Taxonomy annotation and guide tree errors in 16S rRNA databases.
Taxonomy annotation and guide tree errors in 16S rRNA databases.
复制标题
作者：
Edgar R
16S核糖体RNA（rRNA）基因的测序被广泛用于调查微生物群落。已经开发了专门的16S rRNA数据库来支持这种方法，包括Greengenes，RDP和SILVA。这些数据库中的大多数分类学注释都是根据序列预测的，而不是基于模式菌株或分离株研究的权威性分配。在这项工作中，我调查了这些数据库提供的分类注释和指导树。使用盲法测试，我估计RDP数据库的注释错误率为10%。根据RDP提供的训练集（权威参考），发现Greengenes和SILVA指导树的分支顺序彼此之间以及与分类学注释的比率相当，这表明树具有可比的质量。树的分支顺序和模式菌株分类之间的普遍冲突强烈表明，指导树是不可靠的指南，以繁殖。我在SILVA v128和Greengenes v13.5中发现了249，490个具有冲突注释的相同序列，其级别高达门（7，804个冲突），这表明这些数据库中的注释错误率为17%。
Sequencing of the 16S ribosomal RNA (rRNA) gene is widely used to survey microbial communities. Specialized 16S rRNA databases have been developed to support this approach including Greengenes, RDP and SILVA. Most taxonomy annotations in these databases are predictions from sequence rather than authoritative assignments based on studies of type strains or isolates. In this work, I investigated the taxonomy annotations and guide trees provided by these databases. Using a blinded test, I estimated that the annotation error rate of the RDP database is ∼10%. The branching orders of the Greengenes and SILVA guide trees were found to disagree at comparable rates with each other and with taxonomy annotations according to the training set (authoritative reference) provided by RDP, indicating that the trees have comparable quality. Pervasive conflicts between tree branching order and type strain taxonomies strongly suggest that the guide trees are unreliable guides to phylogeny. I found 249,490 identical sequences with conflicting annotations in SILVA v128 and Greengenes v13.5 at ranks up to phylum (7,804 conflicts), indicating that the annotation error rate in these databases is ∼17%.
登录
查看更多内容
影响因子：
2.7
作者：
Edgar RC
通讯作者：
Edgar RC
影响因子：
14.9
作者：
Pruesse E;Quast C;Knittel K;Fuchs BM;Ludwig W;Peplies J;Glöckner FO
通讯作者：
Glöckner FO
影响因子：
4.4
作者：
Webster, G;Parkes, RJ;Weightman, AJ
通讯作者：
Weightman, AJ
影响因子：
56.9
作者：
Huelsenbeck, JP;Rannala, B;Masly, JP
通讯作者：
Masly, JP
DOI：
10.1038/nrg3182
发表时间：
2012-03-13
期刊：
Nature reviews. Genetics
影响因子：
--
作者：
通讯作者：
--