3.3 Actinopterygii (Ray-finned fishes)
A total of 324 sequences were generated belonging to 15 orders, 66 families, 133 genera and 164 species (Table 1). The sequence analysis revealed average nucleotide frequencies to be A: 23.9%, T: 29.6%, G: 18.3% and C: 28.2% (Fig. 3). The base composition analysis for the COI sequence showed that the average T content was the highest and the average G content was the lowest; the AT content (53.50%) was higher than the GC content (46.50%). The GC contents at the first, second and third codon positions for the fish species were 54.62%, 43.66% and 38.04% respectively (Fig. 4). The pattern of %GC content at different codons was 1st>2nd>3rd(p -value <0.005) The K2P genetic distances within each taxonomic level are summarized in Table 3. The average genetic distance within species, genus, family and order were 0.40 ± 0.002%, 6.36 ± 0.008%, 14.10 ± 0.01% and 24.07 ± 0.02%, respectively (Table 3).
The NJ tree of all generated sequences included 164 species is provided in Figure 2. Most of the specimens of the same species were clustered together, which reflected the prior taxonomic assignment based on morphology. No taxonomic deviation was detected at the species level, indicating that the majority of the examined species could be authenticated by the barcode approach.
3.3.1 Order Clupeiformes
This order includes many of the most important forage and food fish. A total of 45 samples were sequenced belonging to three families, 12 genera and 19 species. Among the three families Clupeidae is the most valuable family where a single species Tenualosa ilishacontributes over 12% of total fish production of the country (DoF, 2018). The overall mean nucleotide base frequencies observed for these sequences were T: 28.60%, C: 27.80%, A: 24.20% and G 19.40%. The AT content (52.80%) was higher than the GC content (47.20%) (Fig. 3). The GC contents at the first, second and third codon positions were 49.10%, 48.20% and 44.40% respectively (Fig. 4). The K2P distances of the COI sequence within species, genus and family were 1.81, 6.55 and 13.41, respectively (Table 3). The NJ tree clearly distinguished all the species (Supplementary Fig.1). The species belonging to family Clupeidae, Engraulidae and and Pristigasteridae were represented by three distinct clades.