EukRef-Ciliophora: a manually curated, phylogeny-based database of small subunit rRNA gene sequences of ciliates
EukRef-Ciliophora: a manually curated, phylogeny-based database of small subunit rRNA gene sequences of ciliates
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EukRef-Ciliophora：手动管理的、基于系统发育的纤毛虫小亚基 rRNA 基因序列数据库
DOI：
10.1111/1462-2920.14264
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发表时间：
2018-06-01
影响因子：
5.1
通讯作者：
Keeling, Patrick J.
中科院分区：
文献类型：
--
作者：
Boscaro, Vittorio;Santoferrara, Luciana F.;Keeling, Patrick J.
高通量测序(HTS)调查是目前环境微生物学中最常用的方法之一，需要可靠的参考数据库才能得到正确的解释。EukRef Initiative(eukref.org)是一项社区工作，旨在手动筛选可用的小亚基(SSU)rRNA基因序列，并产生一个基于系统发育的分类注释的公共、高质量和信息丰富的框架。在EukRef的背景下，我们提出了一个关于单系纤毛纲的数据库，纤毛纲是最复杂、最多样化和最普遍的原生类群之一。我们检索了基因库中存在的11500多个纤毛虫序列(28%来自已鉴定的菌株，72%来自环境调查)。我们的方法包括每个纤毛虫谱系的系统发育树的推断，并产生了迄今为止纤毛纲最大的SSU rRNA树。我们标记了大约750个嵌合或低质量的序列，改进了70%的GenBank条目的分类，并将环境和文献元数据丰富了30%。在对全球海洋调查的HTS读数进行分类方面，EukRef-Ciliophora的性能优于当前的Silva数据库。已公开提供全面的产出，使新工具成为非专家的有用指南和专家的快速参考。
High-throughput sequencing (HTS) surveys, among the most common approaches currently used in environmental microbiology, require reliable reference databases to be correctly interpreted. The EukRef Initiative (eukref.org) is a community effort to manually screen available small subunit (SSU) rRNA gene sequences and produce a public, high-quality and informative framework of phylogeny-based taxonomic annotations. In the context of EukRef, we present a database for the monophyletic phylum Ciliophora, one of the most complex, diverse and ubiquitous protist groups. We retrieved more than 11500 sequences of ciliates present in GenBank (28% from identified isolates and 72% from environmental surveys). Our approach included the inference of phylogenetic trees for every ciliate lineage and produced the largest SSU rRNA tree of the phylum Ciliophora to date. We flagged approximately 750 chimeric or low-quality sequences, improved the classification of 70% of GenBank entries and enriched environmental and literature metadata by 30%. The performance of EukRef-Ciliophora is superior to the current SILVA database in classifying HTS reads from a global marine survey. Comprehensive outputs are publicly available to make the new tool a useful guide for non-specialists and a quick reference for experts.