Molecular assessment of proteins encoded by the mitochondrial genome of Clarias batrachus and Clarias gariepinus

Abstract

The population of catfish, Clarias batrachus has substantially diminished in various countries and studies show that another related species Clarias gariepinus is replacing it. The better adaptability and survivability of C. gariepinus over C. batrachus could be attributed to the metabolic differences between these two species, which is primarily regulated by mitochondrial activities. To understand the reasons behind this phenomenon, we performed in silico analyses to decipher the differences between the proteins encoded by the mitochondrial genome of these two related species. Our analysis revealed that out of thirteen, twelve proteins encoded by the mitochondrial genome of these two species have substantial variations between them. We characterised these variations by analysing their effect on secondary structure, intrinsic disorder predisposition, and functional impact on protein and stability parameters. Our data show that most of the parameters are changing between these two closely related species. Altogether, we demonstrate the molecular insights into the mitochondrial genome-encoded proteins of these two species and predict their effect on protein function and stability that might be helping C. gariepinus to gain survivability better than the C. batrachus .

Mitochondriomics of Clarias Fishes (Siluriformes: Clariidae) with a New Assembly of Clarias camerunensis: Insights into the Genetic Characterization and Diversification

“…Various genetic markers (glutamic acid transfer RNA, cytochrome b, and cytochrome c oxidase subunit 1) were used to elucidate the diversity, evolutionary relationship, population structure, and cryptic diversity of Clarias species [ 23 , 24 , 25 ]. Later on, the complete mitogenomes and whole-genome sequences were analyzed to comprehend the in-depth phylogenetic relationship of Clarias species [ 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 ]. Further, with the flourishment of molecular tools in biodiversity research, the non-invasive environmental DNA (eDNA) was also examined by qPCR assay to reveal the genetic diversity of north African sharptooth catfish, C. gariepinus [ 34 ].…”

A computational study on mitogenome-encoded proteins of Pavo cristatus and Pavo muticus identifies key genetic variations with functional implications

“…The multiple sequence alignment of the mitogenome-encoded 13 proteins from P. cristatus and P. muticus were performed by Clustal Omega webserver as described earlier [ 28 , 29 ] .…”

Biology of selected Clarias catfish species used in aquaculture

“…These studies reported basic features, including the overall mitogenome size, ranging from 16,508 to 16,525 base pairs (depending on the species), A+T content, and the identification of coding, tRNA, and rRNA genes in the D-loop or control region for each species. Chand et al (2021) directly compared the mitogenomes of C. batrachus and C. gariepinus. They described variation in 12 of 13 proteins encoded by these genomes that might lead to functional and stability differences.…”