Identification of Hypervariable Domains in 12SrDNA for Enhanced Fish Species Barcoding from the Red Sea Regions of Egypt and Yemen

Ribosomal RNA (rRNA) genes, particularly 12SrDNA, have proven to be effective barcodes for fish species identification due to their secondary structure domains that exhibit interspecific variability. This study focused on identifying hypervariable domains within the 12SrDNA gene that contribute to its barcoding efficiency. Fish samples from Egypt and Yemen, representing various orders and families, were analyzed using 12SrDNA and COI gene sequencing. Four hypervariable domains (D2, D3, D5, D7) within 12SrDNA showed the highest divergence among species. Concatenating these domains significantly increased interspecific genetic distances. COI and 12SrDNA barcodes revealed 3 misidentified species (Plectorhinchus sordidus, Mulloidichthys flavolineatus, and Lethrinus nebulosus.), emphasizing the importance of focusing on specific hypervariable domains for accurate species identification.