Testing three pipelines for 18S rDNA-based metabarcoding of soil faunal diversity  

作　　者：YANG ChenXue JI YingQiu WANG XiaoYang YANG ChunYang YU Douglas W. 

机构地区：[1]Ecology,Conservation,and Environment Center,State Key Laboratory of Genetic Resources and Evolution,Kunming Institute of Zoology,Chinese Academy of Sciences [2]School of Biological Sciences,University of East Anglia

出　　处：《Science China(Life Sciences)》2013年第1期73-81,共9页中国科学（生命科学英文版）

基　　金：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

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.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 com- pare 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 In- sights Into Microbial Ecology） environment.

关 键 词：454 Genome Sequencer FLX System DNA barcoding high-throughput sequencing soil fauna metabarcoding 18SrDNA 

分 类 号：S154.5[农业科学—土壤学]