Affiliations 

  • 1 a School of Applied Sciences, Faculty of Computing, Engineering and Science , University of South Wales , Pontypridd , UK
  • 2 d Biodiversity Research Center, Academia Sinica , Taipei , Taiwan
  • 3 f School of Life and Environmental Sciences , Centre for Integrative Ecology, Deakin University , Geelong , Australia
  • 4 i South China DNA Barcoding Center, Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming , PR China
PMID: 29591722 DOI: 10.1080/24701394.2018.1455189

Abstract

Consensus on the optimal high-throughput sequencing (HTS) approach to examine biodiversity in mixed terrestrial arthropod samples has not been reached. Metatranscriptomics could increase the proportion of taxonomically informative mitochondrial reads in HTS outputs but has not been investigated for terrestrial arthropod samples. We compared the efficiency of 16S rRNA metabarcoding, metagenomics and metatranscriptomics for detecting species in a mixed terrestrial arthropod sample (pooled DNA/RNA from 38 taxa). 16S rRNA metabarcoding and nuclear rRNA-depleted metatranscriptomics had the highest detection rate with 97% of input species detected. Based on cytochrome c oxidase I, metagenomics had the highest detection rate with 82% of input species detected, but metatranscriptomics produced a larger proportion of reads matching (Sanger) reference sequences. Metatranscriptomics with nuclear rRNA depletion may offer advantages over metabarcoding through reducing the number of spurious operational taxonomic units while retaining high detection rates, and offers natural enrichment of mitochondrial sequences which may enable increased species detection rates compared with metagenomics.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.