Testing three pipelines for 18S rDNA-based metabarcoding of soil faunal diversity
作者： ChenXue Yang , YingQiu Ji , XiaoYang Wang , ChunYang Yang , Douglas W. Yu
DOI: 10.1007/S11427-012-4423-7
关键词: Ecology (disciplines) 、 Microbial ecology 、 Phylogenetic diversity 、 DNA sequencing 、 DNA barcoding 、 Taxon 、 Biodiversity 、 Ecology 、 Soil biology 、 Biology
摘要: A number of basic and applied questions in ecology environmental management require the characterization soil leaf litter faunal diversity. Recent advances high-throughput sequencing barcode-gene amplicons (‘metabarcoding’) have made it possible to survey biodiversity a robust efficient way. However, one obstacle widespread adoption this technique is need choose amongst many candidates for bioinformatic processing raw data. We compare three candidate pipelines 18S small subunit rDNA metabarcode data from solid substrates: (i) USEARCH/CROP, (ii) Denoiser/UCLUST, (iii) OCTUPUS. The produced reassuringly similar highly correlated assessments community composition that are dominated by taxa known characterize sampled environments. OCTUPUS appears inflate phylogenetic diversity, because higher sequence noise. therefore recommend either USEARCH/CROP or Denoiser/UCLUST pipelines, both which can be run within QIIME (Quantitative Insights Into Microbial Ecology) environment.
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