Complete Mitochondrial Genome And Phylogenetic Study Of Catfishes Order (Siluriformes) From River Indus Sindh, Pakistan

Natural resources of aquatic organisms are decreasing, due to overfishing,human manipulation and global climate change, through out the world. On the otherhand, demand of aquatic protein is increasing. Thus, lack of resources and increasinghuman population all over the world is a great challenage to ensure the food security.Scientists and researches are engaged to find out the techniques those not only save thenatural creature but increase the production of organisms for welfare of human being.Aquaculutre is one of the developing technique that produce millions tons ofaquaculture species to fulfil the market demand. Aquaculture industry is facing lot ofproblems, such as slow growth rate, diseasese resistance etc, to increase productivityand profitability of aquatic organisms. In this regards efforts had been carried out forlast many decades to improve the important species through conventional breedingmethods to increase the production. It seems an improvement by conventional methodbut could not improve the important desired production. Main draw back ofconventional breeding was that it is time consuming, laborious and environmentalfactor influence the athenticity during breeding process.In the modern developed technology of DNA sequencing have facilitate thebreeders to find out desired economically important aquaculture species in little timeperiod by markers-assisted selection (MAS) breeding. In this regard MAS requires thegene/DNA sequence responsible of controlling the desired trait. This is a moderngenetic technology that has been applied in many aquaculture species, significantprogress have been observed in Taiwan catfish bagridae family phylogeneticrelationship.Freshwater catfishes are important aquaculture species. This farming history ofthese commercial fishes is few decades old. DNA sequencing technology has facilitated to develop the genetic resource of the catfishes. Hence, development ofDNA sequencing facilitate for phylogenetic studeis. Complete mitochondrial genomesof four catfish species were sequenced in this work, and phelogenetic study wascarried out.The complete Rita rita mitogenome sequence is16,449bp in length. Theoverall characteristics, including its overall organization and the gene arrangementpattern, are identical to that of the typical vertebrate mitogenome. The completemitogenome contains13protein-coding genes,2rRNA,22tRNA genes and oneputative control region. The average base composition of the complete mitogenome is33.40%A,27.43%C,14.26%G, and24.89%T. All protein-coding genes except(ND6) were encoded on heavy strand (H strand). Fourteen tRNA were encoded onheavy strand and remainder were encoded on light strand (L strand). The organizationof Rita rita mitochondrial genome conforms to the consensus of gene order of otherfish mitochondrial genome.The complete Sperata seenghala mitogenome sequence is16,588bp in length.The complete mitogenome contains13protein-coding genes,2rRNA,22tRNA genesand one putative control region. The average base composition of the sperata completemitogenome is31.28%A,27.80%C,15.31%G, and25.57%T. All protein-codinggenes except (NADH6) were encoded on heavy strand (H strand). Fourteen tRNAwere encoded on heavy strand and remainder were encoded on light strand (L strand).The S. seenghala mtDNA genome conforms to the consensus gene order of other fish(mtDNA) genome.The complete Bagarius bagarius mitogenome sequence is16,457bp in length.The complete mitogenome contains13protein-coding genes,2rRNA,22tRNA genes and one putative control region. The average base composition of the Bagariuscomplete mitogenome is31.14%A,27.72%C,15.62%G, and25.50%T. All protein-coding genes except (ND6) were encoded on heavy strand (H strand). Fourteen tRNAwere encoded on heavy strand and remainder were encoded on light strand (L strand).The organization of Bagarius bagarius mitochondrial genome conforms to theconsensus of gene order of other fish mitochondrial genome.The complete Wallago attu mitogenome sequence is15639bp in length. Theoverall characteristics, including its overall organization and the gene arrangementpattern, are identical to that of the typical vertebrate mitogenome. The completemitogenome contains13protein-coding genes,2rRNA,22tRNA genes and oneputative control region. The average base composition of the Rita completemitogenome is31.17%A,28.15%C,15.55%G, and25.12%T. All protein-codinggenes except (NADH6) were encoded on heavy strand (H strand). Fourteen tRNAwere encoded on heavy strand and remainder were encoded on light strand (L strand).The organization of Wallago attu, mitochondrial genome conforms to the consensus ofgene order of other fish mitochondrial genome.In the current study we used48species from four families (Bagridae, Pangasiidae,Mochokidae, Sisoridae and Siluridae) of order siluriformes including one out groupfamily (Channidae) respectively.Our target species in present study were Rita rita,Sperata seenghala, Bagarius bagarius and Wallago attu. For phylogenetic analysis weused different methods to confirm genetic relationship (TML, TNJ, TME, TU andTMP). The evolutionary history was inferred by using the Maximum Likelihoodmethod based on the Tamura-Nei model. The tree with the highest log likelihood (-11816.9588) is shown. The percentage of trees in which the associated taxa clustered together is shown above the branches. Initial trees for the heuristic search wereobtained automatically by applying Neighbor-Join and Bio NJ algorithms to a matrixof pairwise distances estimated using the Maximum Composite Likelihood (MCL)approach, and then selecting the topology with superior log likelihood value. The treeis drawn to scale, with branch lengths measured in the number of substitutions per site.The analysis involved48nucleotide sequences. Codon positions included were1st+2nd+3rd+Noncoding. All positions containing gaps and missing data wereeliminated. There were a total of667positions in the final dataset. Evolutionaryanalyses were conducted in MEGA6. Our phylogenetic results confirm that fourspecies from Pakistan belongs to same families which were reported by manyresearchers. In present phylogenetic research shows relationship between species Ritarita is closely related with Rita sacerdotum, Wallago attu is closely related withSilurus soldatovi, Sperata seenghala is genetically related with Hemibagrus spilopterusand Bagarius bagarius is closely related with Bagarus yarrali which were collectedfrom Indus River. Out of four species three are critically endangered. From thisphylogenetic study we can conserve these species by genetic breeding or traditionalbreeding/hyberdization with closely related species.Hopefully, these findings will lead to a better understand the factors thatinfluence on genetic level. Thus the results will promote the species identification tohigher production through marker-assisted breeding.