Abstract
Environmental DNA (eDNA) analysis has advanced conservation biology and biodiversity management. However, accurate estimation of age and origin of eDNA is complicated by particle transport and the presence of legacy genetic material, which can obscure accurate interpretation of eDNA detection and quantification. To understand the state of genomic material within the environment, we investigated the degradation relationships between (a) size of fragments (long vs short), (b) genomic origins (mitochondrial vs nuclear), (c) nucleic acids (eDNA vs eRNA), and (d) RNA types (messenger (m)RNA vs ribosomal (r)RNA) from non-indigenous Dreissena mussels. Initial concentrations of eRNA followed expected transcriptional trends, with rRNAs found at > 1000 × that of eDNA, and a mitosis-associated mRNA falling below detection limits within 24 h. Furthermore, the ratio of eRNA:eDNA significantly decreased throughout degradation, potentially providing an estimate for the age of genomic material. Thus, eRNA quantification can increase detection due to the high concentrations of rRNAs. Furthermore, it may improve interpretation of positive detections through the eRNA:eDNA ratio and/or by detecting low abundant mitosis-associated mRNAs that degrade within ~ 24 h.
Highlights
Environmental (e)DNA collected from aquatic habitats has improved the management and assessment of a species’ distribution and entire community compositions[1,2]
The genetic state of Environmental DNA (eDNA) in the natural environment is composed of both nuclear and mitochondrial genomes, which differ in their structure, and potentially their abundance and detectability[22,23]
RRNA is hypothesized to be less susceptible to degradation compared to mRNA due to structure s tability[33], and gene detection within eRNA is likely dependent upon the RNA type
Summary
Environmental (e)DNA (i.e., genetic material from urine, waste, mucus, or sloughed cells) collected from aquatic habitats has improved the management and assessment of a species’ distribution and entire community compositions[1,2]. Studies comparing environmental degradation rates across the genomic origins are scarce, and knowledge about gene-dependent detection and quantification is necessary for advancing eDNA methodologies. Majority of species-specific eDNA markers use mt-DNA (typically targeting the cytochrome oxidase subunit I (COI) or cytochrome b (Cytb) genes), due to large existing sequence databases[2], expected higher density of mt-DNA compared to nu-DNA (10–1000 s of mitochondria to a single nucleus per cell)[20], and the assumption that the mt-genome is more stable due to it’s circular s tructure[24]. An accurate interpretation of environmental genetic signal is dependent upon knowledge of the shedding and degradation rates between the nu- and mt-genomes, between eDNA and eRNA, and between the RNA types within eRNA
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