An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea.
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea.
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DOI：
10.1038/ismej.2011.139
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发表时间：
2012-03
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参考系统发育是为标记基因和宏基因组调查提供分类框架的关键，它们继续以惊人的速度揭示新物种。Greengenes是一个专门的全长16S rRNA基因数据库，为用户提供基于从头树推断的精心分类。我们开发了一种“分类法到树”的方法，将组名从现有的分类法转移到树拓扑结构，并使用它将Greengenes，国家生物技术信息中心（NCBI）和cyanoDB（仅蓝藻）分类法应用于包含408 315个序列的新生树。我们还将NCBI分类法提供的显式排名信息合并到组名中（通过添加排名名称的前缀），以更好地面向用户和分类一致性。与原始的NCBI分类相比，合并后的分类方法将75%的序列的分类提高了一个或多个等级，其中未分类的环境序列的改进最为明显。我们还评估了目前由NCBI定义的候选门（分部），并提出了34个冗余命名组的合并建议。来自管道的所有中间结果，包括树推断、jackknifing和将供体分类法转移到接收树（tax2tree），都可以下载。改进后的Greengenes分类法将为研究生态系统的大型测序项目提供重要的基础设施，研究范围从我们自己的身体（人类微生物组计划）到整个地球（地球微生物组计划）。该软件的实现可以从http://sourceforge.net/projects/tax2tree/获得。
Reference phylogenies are crucial for providing a taxonomic framework for interpretation of marker gene and metagenomic surveys, which continue to reveal novel species at a remarkable rate. Greengenes is a dedicated full-length 16S rRNA gene database that provides users with a curated taxonomy based on de novo tree inference. We developed a ‘taxonomy to tree' approach for transferring group names from an existing taxonomy to a tree topology, and used it to apply the Greengenes, National Center for Biotechnology Information (NCBI) and cyanoDB (Cyanobacteria only) taxonomies to a de novo tree comprising 408 315 sequences. We also incorporated explicit rank information provided by the NCBI taxonomy to group names (by prefixing rank designations) for better user orientation and classification consistency. The resulting merged taxonomy improved the classification of 75% of the sequences by one or more ranks relative to the original NCBI taxonomy with the most pronounced improvements occurring in under-classified environmental sequences. We also assessed candidate phyla (divisions) currently defined by NCBI and present recommendations for consolidation of 34 redundantly named groups. All intermediate results from the pipeline, which includes tree inference, jackknifing and transfer of a donor taxonomy to a recipient tree (tax2tree) are available for download. The improved Greengenes taxonomy should provide important infrastructure for a wide range of megasequencing projects studying ecosystems on scales ranging from our own bodies (the Human Microbiome Project) to the entire planet (the Earth Microbiome Project). The implementation of the software can be obtained from http://sourceforge.net/projects/tax2tree/.
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影响因子：
12.3
作者：
Knight R;Maxwell P;Birmingham A;Carnes J;Caporaso JG;Easton BC;Eaton M;Hamady M;Lindsay H;Liu Z;Lozupone C;McDonald D;Robeson M;Sammut R;Smit S;Wakefield MJ;Widmann J;Wikman S;Wilson S;Ying H;Huttley GA
通讯作者：
Huttley GA
高度平行的焦索测序者产生的16S rRNA序列的准确分类学分配。
影响因子：
14.9
作者：
Liu Z;DeSantis TZ;Andersen GL;Knight R
通讯作者：
Knight R
影响因子：
14.9
作者：
Ludwig, W;Strunk, O;Schleifer, KH
通讯作者：
Schleifer, KH
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：
14.9
作者：
Cole JR;Wang Q;Cardenas E;Fish J;Chai B;Farris RJ;Kulam-Syed-Mohideen AS;McGarrell DM;Marsh T;Garrity GM;Tiedje JM
通讯作者：
Tiedje JM