| GenBank中裂腹鱼类COI基因序列的分子标记有效性 |
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| 引用本文： | 袁晓倩,迪丽娜·茹斯坦木,张琪,韩洁.GenBank中裂腹鱼类COI基因序列的分子标记有效性[J].中国水产科学,2022,29(7):1073-1090. |
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| 作者姓名： | 袁晓倩 迪丽娜·茹斯坦木 张琪 韩洁 |
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| 作者单位： | 新疆大学生命科学与技术学院, 新疆 乌鲁木齐 830046;北京师范大学生命科学学院, 生物多样性与生态工程教育部重点实验室, 北京 100875;新疆大学生命科学与技术学院, 新疆 乌鲁木齐 830046 ；北京师范大学生命科学学院, 生物多样性与生态工程教育部重点实验室, 北京 100875 |
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| 基金项目： | 科技部国家科技基础资源调查专项(2019FY101700)； 生物多样性与生态工程教育部重点实验室自主课题. |
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| 摘 要： | 裂腹鱼类(Schizothoracids)分布有复杂的水系格局, 在形态学鉴定时有些鱼种容易混淆。线粒体细胞色素 C 氧化酶亚基 I(CO I)基因是动物学研究中常用的物种分子条形码, 分析 GenBank 数据库中裂腹鱼类 CO I 作为分子标记的有效性, 可以加深理解和认识前人用这些数据所做的研究工作, 也为今后更合理地使用这些数据提供参考依据。本研究对 GenBank 数据库中裂腹鱼类 CO I 基因的分子标记有效性进行分析评估, 通过同源性比对、参考序列间遗传分歧的估算和系统发育关系重建等方法, 判断 GenBank 数据库中裂腹鱼类 CO I 基因序列的同源性、序列所属鱼种鉴定的准确性, 以及序列信息对系统发育关系的解析力。通过对下载的 1431 条序列进行多重比对发现, 有 3 条序列与其他序列存在显著差异, 同源性存疑, 数据信息经 BLAST 相似性搜索和核查确认为, 以 CO I 基因的互补链形式提交的序列, 比对前应先进行互补链转换。全部序列的比对结果显示, GenBank 数据库中裂腹鱼类的 CO I 基因片段序列均为该基因近 5?端至中部的序列。权衡序列的数量和长度后, 舍弃较短的 35 条序列, 保留长度为 527 bp 的 1396 条序列进行分析, 结果共定义了 228 个单倍型, 在有多条序列的鱼种中, 普遍存在种内共享单倍型, 还有 41 个单倍型为种间共享。裂腹鱼类 CO I 单倍型的平均 p-距离为 9.5%, 与鱼类的属级水平相当, 原始、 特化和高度特化类群各自的平均 p-距离值更低, 体现近期辐射演化的特征, 可能与它们随着青藏高原演化成种的历史较短有关。GenBank 中一些裂腹鱼类 CO I 基因序列的鱼种鉴定存在错误, 在使用时应先与参考序列对比, 或从系统发育分析的角度做出判断。总体来看, CO I 基因序列能够有力解析裂腹鱼类各演化等级裂腹鱼类之间的亲缘关系, 可用于分类和演化的初步分析。结合形态学、生态学、线粒体和核基因的多样性及系统发育关系等进行综合分析, 将有助于更准确地界定裂腹鱼种类, 同时也为深入探讨杂交和成种过程等问题奠定基础。
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| 关 键 词： | 裂腹鱼类 CO I 分子标记有效性 GenBank |
Validity of the CO I sequences from Schizothoracids in GenBank as a molecular marker |
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| YUAN Xiaoqian,RUSTAM Delar,ZHANG Qi,HAN Jie.Validity of the CO I sequences from Schizothoracids in GenBank as a molecular marker[J].Journal of Fishery Sciences of China,2022,29(7):1073-1090. |
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| Authors: | YUAN Xiaoqian RUSTAM Delar ZHANG Qi HAN Jie |
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| Abstract: | The validity of the mitochondrial cytochrome C oxidase subunit I (CO I) sequences from Schizothoracids in GenBank as a molecular marker was determined in this study. Multiple sequence alignment, divergence from reference sequence assessment, and phylogenetic reconstruction were employed to evaluate the sequence homology, species diagnosis, and phylogenetic resolution of CO I sequences from Schizothoracids in GenBank. The primary alignment result for 1431 downloaded sequences revealed three sequences with significantly large indels; however, their homologous status was questionable. BLAST search and sequence information in GenBank confirmed that these sequences were Schizothoracid CO I sequences that were submitted as complements. Accordingly, prior to alignment, complement transition of these sequences should be carried out. Complete multiple sequence alignment revealed that all Schizothoracid CO I fragments in the GenBank nucleotide database were from near the 5? end to the middle of this coding gene. To retain more variation information, 35 short sequences were eliminated from the dataset. As a result, 1,396 sequences with 527 bp were analyzed, and 228 CO I haplotypes were defined. Intra-specific sharing haplotypes were common in species with multiple available sequences. However, 41 inter-specific sharing haplotypes were shared by more than one species. The average pairwise p-distance within the Schizothoracid CO I haplotypes was 9.5%, which is comparable with the cogeneric species level in fish. The average pairwise p-distances within the primitive, specialized, and highly specialized Schizothoracids were even shorter, a character of recent radiation that may reflect a short speciation history mainly driven by the elevation of the Qinghai-Tibet Plateau. Specimen misidentification was found in some Schizothoracid CO I sequences in GenBank, suggesting confirmation steps before use, such as comparison with reference sequences or inference from the phylogenetic reconstruction. Generally, the CO I sequence is a good molecular marker for Schizothoracids identification and primary evolutionary analysis, and the phylogenetic relationships among the three evolutionary grades of Schizothoracids are well resolved using this marker. Integrative analyses, including morphology, ecology, mitochondrial and nuclear DNA diversity, and phylogeny, would aid in taxonomic resolution and further investigation of hybridization and speciation in Schizothoracids. |
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