BIOINFORMATIC ANALYSIS OF MITOCHONDRIAL GENOME OF HUMPED FEATHERBACK CHITAL FISH, Chitala chitala (HAMILTON, 1822)

Abstract

The present study was about the bioinformatic analysis of mitochondrial genome of an endangered featherback fish, Chitala chitala. Although Chitala chitala plays significant role in inland fishery, but its’ evolution has received little attention. In the current study, the mitogenome of Chitala chitala was retrieved and investigated. Some of the bioinformatics tools were applied to measure important gene parameters including AT/GC-skewness, codon adaptation index (CAI), the effective number of codons (ENc) and GC percentages of each protein coding gene. The majority of AT-skew and GC-skew values of all protein coding genes of the species were negative, and the amplitude of the GC-skew was larger than the AT-skew. On the basis of comparative selective strength analysis with the PCGs of two related mitogenomes, I discovered that most of the PCGs retained the Ka/Ks ratios less than one implying that they evolved under strong negative or purifying selection. Moreover, I analyzed the codon frequency and relative synonymous codon usage (RSCU). Then, I identified a total of 22 RSCU values (>1) and revealed 6 codons as “over-presented” that implied for codon usage bias to engage in highly expressed genes for efficient protein synthesis via translational selection. The phylogenetic tree and time tree were constructed by Maximum Likelihood (ML) method, providing further supplement to the evolution of the fish. Regarding on the facts of the presence of codon usage biasness rolling in translational selection and the signs of purifying selection identified in PCGs indicate obvious conservation of this endangered fish species.