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Genetic evolution and codon usage analysis of NKX-2.5 gene governing heart development in some mammals

Malakar, Arup Kr., Halder, Binata, Paul, Prosenjit, Deka, Himangshu, Chakraborty, Supriyo
Genomics 2020 v.112 no.2 pp. 1319-1329
amino acids, bioinformatics, codons, heart, mammals, mutation, natural selection
NKX-2.5 gene is responsible for cardiac development and its targeted disruption apprehends cardiac development at the linear heart tube stage. Bioinformatic analysis was employed to investigate the codon usage pattern and dN/dS of mammalian NKX-2.5 gene. The relative synonymous codon usage analysis revealed variation in codon usage and two synonymous codons namely ATA (Ile) and GTA (Val) were absent in NKX-2.5 gene across selected mammalian species suggesting that these two codons were possibly selected against during evolution. Parity rule 2 analysis of two and four fold amino acids showed CT bias whereas six-fold amino acids revealed GA bias. Neutrality analysis suggests that selection played a prominent role while mutation had a minor role. The dN/dS analysis suggests synonymous substitution played a significant role and it negatively correlated with p-distance of the gene. Purifying natural selection played a dominant role in the genetic evolution of NKX-2.5 gene in mammals.