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.
Description:
A Thesis
Submitted to the Faculty of Agriculture,
Sher-e-Bangla Agricultural University, Dhaka,
in partial fulfillment of the requirements
for the degree of
MASTER OF SCIENCE
IN
BIOTECHNOLOGY
SEMESTER: JULY-DECEMBER, 2021
