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Taxonomic and Functional Compositions Impacted by the Quality of Metatranscriptomic Assemblies
Lau, Maggie C. Y.1,5; Harris, Rachel L.1; Oh, Youmi2,6; Yi, Min Joo3; Behmard, Aida4,7; Onstott, Tullis C.1
2018-06-20
发表期刊FRONTIERS IN MICROBIOLOGY
ISSN1664-302X
卷号9页码:17
摘要Metatranscriptomics has recently been applied to investigate the active biogeochemical processes and elemental cycles, and in situ responses of microbiomes to environmental stimuli and stress factors. De novo assembly of RNA-Sequencing (RNA-Seq) data can reveal a more detailed description of the metabolic interactions amongst the active microbial communities. However, the quality of the assemblies and the depiction of the metabolic network provided by various de novo assemblers have not yet been thoroughly assessed. In this study, we compared 15 de novo metatranscriptomic assemblies for a fracture fluid sample collected from a borehole located at 1.34 km below land surface in a South African gold mine. These assemblies were constructed from total, non-coding, and coding reads using five de novo transcriptomic assemblers (Trans-ABySS, Trinity, Oases, IDBA-tran, and Rockhopper). They were evaluated based on the number of transcripts, transcript length, range of transcript coverage, continuity, percentage of transcripts with confident annotation assignments, as well as taxonomic and functional diversity patterns. The results showed that these parameters varied considerably among the assemblies, with Trans-ABySS and Trinity generating the best assemblies for non-coding and coding RNA reads, respectively, because the high number of transcripts assembled covered a wide expression range, and captured extensively the taxonomic and metabolic gene diversity, respectively. We concluded that the choice of de novo transcriptomic assemblers impacts substantially the taxonomic and functional compositions. Care should be taken to obtain high-quality assemblies for informing the in situ metabolic landscape.
关键词RNA-Sequencing de novo metatranscriptomics taxonomic composition metabolic functions metaproteomics
DOI10.3389/fmicb.2018.01235
资助者National Science Foundation ; Deep Carbon Observatory (Alfred P. Sloan Foundation) ; NSF Graduate Research Fellowship
语种英语
关键词[WOS]DE-BRUIJN GRAPH ; RNA-SEQ DATA ; EXPRESSION LEVELS ; SUBSURFACE ; DIVERSITY ; COMMUNITY ; GENOME ; CONTAMINATION ; SEQUENCE ; CARBON
资助项目National Science Foundation[EAR-1739151] ; National Science Foundation[DEB-1441646] ; Deep Carbon Observatory (Alfred P. Sloan Foundation)[Sloan 2013-10-03] ; Deep Carbon Observatory (Alfred P. Sloan Foundation)[48045] ; NSF Graduate Research Fellowship[DGE-1148900]
WOS研究方向Microbiology
WOS类目Microbiology
WOS记录号WOS:000435690000001
出版者FRONTIERS MEDIA SA
引用统计
文献类型期刊论文
条目标识符http://ir.idsse.ac.cn/handle/183446/5973
专题深海科学研究部_地外海洋系统研究室
通讯作者Lau, Maggie C. Y.
作者单位1.Princeton Univ, Dept Geosci, Princeton, NJ 08544 USA
2.Princeton Univ, Program Atmospher & Ocean Sci, Princeton, NJ 08544 USA
3.Princeton Univ, Dept Ecol & Evolutionary Biol, Princeton, NJ 08544 USA
4.Princeton Univ, Dept Astrophys Sci, Princeton, NJ 08544 USA
5.Chinese Acad Sci, Inst Deep Sea Sci & Engn, Lab Extraterr Ocean Syst, Sanya, Peoples R China
6.Purdue Univ, Earth Atmospher & Planetary Sci, W Lafayette, IN 47907 USA
7.CALTECH, Div Geol & Planetary Sci, Pasadena, CA 91125 USA
第一作者单位中国科学院深海科学与工程研究所
通讯作者单位中国科学院深海科学与工程研究所
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GB/T 7714
Lau, Maggie C. Y.,Harris, Rachel L.,Oh, Youmi,et al. Taxonomic and Functional Compositions Impacted by the Quality of Metatranscriptomic Assemblies[J]. FRONTIERS IN MICROBIOLOGY,2018,9:17.
APA Lau, Maggie C. Y.,Harris, Rachel L.,Oh, Youmi,Yi, Min Joo,Behmard, Aida,&Onstott, Tullis C..(2018).Taxonomic and Functional Compositions Impacted by the Quality of Metatranscriptomic Assemblies.FRONTIERS IN MICROBIOLOGY,9,17.
MLA Lau, Maggie C. Y.,et al."Taxonomic and Functional Compositions Impacted by the Quality of Metatranscriptomic Assemblies".FRONTIERS IN MICROBIOLOGY 9(2018):17.
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