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Exhaustive reanalysis of barcode sequences from public repositories highlights ongoing misidentifications and impacts taxa diversity and distribution
Molecular Ecology Resources ( IF 5.5 ) Pub Date : 2021-06-21 , DOI: 10.1111/1755-0998.13453
Antoine Fort 1 , Marcus McHale 1 , Kevin Cascella 2 , Philippe Potin 2 , Marie-Mathilde Perrineau 3 , Philip D Kerrison 3 , Elisabete da Costa 4 , Ricardo Calado 5 , Maria do Rosário Domingues 4 , Isabel Costa Azevedo 6 , Isabel Sousa-Pinto 6, 7 , Claire Gachon 3, 8 , Adrie van der Werf 9 , Willem de Visser 9 , Johanna E Beniers 9 , Henrice Jansen 9 , Michael D Guiry 10 , Ronan Sulpice 1
Affiliation  

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.

中文翻译:

对公共存储库中条形码序列的详尽重新分析突出了持续的错误识别并影响了分类群的多样性和分布

准确的物种识别通常依赖于公共存储库来比较被调查个体的条形码序列与分类指定的序列。然而,公共存储库中标识的准确性常常受到质疑,并且最初给出的名称很少更新。例如,海生菜的种类(石莼属;石莼科、石莼科、石莼科)经常在公共存储库中被错误识别,包括植物标本馆和基因库,使得基于传统条形码的物种识别变得不可靠。我们DNA条形码的295个人distromatic叶状株石莼从东北大西洋的三个位点(RBC L,TUFA,ITS1)。发现了七个不同的物种,我们将我们的结果与全世界所有的石莼属进行了比较。序列存在于NCBI数据库的三个条形码RBC L,TUF A和ITS1。我们的结果表明存在很大程度的物种错误识别,我们估计与叶类物种有关的条目中有 24%–32% 被错误注释,并提供了详尽的 NCBI 序列重新注释列表。对叶类物种登记样本的全球分布的分析也表明某些物种可能存在地理隔离,并且没有来自北欧的U. lactuca。我们将我们的分析框架扩展到其他三个属,墨角藻属,紫菜Pyropia并且还确定了错误标记的种质和可能的新同义词,尽管少于Ulva spp。总而言之,通过聚合条形码序列库进行详尽的分类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。
更新日期:2021-06-21
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