EukRef-Ciliophora: a manually curated, phylogeny-based database of small subunit rRNA gene sequences of ciliates

Autor: Eleni Gentekaki, Javier del Campo, Vittorio Boscaro, Mitchell J. Syberg-Olsen, Qianqian Zhang, Luciana F. Santoferrara, Patrick J. Keeling
Přispěvatelé: Tula Foundation, National Science Foundation (US), National Natural Science Foundation of China, European Commission, Natural Sciences and Engineering Research Council of Canada
Rok vydání: 2018
Předmět:
Zdroj: Digital.CSIC. Repositorio Institucional del CSIC
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ISSN: 1462-2920
Popis: Special Issue EMI is 20!.-- 13 pages, 5 figures, 1 table, supporting information https://dx.doi.org/10.1111/1462-2920.14264
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 11 500 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
This work was supported by a grant (RGPIN‐2014‐03994) from the Natural Sciences and Engineering Research Council of Canada to PJK. VB and JdC were supported by grants to the Centre for Microbial Diversity and Evolution from the Tula Foundation. LFS was supported by grant OCE1435515 from the U.S. National Science Foundation to Dr. George McManus (University of Connecticut). QZ was supported by the grant 31672251 from the National Natural Science Foundation of China. JdC was supported by a Marie Curie International Outgoing Fellowship grant (FP7‐PEOPLE‐2012‐IOF‐331450 CAARL)
Databáze: OpenAIRE
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