Journal of Environmental Biology

RNA editing sites and compositional features in mitochondrial genes of two freshwater fish species Clarias batrachus and Heteropneustes fossilis 

J.C. Das, V. Dey and S. Chakraborty*     

Department of Biotechnology, Assam University, Silchar-788 011, India

Received: 01 April 2025                   Revised: 09 July 2025                   Accepted: 15 October 2025

*Corresponding Author Email : biotechnology700@gmail.com                  *ORCiD: https://orcid.org/0009-0005-7853-9553

Abstract

Aim: This study explores the codon usage bias (CUB) in the mitochondrial genes of two economically significant catfish species, Clarias batrachus and Heteropneustes fossilis, providing valuable insights for genetic and evolutionary research.

Methodology: Effective Number of Codons (ENC), RSCU values, Compositional analysis, Correspondence and PR2 analysis, Neutrality plot, RNA editing etc., were conducted.

Results: A low CUB was observed in both species, with average Effective Number of Codons (ENC) values 43.46 for C. batrachus and 44.08 for H. fossilis. In C. batrachus, 12 codons were over-represented, while 19 were under-represented; in H. fossilis, 11 codons were over-represented and 17 under-represented. Compositional analysis showed an AT-rich bias at third codon position in both the species. Correspondence and parity rule 2 (PR2) analyses suggested that mutational pressure and natural selection contribute to CUB. Neutrality plots indicated that natural selection plays a significant role than mutation in shaping CUB in the mitochondrial genes. Additionally, high C to T transitions was observed at RNA editing sites. Positive GRAVY scores pointed to the hydrophobic nature of mitochondrial proteins. Phylogenetic analysis revealed the evolutionary relationships between these species.

Interpretation: This study provides valuable insights into the genetic evolution of these catfish species, with implications for aquaculture and evolutionary biology.

Key words: Codon usage bias, Natural selection, Phylogenetic, RNA editing sites

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