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

Area of Science:

• Ecology
• Genomics
• Bioinformatics

Background:

• Optimal high-throughput sequencing (HTS) for terrestrial arthropod biodiversity assessment remains debated.
• Metatranscriptomics, which analyzes RNA, has potential to enrich mitochondrial reads for improved taxonomic resolution but is understudied in this context.

Purpose of the Study:

• To compare the effectiveness of 16S rRNA metabarcoding, metagenomics, and metatranscriptomics for species detection in mixed terrestrial arthropod samples.
• To evaluate metatranscriptomics' potential for enhancing taxonomic information from mitochondrial DNA sequences.

Main Methods:

• A mixed terrestrial arthropod sample (pooled DNA/RNA from 38 taxa) was analyzed using three HTS approaches: 16S rRNA metabarcoding, metagenomics, and metatranscriptomics (with nuclear rRNA depletion).
• Species detection rates and the proportion of taxonomically informative reads were compared across methods.

Main Results:

• 16S rRNA metabarcoding and nuclear rRNA-depleted metatranscriptomics achieved the highest species detection rate (97%).
• Metagenomics, targeting cytochrome c oxidase I, detected 82% of species but yielded a lower proportion of matching reads compared to metatranscriptomics.
• Metatranscriptomics generated a greater proportion of reads that matched reference sequences.

Conclusions:

• Nuclear rRNA-depleted metatranscriptomics shows promise for arthropod biodiversity studies, offering high detection rates while potentially reducing spurious operational taxonomic units.
• Metatranscriptomics may surpass metagenomics in species detection by naturally enriching mitochondrial sequences.