Fastq sequence files supporting: Assessing the degradation of environmental DNA and RNA based on genomic origin in a metabarcoding context

Molecular tools of species identification based on eNAs (environmental
nucleic acids; eDNA and eRNA) have the potential to greatly transform
biodiversity science. However, the ability of eNAs to obtain “real-time”
biodiversity estimates may be complicated by the differential persistence
and degradation dynamics of the molecular template (eDNA or eRNA) and the
barcode marker used. Here, we collected water samples over a 28-day period
to comparatively assess species detection using eDNA and eRNA
metabarcoding of two distinct barcode markers—a mitochondrial mRNA marker
(COI) and a nuclear rRNA marker (18S)—following complete removal
of Arthropoda taxa in a semi-natural freshwater system.
Our findings demonstrate that Arthropoda community
composition was largely influenced by marker choice, rather than molecular
template, individual microcosm, or sampling time point. Further, although
eRNA may capture similar species diversity as the established eDNA method,
this finding may be marker dependent. Although we found little to
no difference in decay rates observed among sample groups (COI eDNA, COI
eRNA, 18S eDNA, 18S eRNA), this result is likely due to limitations in the
ability of eNA-based metabarcoding to provide a strong
correlation between true eNA copy numbers present in the
environment and final read counts obtained (following the metabarcoding
workflow). Collectively, our findings provide further support for
the use of multi-marker assessments in metabarcoding surveys to unravel
the broadest taxonomic diversity possible, highlight the limitations
of eNA metabarcoding methods in providing accurate decay
rate estimates, as well as establish the need for further comparative
studies using both metabarcoding and single-species detection methods to
assess the persistence and degradation dynamics of eNAs for a diverse
range of taxa.