Transitioning from environmental genetics to genomics using mitogenome reference databases

Abstract

Species detection using eDNA is revolutionizing the 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 complete mitogenomic sequence information to evaluate the effectiveness of such data to differentiate, identify and detect taxa. We created the Oregon Biodiversity Genome Project working group to utilize recent advances in sequencing technology to create a database of complete, near error-free mitogenomic sequences for all of Oregon’s resident freshwater fishes. So far, we have successfully assembled the complete mitogenomes of 313 specimens of freshwater fish representing 7 families, 55 genera, and 129 (88%) of the 146 resident species and lineages. Our comparative analyses of these sequences illustrate that the short (~150 bp) mitochondrial “barcode” regions typically used for eDNA assays are not consistently diagnostic for species-level identification and that no single region is best for metabarcoding Oregon’s fishes. However, often-overlooked intergenic regions of the mitogenome such as the D-loop have the potential to reliably diagnose and differentiate species. This project provides a blueprint for other researchers to follow as they build regional databases. It also illustrates the taxonomic value and limits of complete mitogenomic sequences, and how current eDNA assays and the “PCR-free” environmental genomics methods of the future can best leverage this information.

NAMERS: a purpose-built reference DNA sequence database to support applied eDNA metabarcoding

“…The NAMERS repository is presented here as a framework or foundation to inspire this investment and motivate the considerable coordination that will be necessary to extend it to include larger geographic and taxonomic scales. The NAMERS database echoes Dziedzic et al 17 in demonstrating that a small research group can generate a comprehensive set of high quality mitogenome reference sequences for a geographically relevant area, which can be impactful on it’s own or within a larger framework. We acknowledge that long term support and continued augmentation of any database like NAMERS requires dedicated resources, and yet argue the need for this and the plausibility of this given the increased need for metabarcoding for real-world applications.…”

“…The NAMERS repository is presented here as a framework or foundation to inspire this investment and motivate the considerable coordination that will be necessary to extend it to include larger geographic and taxonomic scales. The NAMERS database echoes Dziedzic et al 17 in demonstrating that a small research group can generate a comprehensive set of high quality mitogenome reference sequences for a geographically relevant area, which can be impactful on it's own or within a larger framework.…”

“…It has been known since the inception of eDNA metabarcoding that standardized DNA barcoding markers will not suffice given the need for marker choice flexibility and that comprehensive databases of whole organellular genomes are required 14 . Regardless, most references to DNA sequence databases for eDNA metabarcoding focus on filling gaps in existing single gene repositories 17,18 . There has been a lack of recognition of the need for innovation around reference DNA sequence databases to meet the unique needs of applied eDNA metabarcoding.…”

Environmental DNA: The next chapter

“…Due to the unprecedented effort over the last 10 years to sequence biodiversity, reference databases are now substantially more exhaustive and even include complete -or near to complete -references for some restricted taxonomic groups and geographical areas (e.g. Dziedzic et al, 2023).…”