| 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.
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| 发表期刊 | ENVIRONMENTAL MICROBIOLOGY
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| ISSN | 1462-2912 |
| 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 |
| 研究领域 | Microbiology |
| 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 |
| 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 | |
| 文献类型 | 期刊论文 |
| 条目标识符 | http://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 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. |
| 条目包含的文件 | ||||||
| 文件名称/大小 | 文献类型 | 版本类型 | 开放类型 | 使用许可 | ||
| EukRef-Ciliophora a （774KB） | 期刊论文 | 出版稿 | 开放获取 | CC BY-NC-SA | 浏览 请求全文 | |
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