Testing three pipelines for 18S rDNA-based metabarcoding of soil faunal diversity
文献类型：期刊论文
| 作者 | Yang CX1; Ji YQ1; Wang XY1; Yang CY1; Yu DW[*]1,2 |
| 刊名 | SCIENCE CHINA-LIFE SCIENCES
 |
| 出版日期 | 2013 |
| 卷号 | 56期号:1页码:73-81 |
| 关键词 | 454 Genome Sequencer FLX System DNA barcoding high-throughput sequencing soil fauna metabarcoding 18S rDNA |
| 通讯作者 | dougwyu@gmail.com |
| 合作状况 | 其它 |
| 英文摘要 | A number of basic and applied questions in ecology and environmental management require the characterization of soil and leaf litter faunal diversity. Recent advances in high-throughput sequencing of barcode-gene amplicons ('metabarcoding') have made it possible to survey biodiversity in a robust and efficient way. However, one obstacle to the widespread adoption of this technique is the need to choose amongst many candidates for bioinformatic processing of the raw sequencing data. We compare three candidate pipelines for the processing of 18S small subunit rDNA metabarcode data from solid substrates: (i) USEARCH/CROP, (ii) Denoiser/UCLUST, and (iii) OCTUPUS. The three pipelines produced reassuringly similar and highly correlated assessments of community composition that are dominated by taxa known to characterize the sampled environments. However, OCTUPUS appears to inflate phylogenetic diversity, because of higher sequence noise. We therefore recommend either the USEARCH/CROP or Denoiser/UCLUST pipelines, both of which can be run within the QIIME (Quantitative Insights Into Microbial Ecology) environment. |
| 收录类别 | SCI |
| 资助信息 | This work was supported by Yunnan Province (20080A001), Chinese Academy of Sciences (0902281081, KSCX2-YW-Z-1027), the National Natural Science Foundation of China (31170498), Ministry of Science and Technology of China (2012FY110800), Kunming Institute of Zoology, and the University of East Anglia. |
| 语种 | 英语 |
| WOS记录号 | WOS:000313447000010 |
| 公开日期 | 2013-03-08 |
| 源URL | [http://159.226.149.42:8088/handle/152453/7272]  |
| 专题 | 昆明动物研究所_动物生态学研究中心 昆明动物研究所_遗传资源与进化国家重点实验室 |
| 作者单位 | 1.Ecology, Conservation, and Environment Center, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China 2.School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR47TJ, UK |
| 推荐引用方式 GB/T 7714 | Yang CX,Ji YQ,Wang XY,et al. Testing three pipelines for 18S rDNA-based metabarcoding of soil faunal diversity[J]. SCIENCE CHINA-LIFE SCIENCES,2013,56(1):73-81. |
| APA | Yang CX,Ji YQ,Wang XY,Yang CY,&Yu DW[*].(2013).Testing three pipelines for 18S rDNA-based metabarcoding of soil faunal diversity.SCIENCE CHINA-LIFE SCIENCES,56(1),73-81. |
| MLA | Yang CX,et al."Testing three pipelines for 18S rDNA-based metabarcoding of soil faunal diversity".SCIENCE CHINA-LIFE SCIENCES 56.1(2013):73-81. |
入库方式： OAI收割
来源：昆明动物研究所
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