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Difference in synonymous polymorphism related to codon degeneracy between co-transcribed genes in the genome of Escherichia coli


Affiliations
1 Department of Molecular Biology and Biotechnology, Tezpur University, Napaam 784 028, India , India
2 Department of Computer Science and Engineering, Tezpur University, Napaam 784 028, India, India
3 Department of Electronics and Communication Engineering, National Institute of Technology, Jote, Papum Pare 791 113, India, India
4 Department of Computer Science and Engineering, Tezpur University, Napaam 784 028, India; Centre for Multidisciplinary Research, Tezpur University, Napaam 784 028, India, India
5 Department of Molecular Biology and Biotechnology, Tezpur University, Napaam 784 028, India; Centre for Multidisciplinary Research, Tezpur University, Napaam 784 028, India, India

In our study, we compared synonymous polymorphism in co-transcribed gene pairs within five well-known Escherichia coli operons (rpoB/C, lacZ/Y, kdpA/B, araB/A and bcsA/B). Interestingly, the transition to transversion ratio between gene pairs were different due to their compositional differences of two-fold and four-fold degenerate codons. The differences in polymorphism spectra were more pronounced in four-fold and six-fold codons compared to two-fold degenerate codons. Notably, rpoB and rpoC showed significant distinctions in UCC, GUA, CCG, GCU, GGC and CGC codons. Similar trends were observed in other gene pairs, particularly in higher degenerate codons. Notably, two-fold degenerate codons primarily exhibited synonymous polymorphisms through transitions, while higher degenerate codons encompassed both transition and transversion events. This underscores the intriguing role of degenerate codons in molecular evolution
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Abstract Views: 221




  • Difference in synonymous polymorphism related to codon degeneracy between co-transcribed genes in the genome of Escherichia coli

Abstract Views: 221  | 

Authors

Pratyush Kumar Beura
Department of Molecular Biology and Biotechnology, Tezpur University, Napaam 784 028, India , India
Piyali Sen
Department of Computer Science and Engineering, Tezpur University, Napaam 784 028, India, India
Ruksana Aziz
Department of Molecular Biology and Biotechnology, Tezpur University, Napaam 784 028, India , India
Chayanika Chetia
Department of Molecular Biology and Biotechnology, Tezpur University, Napaam 784 028, India , India
Madhusmita Dash
Department of Electronics and Communication Engineering, National Institute of Technology, Jote, Papum Pare 791 113, India, India
Siddhartha Shankar Satapathy
Department of Computer Science and Engineering, Tezpur University, Napaam 784 028, India; Centre for Multidisciplinary Research, Tezpur University, Napaam 784 028, India, India
Suvendra Kumar Ray
Department of Molecular Biology and Biotechnology, Tezpur University, Napaam 784 028, India; Centre for Multidisciplinary Research, Tezpur University, Napaam 784 028, India, India

Abstract


In our study, we compared synonymous polymorphism in co-transcribed gene pairs within five well-known Escherichia coli operons (rpoB/C, lacZ/Y, kdpA/B, araB/A and bcsA/B). Interestingly, the transition to transversion ratio between gene pairs were different due to their compositional differences of two-fold and four-fold degenerate codons. The differences in polymorphism spectra were more pronounced in four-fold and six-fold codons compared to two-fold degenerate codons. Notably, rpoB and rpoC showed significant distinctions in UCC, GUA, CCG, GCU, GGC and CGC codons. Similar trends were observed in other gene pairs, particularly in higher degenerate codons. Notably, two-fold degenerate codons primarily exhibited synonymous polymorphisms through transitions, while higher degenerate codons encompassed both transition and transversion events. This underscores the intriguing role of degenerate codons in molecular evolution


DOI: https://doi.org/10.18520/cs%2Fv125%2Fi8%2F871-877