialis	AP010860
	副康吉鳗属Paraconger	尾边副康吉鳗Paraconger caudilimbatus	OR582666
异康吉鳗亚科Heterocongrinae	异康吉鳗属Heteroconger	哈氏异康吉鳗Heteroconger hassi	AP010859
康吉鳗亚科Congrinae	康吉鳗属Conger	暗康吉鳗Conger erebennus	OM691699
		星康吉鳗Conger myriaster	AB038381
		美洲康吉鳗Conger oceanicus	OR546244
		日本康吉鳗Conger japonicus	KR131863
	异唇鳗属Xenomystax	似康吉异唇鳗Xenomystax congroides	OR482507
	异唇鳗属Xenomystax	异唇鳗Xenomystax atrarius	OR482465
	吻鳗属Rhynchoconger	黑尾吻鳗Rhynchoconger ectenurus	MN256490
	尖尾鳗属Uroconger	尖尾鳗Uroconger lepturus	OR581023
	尖尾鳗属Uroconger	丝尾鳗Uroconger syringinus	OP056976
	深海尾鳗属Bathyuroconger	深海尾鳗Bathyuroconger vicinus	OP035192
	深海尾鳗属Bathyuroconger	深海尾鳗Bathyuroconger vicinus	本研究

亚科	属	种	GenBank序列号
深海康吉鳗亚科Bathymyrinae	美体鳗属Ariosoma	梅氏美体鳗Ariosoma meeki	OK585090
	美体鳗属Ariosoma	细美体鳗Ariosoma shiroanago	AP010861
	副康吉鳗属Paraconger	几内亚副康吉鳗Paraconger notialis	AP010860
	副康吉鳗属Paraconger	尾边副康吉鳗Paraconger caudilimbatus	OR582666
异康吉鳗亚科Heterocongrinae	异康吉鳗属Heteroconger	哈氏异康吉鳗Heteroconger hassi	AP010859
康吉鳗亚科Congrinae	康吉鳗属Conger	暗康吉鳗Conger erebennus	OM691699
		星康吉鳗Conger myriaster	AB038381
		美洲康吉鳗Conger oceanicus	OR546244
		日本康吉鳗Conger japonicus	KR131863
	异唇鳗属Xenomystax	似康吉异唇鳗Xenomystax congroides	OR482507
	异唇鳗属Xenomystax	异唇鳗Xenomystax atrarius	OR482465
	吻鳗属Rhynchoconger	黑尾吻鳗Rhynchoconger ectenurus	MN256490
	尖尾鳗属Uroconger	尖尾鳗Uroconger lepturus	OR581023
	尖尾鳗属Uroconger	丝尾鳗Uroconger syringinus	OP056976
	深海尾鳗属Bathyuroconger	深海尾鳗Bathyuroconger vicinus	OP035192
	深海尾鳗属Bathyuroconger	深海尾鳗Bathyuroconger vicinus	本研究

组装级别	总长度/bp	序列数量	序列数量(≥2 kb)	N₅₀值/bp	GC含量/%
Contig	1895343751	12514712	42840	238	43.1
Scaffold	1424281181	3643303	104841	828	40.6

组装级别	总长度/bp	序列数量	序列数量(≥2 kb)	N₅₀值/bp	GC含量/%
Contig	1895343751	12514712	42840	238	43.1
Scaffold	1424281181	3643303	104841	828	40.6

重复类型	数量	出现频率/%	相对丰度/(个/Mb)	平均长度/bp	总长度/bp
单碱基重复	296884	8.15	208.44	10.73	3186246
二碱基重复	804493	22.08	564.84	7.25	5835940
三碱基重复	77485	2.13	54.40	14.61	1132785
四碱基重复	32633	0.90	22.91	17.36	566572
五碱基重复	5852	0.16	4.11	23.21	135805
六碱基重复	4087	0.11	2.87	19.45	79500
总计	1221434	33.53	857.57	92.61	10936848

基于基因组Survey数据的深海尾鳗微卫星特征及系统发育关系分析

Analysis of Microsatellites Characterization and Phylogenetic Relationship for Bathyuroconger vicinus Based on Genomic Survey Data

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重复次数	单碱基重复/个	二碱基重复/个	三碱基重复/个	四碱基重复/个	五碱基重复/个	六碱基重复/个	合计/个	占比/%
5	0	0	24332	15525	3615	1746	45218	3.70
6	0	221468	13981	7176	1041	851	244517	20.02
7	0	139104	9972	3520	496	595	153687	12.58
8	0	98297	7153	1851	280	889	108470	8.88
9	0	75633	5270	1179	200	6	82288	6.74
10	110388	61055	4006	908	220	0	176577	14.46
11	58531	50354	2920	890	0	0	112695	9.23
12	37803	41211	2295	1472	0	0	82781	6.78
13	25846	31658	1881	112	0	0	59497	4.87
14	18068	23904	1614	0	0	0	43586	3.57
15	12542	17012	2355	0	0	0	31909	2.61
16	9291	11955	1629	0	0	0	22875	1.87
17	6651	8163	77	0	0	0	14891	1.22
18	4814	5869	0	0	0	0	10683	0.87
19	3501	4235	0	0	0	0	7736	0.63
20	2384	3340	0	0	0	0	5724	0.47
21	1807	2825	0	0	0	0	4632	0.38
22	1313	2852	0	0	0	0	4165	0.34
23	897	3860	0	0	0	0	4757	0.39
24	634	1635	0	0	0	0	2269	0.19
>25	2414	63	0	0	0	0	2477	0.20

重复类型	种类/种	最多重复基元			最少重复基元
重复类型	种类/种	重复基元	数量/个	占比/%	重复基元	数量/个	占比/%
单碱基重复	4	A	128843	43.40	G	29248	9.85
二碱基重复	12	CA	239966	29.83	GC	522	0.06
三碱基重复	60	AAT	9533	12.30	ACG	14	0.02
四碱基重复	231	AAAT	2663	8.16	ACGA/ACGT/ATCG/ CCCA/CCGA/CGAA/ CGAT/CGTA/TACG/TCGG	1	0.00
五碱基重复	583	CATTA	316	5.40	—	1	0.02
六碱基重复	668	CACACT	268	6.56	—	1	0.02

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