对GenBank分类输入错误的更正提出了一个关于Salangidae (osmeriforma: Salangidae)间属间关系的新问题。

IF 0.9 Q3 AGRICULTURE, MULTIDISCIPLINARY
E S Balakirev
{"title":"对GenBank分类输入错误的更正提出了一个关于Salangidae (osmeriforma: Salangidae)间属间关系的新问题。","authors":"E S Balakirev","doi":"10.18699/vjgb-25-29","DOIUrl":null,"url":null,"abstract":"<p><p>The GenBank database of publicly available nucleotide sequences is the largest genetic repository providing vitally important resources for downstream applications in biology and medicine. The concern raised about reliability of GenBank data necessitates monitoring of possible taxonomic entry errors. A case of mitochondrial genome (or mitogenome) misidentification for a salangid fish belonging to the genus Neosalanx (Osmeriformes, Salangidae) is considered in this report. The GenBank database contains four complete mitogenome sequences of N. taihuensis with the accession numbers JX524196, KP170510, MH348204, and MW291630. The overall mean p-distance for these sequences is quite high (7.01 ± 0.14 %) but becomes 29-fold lower (0.24 ± 0.05 %) after excluding the MW291630 mitogenome. An analysis of all available nucleotide sequences of salangids has shown that the observed inconsistency in the level of divergence between N. taihuensis mitogenomes is due to species misidentification. It has turned out that the mitogenome MW291630 available in GenBank does not belong to N. taihuensis, but is, in fact, a mitogenome of N. jordani misidentified as N. taihuensis. The resolved taxonomic identity of the MW291630 mitogenome, as well as an extended sample of species with investigated single-marker sequences, has raised some new issues regarding intergeneric relationships in salangid fishes. In particular, the obtained data do not support synonymization of the genus Neosalanx with Protosalanx, as was suggested in the last revision of the salangid classification. As the comparative analysis of interspecific and intergeneric divergences shows, Protosalanx is not an all-inclusive clade that includes all Neosalanx species. Instead, it consists of (at least) two evolutionary distinct lineages with the level of genetic divergence between them matching well the mean value of divergence between the other salangid genera. Further analysis using nuclear genome-wide data is required to have new insights into the evolution of salangid fishes.</p>","PeriodicalId":44339,"journal":{"name":"Vavilovskii Zhurnal Genetiki i Selektsii","volume":"29 2","pages":"259-267"},"PeriodicalIF":0.9000,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12010254/pdf/","citationCount":"0","resultStr":"{\"title\":\"Correction of GenBank's taxonomic entry error raises a new issue regarding intergeneric relationships among salangid fishes (Osmeriformes: Salangidae).\",\"authors\":\"E S Balakirev\",\"doi\":\"10.18699/vjgb-25-29\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>The GenBank database of publicly available nucleotide sequences is the largest genetic repository providing vitally important resources for downstream applications in biology and medicine. The concern raised about reliability of GenBank data necessitates monitoring of possible taxonomic entry errors. A case of mitochondrial genome (or mitogenome) misidentification for a salangid fish belonging to the genus Neosalanx (Osmeriformes, Salangidae) is considered in this report. The GenBank database contains four complete mitogenome sequences of N. taihuensis with the accession numbers JX524196, KP170510, MH348204, and MW291630. The overall mean p-distance for these sequences is quite high (7.01 ± 0.14 %) but becomes 29-fold lower (0.24 ± 0.05 %) after excluding the MW291630 mitogenome. An analysis of all available nucleotide sequences of salangids has shown that the observed inconsistency in the level of divergence between N. taihuensis mitogenomes is due to species misidentification. It has turned out that the mitogenome MW291630 available in GenBank does not belong to N. taihuensis, but is, in fact, a mitogenome of N. jordani misidentified as N. taihuensis. The resolved taxonomic identity of the MW291630 mitogenome, as well as an extended sample of species with investigated single-marker sequences, has raised some new issues regarding intergeneric relationships in salangid fishes. In particular, the obtained data do not support synonymization of the genus Neosalanx with Protosalanx, as was suggested in the last revision of the salangid classification. As the comparative analysis of interspecific and intergeneric divergences shows, Protosalanx is not an all-inclusive clade that includes all Neosalanx species. Instead, it consists of (at least) two evolutionary distinct lineages with the level of genetic divergence between them matching well the mean value of divergence between the other salangid genera. Further analysis using nuclear genome-wide data is required to have new insights into the evolution of salangid fishes.</p>\",\"PeriodicalId\":44339,\"journal\":{\"name\":\"Vavilovskii Zhurnal Genetiki i Selektsii\",\"volume\":\"29 2\",\"pages\":\"259-267\"},\"PeriodicalIF\":0.9000,\"publicationDate\":\"2025-04-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12010254/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Vavilovskii Zhurnal Genetiki i Selektsii\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.18699/vjgb-25-29\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q3\",\"JCRName\":\"AGRICULTURE, MULTIDISCIPLINARY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Vavilovskii Zhurnal Genetiki i Selektsii","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.18699/vjgb-25-29","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"AGRICULTURE, MULTIDISCIPLINARY","Score":null,"Total":0}
引用次数: 0

摘要

基因库是最大的遗传资源库,为生物学和医学的下游应用提供了至关重要的资源。对GenBank数据可靠性的担忧要求对可能出现的分类输入错误进行监测。一个线粒体基因组(或有丝分裂基因组)误认的情况下,属于新salanx属的salangid鱼(Osmeriformes, Salangidae)在这个报告中被考虑。GenBank数据库包含4个完整的太湖白鲟有丝分裂基因组序列,登录号为JX524196、KP170510、MH348204和MW291630。这些序列的总体平均p-距离很高(7.01±0.14%),但在排除MW291630有丝分裂基因组后,p-距离降低了29倍(0.24±0.05%)。对所有可用的salangids核苷酸序列的分析表明,在不同的有丝分裂基因组之间观察到的差异水平的不一致是由于物种错误识别。结果表明,GenBank中的有丝分裂基因组MW291630不属于太湖北蝽,而实际上是被误认为太湖北蝽的N. jordani的有丝分裂基因组。MW291630有丝分裂基因组的分类鉴定,以及已研究的单标记序列物种的扩展样本,提出了一些关于salangid鱼类属间关系的新问题。特别是,获得的数据不支持Neosalanx属与Protosalanx属同义,正如上次修订的salanid分类所建议的那样。种间和属间差异的比较分析表明,原salanx并不是一个包括所有新salanx物种的包罗万象的进化支。相反,它由(至少)两个进化上截然不同的谱系组成,它们之间的遗传差异水平与其他salangid属之间差异的平均值很好地匹配。为了对萨兰科鱼类的进化有新的认识,需要使用核基因组数据进行进一步的分析。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Correction of GenBank's taxonomic entry error raises a new issue regarding intergeneric relationships among salangid fishes (Osmeriformes: Salangidae).

The GenBank database of publicly available nucleotide sequences is the largest genetic repository providing vitally important resources for downstream applications in biology and medicine. The concern raised about reliability of GenBank data necessitates monitoring of possible taxonomic entry errors. A case of mitochondrial genome (or mitogenome) misidentification for a salangid fish belonging to the genus Neosalanx (Osmeriformes, Salangidae) is considered in this report. The GenBank database contains four complete mitogenome sequences of N. taihuensis with the accession numbers JX524196, KP170510, MH348204, and MW291630. The overall mean p-distance for these sequences is quite high (7.01 ± 0.14 %) but becomes 29-fold lower (0.24 ± 0.05 %) after excluding the MW291630 mitogenome. An analysis of all available nucleotide sequences of salangids has shown that the observed inconsistency in the level of divergence between N. taihuensis mitogenomes is due to species misidentification. It has turned out that the mitogenome MW291630 available in GenBank does not belong to N. taihuensis, but is, in fact, a mitogenome of N. jordani misidentified as N. taihuensis. The resolved taxonomic identity of the MW291630 mitogenome, as well as an extended sample of species with investigated single-marker sequences, has raised some new issues regarding intergeneric relationships in salangid fishes. In particular, the obtained data do not support synonymization of the genus Neosalanx with Protosalanx, as was suggested in the last revision of the salangid classification. As the comparative analysis of interspecific and intergeneric divergences shows, Protosalanx is not an all-inclusive clade that includes all Neosalanx species. Instead, it consists of (at least) two evolutionary distinct lineages with the level of genetic divergence between them matching well the mean value of divergence between the other salangid genera. Further analysis using nuclear genome-wide data is required to have new insights into the evolution of salangid fishes.

求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
Vavilovskii Zhurnal Genetiki i Selektsii
Vavilovskii Zhurnal Genetiki i Selektsii AGRICULTURE, MULTIDISCIPLINARY-
CiteScore
1.90
自引率
0.00%
发文量
119
审稿时长
8 weeks
期刊介绍: The "Vavilov Journal of genetics and breeding" publishes original research and review articles in all key areas of modern plant, animal and human genetics, genomics, bioinformatics and biotechnology. One of the main objectives of the journal is integration of theoretical and applied research in the field of genetics. Special attention is paid to the most topical areas in modern genetics dealing with global concerns such as food security and human health.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信