High-throughput terrestrial biodiversity assessments: mitochondrial metabarcoding, metagenomics or metatranscriptomics?

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.

Keywords:

• Arthropods
• DNA barcodes
• genome skimming
• mitogenomics
• transcriptomics

Acknowledgements

This study was initiated when JJW, BMGJ and KWS were at the Institute of Biological Sciences, Faculty of Science, University of Malaya. Men-How Cheah assisted in collection of specimens. This project was in part inspired by a presentation by Ryuji Machida at the University of Malaya-Academia Sinica Symposium 2015. HMG is grateful to the Monash University Malaysia Tropical Medicine and Biology Platform for infrastructure and financial support. KWS is supported by Chinese Academy of Sciences President’s International Fellowship Initiative (CAS-PIFI).

Disclosure statement

The authors report no conflicts of interest.

Additional information

Funding

This study was supported by a High Impact Research grant from the University of Malaya to JJW.