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对来自公共数据库的条形码序列进行详尽的重新分析,凸显了持续存在的错误识别情况,并影响了分类群的多样性和分布。

Exhaustive reanalysis of barcode sequences from public repositories highlights ongoing misidentifications and impacts taxa diversity and distribution.

作者信息

Fort Antoine, McHale Marcus, Cascella Kevin, Potin Philippe, Perrineau Marie-Mathilde, Kerrison Philip D, da Costa Elisabete, Calado Ricardo, Domingues Maria do Rosário, Costa Azevedo Isabel, Sousa-Pinto Isabel, Gachon Claire, van der Werf Adrie, de Visser Willem, Beniers Johanna E, Jansen Henrice, Guiry Michael D, Sulpice Ronan

机构信息

National University of Ireland - Galway, Plant Systems Biology Laboratory, Ryan Institute & MaREI Centre for Marine, Climate and Energy, School of Natural Sciences, Galway, Ireland.

CNRS, Sorbonne Université Sciences, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France.

出版信息

Mol Ecol Resour. 2022 Jan;22(1):86-101. doi: 10.1111/1755-0998.13453. Epub 2021 Jul 5.

DOI:10.1111/1755-0998.13453
PMID:34153167
Abstract

Accurate species identification often relies on public repositories to compare the barcode sequences of the investigated individual(s) with taxonomically assigned sequences. However, the accuracy of identifications in public repositories is often questionable, and the names originally given are rarely updated. For instance, species of the Sea Lettuce (Ulva spp.; Ulvophyceae, Ulvales, Ulvaceae) are frequently misidentified in public repositories, including herbaria and gene banks, making species identification based on traditional barcoding unreliable. We DNA barcoded 295 individual distromatic foliose strains of Ulva from the North-East Atlantic for three loci (rbcL, tufA, ITS1). Seven distinct species were found, and we compared our results with all worldwide Ulva spp. sequences present in the NCBI database for the three barcodes rbcL, tufA and the ITS1. Our results demonstrate a large degree of species misidentification, where we estimate that 24%-32% of the entries pertaining to foliose species are misannotated and provide an exhaustive list of NCBI sequences reannotations. An analysis of the global distribution of registered samples from foliose species also indicates possible geographical isolation for some species, and the absence of U. lactuca from Northern Europe. We extended our analytical framework to three other genera, Fucus, Porphyra and Pyropia and also identified erroneously labelled accessions and possibly new synonymies, albeit less than for Ulva spp. Altogether, exhaustive taxonomic clarification by aggregation of a library of barcode sequences highlights misannotations and delivers an improved representation of species diversity and distribution.

摘要

准确的物种鉴定通常依赖于公共数据库,以便将被调查个体的条形码序列与分类学上已确定的序列进行比较。然而,公共数据库中鉴定的准确性往往存疑,而且最初给出的名称很少更新。例如,海莴苣属(Ulva spp.;石莼科、石莼目、石莼科)的物种在包括植物标本馆和基因库在内的公共数据库中经常被错误鉴定,这使得基于传统条形码技术的物种鉴定不可靠。我们对来自东北大西洋的295个石莼属的二分叶状叶状体菌株进行了三个基因座(rbcL、tufA、ITS1)的DNA条形码分析。发现了七个不同的物种,我们将我们的结果与NCBI数据库中存在的所有全球石莼属物种的rbcL、tufA和ITS1这三个条形码序列进行了比较。我们的结果表明存在大量的物种误鉴定情况,我们估计与叶状物种相关的条目中有24%-32%被错误注释,并提供了一份NCBI序列重新注释的详尽列表。对叶状物种登记样本的全球分布分析还表明,一些物种可能存在地理隔离,并且北欧没有皱波角叉菜。我们将分析框架扩展到其他三个属,即墨角藻属、紫菜属和条斑紫菜属,也鉴定出了错误标记的登录号以及可能的新同义词,尽管比石莼属的情况要少。总之,通过条形码序列库的汇总进行详尽的分类学澄清突出了错误注释,并提供了对物种多样性和分布的改进表示。

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