大吻斜齿鲨基因组遗传资源调研分析

doi:10.11924/j.issn.1000-6850.casb2025-0473

中国农学通报 ›› 2025, Vol. 41 ›› Issue (28): 139-145.doi: 10.11924/j.issn.1000-6850.casb2025-0473

大吻斜齿鲨基因组遗传资源调研分析

刘晓茹(), 李明僧, 张耀仁, 徐胜勇()

浙江海洋大学水产学院，浙江舟山 316022

收稿日期:2025-06-12 修回日期:2025-08-18 出版日期:2025-10-05 发布日期:2025-10-10
通讯作者:
徐胜勇，男，1989年出生，山东青岛人，副研究员，博士，主要从事海洋鱼类基因组学研究。通信地址：316022 浙江省舟山市浙江海洋大学新城校区浙江海洋大学水产学院，Tel：0580-2556416，E-mail：shengyong@zjou.edu.cn。
作者简介:
刘晓茹，女，2002年出生，四川雅安人，在读硕士研究生，研究方向：海洋鱼类基因组学。通信地址：316022 浙江省舟山市浙江海洋大学新城校区浙江海洋大学水产学院，E-mail：Liuxiaoru@zjou.edu.cn。
基金资助:
国家自然科学基金项目“基于群体基因组学的条纹斑竹鲨种群遗传格局及生态适应研究”(32200413); 国家重点研发计划项目“东海渔业资源一体化修复与海洋牧场构建技术”(2023YFD2401901)

Genomic Profiling and Genetic Resource Evaluation of Scoliodon macrorhynchos

LIU Xiaoru(), LI Mingseng, ZHANG Yaoren, XU Shengyong()

School of Fisheries of Zhejiang Ocean University, Zhoushan, Zhejiang 316022

Received:2025-06-12 Revised:2025-08-18 Published:2025-10-05 Online:2025-10-10

摘要/Abstract

摘要： 大吻斜齿鲨(Scoliodon macrorhynchos)是中国近海常见的软骨鱼类，近年来其种群资源持续衰退，已被IUCN红色名录列为近危物种。为深入了解该物种并为其科学管理和保护提供依据，对其基因组遗传资源进行调研分析。利用全基因组重测序对大吻斜齿鲨基因组DNA序列进行测序，并利用重测序数据进行基因组初步组装和质量评估。在全基因组范围内识别微卫星简单序列重复位点，并计算其相对丰度。使用生物信息学软件从头组装线粒体基因组全序列，并将其与已发布的GenBank参考序列进行比较分析，识别变异位点，确定这些变异位点在基因组上的位置（蛋白质编码基因、tRNA基因、控制区），并分析非同义替换的情况。结果显示，大吻斜齿鲨基因组大小、杂合率、重复序列比例和GC含量分别为2991.63 Mb、0.46%、63.37%、44.34%。基因组初步组装长度为2482 Mb，scaffold N₅₀为3342 bp。基于组装的基因组序列共识别出470542个微卫星位点，其相对丰度约为189.58个/Mb。从头组装获得的大吻斜齿鲨线粒体基因组全序列长度为16693 bp，与已发布的GenBank参考序列一致。线粒体全序列比较分析共检测到19个变异位点，其中16个位于蛋白质编码基因、2个位于tRNA基因、1个位于控制区。在蛋白质编码基因的变异位点中，共有4个非同义替换位点，分别位于COIII、ND4、ND5和Cyt b基因。本研究表明，大吻斜齿鲨基因组应为复杂型基因组。线粒体基因组的比较分析显示，蛋白质编码基因区域具有较高的变异性。在线粒体关键功能基因(COIII、ND4、ND5、Cyt b)中均检测到多个非同义替换位点，提示松散的净化选择可能是该物种线粒体基因组进化的主要驱动力。本研究首次构建了大吻斜齿鲨的基因组草图，开发了大量微卫星标记，揭示了其线粒体基因组变异特征，为后续开展大吻斜齿鲨的种群遗传结构解析、适应性进化研究及制定针对性生物多样性保护策略提供了重要的遗传资源和分子工具。

关键词: 大吻斜齿鲨, 基因组调研分析, 基因组组装, 微卫星位点, 线粒体全序列

Abstract:

The Pacific spadenose shark (Scoliodon macrorhynchos) is a cartilaginous fish commonly found in China's coastal waters. In recent years, the population resources of this species are continuously declining and it has been listed as Near Threatened on the IUCN Red List. In order to further understand the species and provide a basis for its scientific management and protection, this study investigated and analyzed genomic genetic resources of S. macrorhynchos. In this study, whole-genome resequencing was performed on the genomic DNA of the S. macrorhynchos. Using the resequencing data, preliminary genome assembly was conducted and its quality was evaluated. Genome-wide identification of microsatellite loci was carried out with calculation of their relative abundance. The complete mitochondrial genome sequence was de novo assembled using bioinformatics software. The assembled mitochondrial sequence was comparatively analyzed against published GenBank reference sequences to identify variant sites; variations were annotated by genomic location (protein-coding genes, tRNA genes, and the control region) and analyzed for nonsynonymous substitutions. The results showed that the genome of the S. macrorhynchos exhibited the following characteristics: size= 2991.63 Mb, heterozygosity rate= 0.46%, repetitive sequence proportion= 63.37% and GC content= 44.34%. The preliminary genome assembly yielded a total length of 2482 Mb with a scaffold N₅₀ of 3342 bp. A total of 470542 microsatellite loci were identified genome-wide, with a relative abundance of about 189.58 loci/Mb. The complete mitochondrial genome sequence (16693 bp) was de novo assembled using bioinformatics tools, consistent with published GenBank reference sequences. Comparative analysis revealed 19 variant sites in the mitochondrial genome: 16 in protein-coding genes, 2 in tRNA genes, and 1 in the control region. Among variants in protein-coding genes, 4 were nonsynonymous substitutions located in the COIII, ND4, ND5, and Cyt b genes. The genome of the S. macrorhynchos is likely of a complex type. This study obtained foundational genetic resources including a draft genome assembly, genome-wide microsatellite markers, and mitochondrial genome data. Comparative mitochondrial genome analysis revealed heightened variability in protein-coding regions. Multiple nonsynonymous substitutions detected in key mitochondrial genes (COIII, ND4, ND5, Cyt b) suggest that relaxed purifying selection may be the primary evolutionary driver of the mitochondrial genome in this species. This research aims to provide essential genetic resources for advancing S. macrorhynchos genomics studies, investigations of genetic evolution, and conservation initiatives.

Key words: Scoliodon macrorhynchos, genomic survey analysis, genome assembly, microsatellite loci, complete mitochondrial genome

刘晓茹, 李明僧, 张耀仁, 徐胜勇. 大吻斜齿鲨基因组遗传资源调研分析[J]. 中国农学通报, 2025, 41(28): 139-145.

LIU Xiaoru, LI Mingseng, ZHANG Yaoren, XU Shengyong. Genomic Profiling and Genetic Resource Evaluation of Scoliodon macrorhynchos[J]. Chinese Agricultural Science Bulletin, 2025, 41(28): 139-145.

图/表 7

参考文献 38

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文库	原始数据/bp	有效率/%	错误率/%	Q₂₀/%	Q₃₀/%	GC含量/%
文库1	51352795200	84.85	0.03	96.19	90.92	43.04
文库2	52587060600	84.77	0.03	96.00	90.33	43.04

文库	原始数据/bp	有效率/%	错误率/%	Q₂₀/%	Q₃₀/%	GC含量/%
文库1	51352795200	84.85	0.03	96.19	90.92	43.04
文库2	52587060600	84.77	0.03	96.00	90.33	43.04

组装水平	全长/bp	总数	最大长度/bp	N₅₀长度/bp
Contig	2459384968	3119882	49092	2759
Scaffold	2482038903	2855390	76040	3342

组装水平	全长/bp	总数	最大长度/bp	N₅₀长度/bp
Contig	2459384968	3119882	49092	2759
Scaffold	2482038903	2855390	76040	3342

基因	变异位点数量	非同义位点数量	同义位点数量
ND1	1	0	1
tRNA-Ile	1	—	—
ND2	3	0	3
COI	1	0	1
ATP6	2	0	2
COIII	2	1	1
ND3	2	0	2
tRNA-Arg	1	—	—
ND4	2	1	1
ND5	2	1	1
Cyt b	1	1	0
CR	1	—	—

大吻斜齿鲨基因组遗传资源调研分析

Genomic Profiling and Genetic Resource Evaluation of Scoliodon macrorhynchos

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