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

doi:10.1111/1462-2920.14264

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	EukRef-Ciliophora: a manually curated, phylogeny-based database of small subunit rRNA gene sequences of ciliates
	Boscaro, Vittorio ; Santoferrara, Luciana F.; Zhang, Qianqian ; Gentekaki, Eleni ; Syberg-Olsen, Mitchell J.; del Campo, Javier ; Keeling, Patrick J.
刊名	ENVIRONMENTAL MICROBIOLOGY
	2018-07
卷号	20 期号:6 SI 页码:2218-2230
关键词	DEEP-SEA PROTIST DIVERSITY REVISED CLASSIFICATION COMMUNITIES PATTERNS TAXON MORPHOLOGY ARMOPHOREA INSIGHTS NASSOPHOREA
ISSN号	1462-2912
DOI	10.1111/1462-2920.14264
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
文献子类	Article
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.
WOS关键词	DEEP-SEA ; PROTIST DIVERSITY ; REVISED CLASSIFICATION ; COMMUNITIES ; PATTERNS ; TAXON ; MORPHOLOGY ; ARMOPHOREA ; INSIGHTS ; NASSOPHOREA
WOS研究方向	Microbiology
语种	英语
WOS记录号	WOS:000441876900034
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]
内容类型	期刊论文
源URL	[http://ir.yic.ac.cn/handle/133337/24501]
专题	海岸带生物资源高效利用研究与发展中心烟台海岸带研究所_海岸带生物学与生物资源利用所重点实验室
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 7714	Boscaro, 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.
APA	Boscaro, 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.
MLA	Boscaro, 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.