Boscaro, Vittorio; Santoferrara, Luciana F.; Zhang, Qianqian
; Gentekaki, Eleni; Syberg-Olsen, Mitchell J.; del Campo, Javier; Keeling, Patrick J.发表期刊ENVIRONMENTAL MICROBIOLOGY
ISSN1462-2912
2018-07
卷号20期号:6 SI页码:2218-2230
关键词DEEP-SEAPROTIST DIVERSITYREVISED CLASSIFICATIONCOMMUNITIESPATTERNSTAXONMORPHOLOGYARMOPHOREAINSIGHTSNASSOPHOREA
研究领域Microbiology
DOI10.1111/1462-2920.14264
产权排序[Boscaro, Vittorio; Syberg-Olsen, Mitchell J.; del Campo, Javier; Keeling, Patrick J.] Univ British Columbia, Dept Bot, Vancouver, BC, Canada; [Santoferrara, Luciana F.] Univ Connecticut, Dept Marine Sci, Stamford, CT USA; [Santoferrara, Luciana F.] Univ Connecticut, Dept Ecol & Evolutionary Biol, Stamford, CT USA; [Zhang, Qianqian] Chinese Acad Sci, Yantai Inst Coastal Zone Res, Key Lab Coastal Biol & Bioresource Utilizat, Yantai, Peoples R China; [Gentekaki, Eleni] Mae Fah Luang Univ, Sch Sci, Chiang Rai, Thailand; [del Campo, Javier] CSIC, Dept Marine Biol & Oceanog, Inst Ciencias Mar, Barcelona, Spain
作者部门海岸带生物资源高效利用研究与发展中心
英文摘要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.
文章类型Article
资助机构Natural Sciences and Engineering Research Council of Canada [RGPIN-2014-03994]; Tula Foundation; U.S. National Science Foundation [OCE1435515]; National Natural Science Foundation of China [31672251]; Marie Curie International Outgoing Fellowship grant [FP7-PEOPLE-2012-IOF-331450 CAARL]
收录类别SCI
语种英语
关键词[WOS]DEEP-SEA; PROTIST DIVERSITY; REVISED CLASSIFICATION; COMMUNITIES; PATTERNS; TAXON; MORPHOLOGY; ARMOPHOREA; INSIGHTS; NASSOPHOREA
研究领域[WOS]Microbiology
WOS记录号WOS:000441876900034
引用统计被引频次：16[WOS][WOS记录][WOS相关记录]
文献类型期刊论文
条目标识符http://ir.yic.ac.cnhttp://ir.yic.ac.cn/handle/133337/24501
专题海岸带生物学与生物资源利用重点实验室_海岸带生物资源高效利用研究与发展中心
海岸带生物学与生物资源利用重点实验室_海岸带生物学与生物资源保护实验室
作者单位1.Univ British Columbia, Dept Bot, Vancouver, BC, Canada;
2.Univ Connecticut, Dept Marine Sci, Stamford, CT USA;
3.Univ Connecticut, Dept Ecol & Evolutionary Biol, Stamford, CT USA;
4.Chinese Acad Sci, Yantai Inst Coastal Zone Res, Key Lab Coastal Biol & Bioresource Utilizat, Yantai, Peoples R China;
5.Mae Fah Luang Univ, Sch Sci, Chiang Rai, Thailand;
6.CSIC, Dept Marine Biol & Oceanog, Inst Ciencias Mar, Barcelona, Spain
推荐引用方式
GB/T 7714Boscaro, Vittorio,Santoferrara, Luciana F.,Zhang, Qianqian,et al. EukRef-Ciliophora: a manually curated, phylogeny-based database of small subunit rRNA gene sequences of ciliates[J]. ENVIRONMENTAL MICROBIOLOGY,2018,20(6 SI):2218-2230.
APABoscaro, Vittorio.,Santoferrara, Luciana F..,Zhang, Qianqian.,Gentekaki, Eleni.,Syberg-Olsen, Mitchell J..,...&Keeling, Patrick J..(2018).EukRef-Ciliophora: a manually curated, phylogeny-based database of small subunit rRNA gene sequences of ciliates.ENVIRONMENTAL MICROBIOLOGY,20(6 SI),2218-2230.
MLABoscaro, Vittorio,et al."EukRef-Ciliophora: a manually curated, phylogeny-based database of small subunit rRNA gene sequences of ciliates".ENVIRONMENTAL MICROBIOLOGY 20.6 SI(2018):2218-2230.
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