Thomas Desvignes
The University of Alabama at Birmingham
Back to Projects
Status: Current
Type:
Focus Area(s):
Project Leaders
Sea Grant Funds: $9,998
Matching Funds: $5,002
Project Date Range: 02-01-2026 to 12-31-2027
Abstract
The objective of this project development proposal is to generate full mitochondrial reference genomes for at least 50 species of fishes from Alabama, Mississippi, and neighboring Gulf states. This project aims to demonstrate that novel sequencing technologies such as low-coverage Whole Genome Sequencing (lcWGS) can produce in a short time and at low cost the reliable data needed to apply environmental DNA (eDNA) techniques to survey and monitor fish species in marine environments of the Gulf states.
Objectives
The proposed activities will make use of previously collected DNA samples deposited in museum collections and potentially of DNA samples freshly collected during the span of the proposal. DNA of at least 50 fish species will be extracted at our laboratory at the University of Alabama at Birmingham (UAB) and DNA extract quality will be assessed on agarose gels. An aliquot of each high-quality DNA extract will be sent for lcWGS library preparation at a US genomic facility offering the service. All libraries will be individually barcoded, multiplexed, and sequenced together on one lane of the most cost-effective available Illumina sequencing platform. Full mitochondrial genomes of these 50 species will then be either assembled through a guided-assembly process based on complete mitochondrial genomes of closely related species, or de novo assembled using bioinformatic tools such as NOVOPlasty, GetOrganelle, or MitoZ for species that do not have closely related species with a complete mitochondrial genome sequence. Finally, resulting assembled mitochondrial genomes will be annotated using MitoAnnotator and publicly deposited in NCBI GenBank.
Methodology
Emerging genetic technologies such as environmental DNA (eDNA) analyses provide complementary approaches and even sometimes alternatives to logistically complex and costly traditional biodiversity surveys because eDNA can detect the presence of species and characterize fish community assemblages in coastal and marine environments, even where traditional methods are hard or impossible to deploy due to currents, bottom structure, or visibility for example. To date, eDNA studies have often targeted single or few species at a time, but metabarcoding methods can in theory be applied to any fish species, however, a technical gap preventing the broad use of eDNA to monitor fish in the Gulf is the incompleteness of reference genetic databases because accurate species identification relies entirely on the presence in public databases of trusted reference sequences for each species. This project will thus produce novel reliable data needed to more frequently and broadly apply eDNA techniques to survey and monitor fish species in marine environments of the Gulf states.