In silico DNA barcoding by the COI gene of Crassostrea virginica in the Atlantic Ocean and Caribbean Sea

Background: "Crassostrea virginica belongs to a class of bivalve mollusks that play vital roles in the marine ecosystem. This species holds economic and biological significance, making it a key species in the Atlantic, Caribbean, and Gulf of Mexico. This study aimed to understand the genetic diversity of virginica by barcoding techniques and if the distribution of oysters in the Atlantic Ocean is known, it would indicate which areas require further study.
Methods: Two thousand and eight sequences of virginica COI gene were downloaded from BOLD, aligned, and trimmed using BioEdit and ClustalW. For the haplotypes and their networks, MJN used Network and PopArt. DnaSP was used for sequence grouping and population genetic analysis. The p-Distance and Tajima-Nei values were obtained by Mega v11 software. Finally, to generate the phylogenetic tree, IQTree using maximum likelihood and FigTree were utilized.

Results: The three most abundant haplotypes were AY5422 (58.937%), GB8915 (9.661%), and GB1513 (5.314%). Four sets of sequences have been generated by the origin of capture: 176 for the United States, 9 for Canada, 17 for Cuba, and 4 for Panama. The results revealed two haplotype networks based on region and frequency. A total of 42 different haplotypes. The haplotype network showed that they were grouped by regions, with Canada and the US mixed, as well as Cuba and Panama. Genetic diversity values were nearly zero for individuals within the same geographic populations, while there were higher values among the four regions described (0.01 < FST < 0.9). The Tajima-Nei analysis revealed values ranging from approximately 0.001 to 0.029 within regions and between regions, respectively.

Conclusions: This study revealed that among the 4 regions examined, there were significant genetic differences, indicating the need to explore additional regions in the Gulf of Mexico to develop conservation and commercialization initiatives for virginica.