Modified dN/dS for accounting transition and transversion frequency difference and non-sense substitution in genomes

Abstract

The dN/dS value is estimated in homologous protein coding gene sequences between two closely related organisms for studying selection on the genes. In the usual method of calculation of synonymous (S) and non-synonymous (NS) sites in codons, the transition and transversion rates are considered same as well as no difference of pretermination codons from the other codons regarding NS substitutions is considered. In this study we are proposing a modification in the method by estimating the S and the NS sites in codons by considering difference between the transition and transversion rates and the NS substitutions leading to non-sense codons in pretermination codons. So, the dN/dS value calculated by our approach was higher than that calculated by the earlier method. The modified method was applied in estimating dN/dS in 29 homologous gene sequences of Escherichia coli and Salmonella enterica. Impact of codon degeneracy and pretermination codons on the dN/dS values estimated by our method were observed clearly. Our method of estimation that considers the above features is a realistic representation of dN/dS values in coding sequences.

Transcriptomic Analysis Reveals Adaptive Evolution and Conservation Implications for the Endangered Magnolia lotungensis

“…Examining codon usage bias allows us to discern the distinct roles played by these forces in shaping the genetic architecture of the species [ 17 , 18 ]. Moreover, by scrutinizing the dN/dS substitution rates among paralogous genes within M. lotungensis , we can shed light on the evolutionary trajectory of gene families, gaining insights into the molecular mechanisms that underpin the species’ adaptations and vulnerabilities [ 19 , 20 , 21 ].…”