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

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

Abstract

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

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.

Figures/Tables 12

References 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