Creating, curating, and evaluating a mitogenomic reference database to
improve regional species identification using environmental DNA
Abstract
Species detection using eDNA is revolutionizing global capacity to
monitor biodiversity. However, the lack of regional, vouchered, genomic
sequence information—especially sequence information that includes
intraspecific variation—creates a bottleneck for management agencies
wanting to harness the complete power of eDNA to monitor taxa and
implement eDNA analyses. eDNA studies depend upon regional databases of
mitogenomic sequence information to evaluate the effectiveness of such
data to detect and identify taxa. We created the Oregon Biodiversity
Genome Project to create a database of complete, nearly error-free
mitogenomic sequences for all of Oregon’s fishes. We have successfully
assembled the complete mitogenomes of 313 specimens of freshwater,
anadromous, and estuarine fishes representing 24 families, 55 genera,
and 128 species and lineages. Comparative analyses of these sequences
illustrate that many regions of the mitogenome are taxonomically
informative, that the short (~150 bp) mitochondrial
“barcode” regions typically used for eDNA assays do not consistently
diagnose for species, and that complete single or multiple genes of the
mitogenome are preferable for identifying Oregon’s fishes. This project
provides a blueprint for other researchers to follow as they build
regional databases, illustrates the taxonomic value and limits of
complete mitogenomic sequences, and offers clues as to how current eDNA
assays and environmental genomics methods of the future can best
leverage this information.