Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan.
Mol Biol Evol. 2024 Aug 2;41(8). doi: 10.1093/molbev/msae111.
We developed phyloBARCODER (https://github.com/jun-inoue/phyloBARCODER), a new web tool that can identify short DNA sequences to the species level using metabarcoding. phyloBARCODER estimates phylogenetic trees based on the uploaded anonymous DNA sequences and reference sequences from databases. Without such phylogenetic contexts, alternative, similarity-based methods independently identify species names and anonymous sequences of the same group by pairwise comparisons between queries and database sequences, with the caveat that they must match exactly or very closely. By putting metabarcoding sequences into a phylogenetic context, phyloBARCODER accurately identifies (i) species or classification of query sequences and (ii) anonymous sequences associated with the same species or even with populations of query sequences, with clear and accurate explanations. Version 1 of phyloBARCODER stores a database comprising all eukaryotic mitochondrial gene sequences. Moreover, by uploading their own databases, phyloBARCODER users can conduct species identification specialized for sequences obtained from a local geographic region or those of nonmitochondrial genes, e.g. ITS or rbcL.
我们开发了 phyloBARCODER（https://github.com/jun-inoue/phyloBARCODER），这是一个新的网络工具，可使用宏条形码识别短 DNA 序列到物种水平。phyloBARCODER 基于上传的匿名 DNA 序列和数据库中的参考序列估计系统发育树。在没有这种系统发育背景的情况下，替代的、基于相似性的方法通过查询和数据库序列之间的两两比较独立地识别相同组的物种名称和匿名序列，但前提是它们必须完全匹配或非常接近。通过将宏条形码序列放入系统发育背景中，phyloBARCODER 可以准确地识别 (i) 查询序列的物种或分类，以及 (ii) 与同一物种相关的匿名序列，甚至是查询序列的种群，具有清晰准确的解释。phyloBARCODER 的 1.0 版本存储了一个包含所有真核线粒体基因序列的数据库。此外，通过上传自己的数据库，phyloBARCODER 用户可以针对从本地地理区域获得的序列或非线粒体基因（例如 ITS 或 rbcL）进行物种识别。
