Nucleotide sequence of 16S rRNA gene of Clarias gariepinus and its molecular phylogeny with other catfishes

Clarias gariepinus commonly known as the North American catfish, belong to a diverse group of ray finned fish. They are of considerable commercial importance; many of the larger species are farmed or fished for food. Partial sequence of 16S rRNA gene of the mitochondrial genome in the catfish Clarias gariepinus was determined that contained 561 base pairs (bp). Genomic DNA was isolated successfully by CTAB method. Amplification of DNA was carried out using universal set of primers which amplified partial region of the mitochondrial 16S rRNA gene. Nucleotide sequence was determined using the Sanger dideoxy sequencing method. The sequence was 561 bp long and the A+T base composition of the gene was about 53%. Interspecific and intraspecific comparison between two catfishes namely C. gariepinus and C. batrachus based on the 16S rRNA gene. The intraspecific sequences of 16S rRNA gene of C. gariepinus was aligned and 8 of polymorphic sites were observed. However, 21 polymorphic sites were revealed after comparing the interspecific sequence between C. gariepinus and C. batrachus. These polymorphic sites could be used as a molecular tool for identification of these two catfishes. Furthermore, partial 16S rRNA sequences of a few different locally found catfishes from Bangladesh and India were collected from the GenBank database, all of which were over 500 bp long. A phylogenic tree was constructed using the multiple sequence alignment data of the 8 catfish sequences to determine their phylogenic relationship. All eight catfishes form a monophylic group that belong to the order Siluriformes. Among different species of catfish C. gariepinus and C. batrachus form a monophylic group with high bootstrap value (98). Both of these fishes are consistent with phylogeny based on morphology and they belong to the family Clariidae. Labeo rohita and Channa striata were used as out groups. This research demonstrates that partial sequences of this gene can identify the different species of catfish, indicating the usefulness of mtDNA-based approach in species identification.