DNA barcoding and phylogenetic analysis to characterize biodiversity of some freshwater fish species in Lake Nasser and River Nile

The present study aims to provide an inventory of eight freshwater fish species that represent 6 families obtained from Lake Nasser and the River Nile using DNA barcoding, using analysis of cytochrome oxidase subunit I (COI) gene sequences. Fish samples were identified morphologically as Ctenopharyngodon idella, Oreochromis niloticus, Bagrus bajad, Sarotherodon galilaeus, Auchenoglanis occidentalis, Lates niloticus, Sardinella tawilis, and Coptodon zillii. COI gene was successfully amplified for using PCR, showing a readable fragment length of ~ 700 base pairs (bp). The obtained sequences were compared to GenBank and the Barcode of Life Data System (BOLD). The GenBank and BOLD resulted in a total of 6 fish samples finding their best hits with similarity scores ranging from 99.29 to 100%. The average AT content (53.12%) was higher than the average GC content (46.88%) in the studied fish species. The minimum genetic Kimura 2-parameter (K2P) distance between species was 0.089 and the maximum distance was 0.313. According to phylogenetic tree analysis, the majority of fish species were grouped into monophyletic units. The current study confirms that DNA barcoding is a useful method to identify the vast majority of fish species in Lake Nasser and the River Nile. However, the morphological identification remains crucial.