Incorporation of transition to transversion ratio and nonsense mutations, improves the estimation of the number of synonymous and non-synonymous sites in codons

Ruksana Aziz; Piyali Sen; Pratyush Kumar Beura; Saurav Das; Debapriya Tula; Madhusmita Dash; Nima Dondu Namsa; Ramesh Chandra Deka; Edward J. Feil; Siddhartha Sankar Satapathy; Suvendra Kumar Ray

doi:10.1093/dnares/dsac023

Incorporation of transition to transversion ratio and nonsense mutations, improves the estimation of the number of synonymous and non-synonymous sites in codons

Ruksana Aziz, Piyali Sen, Pratyush Kumar Beura, Saurav Das, Debapriya Tula, Madhusmita Dash, Nima Dondu Namsa, Ramesh Chandra Deka, Edward J. Feil, Siddhartha Sankar Satapathy, Suvendra Kumar Ray

Research output: Contribution to journal › Article › peer-review

6 Citations (SciVal)

Abstract

A common approach to estimate the strength and direction of selection acting on protein coding sequences is to calculate the dN/dS ratio. The method to calculate dN/dS has been widely used by many researchers and many critical reviews have been made on its application after the proposition by Nei and Gojobori in 1986. However, the method is still evolving considering the non-uniform substitution rates and pretermination codons. In our study of SNPs in 586 genes across 156 Escherichia coli strains, synonymous polymorphism in 2-fold degenerate codons were higher in comparison to that in 4-fold degenerate codons, which could be attributed to the difference between transition (Ti) and transversion (Tv) substitution rates where the average rate of a transition is four times more than that of a transversion in general. We considered both the Ti/Tv ratio, and nonsense mutation in pretermination codons, to improve estimates of synonymous (S) and non-synonymous (NS) sites. The accuracy of estimating dN/dS has been improved by considering the Ti/Tv ratio and nonsense substitutions in pretermination codons. We showed that applying the modified approach based on Ti/Tv ratio and pretermination codons results in higher values of dN/dS in 29 common genes of equal reading-frames between E. coli and Salmonella enterica. This study emphasizes the robustness of amino acid composition with varying codon degeneracy, as well as the pretermination codons when calculating dN/dS values.

Original language	English
Article number	dsac023
Journal	DNA research : an international journal for rapid publication of reports on genes and genomes
Volume	29
Issue number	4
DOIs	https://doi.org/10.1093/dnares/dsac023
Publication status	Published - 3 Aug 2022

Bibliographical note

We are very much thankful to the anonymous reviewers for their critical comments that helped us to revise the article and improve its quality. R.A. is thankful for the JRF fellowship from the DBT grant (BT/511/NE/TBP/2013) and (BT/403/NE/U-Excel/2013). P.S. is thankful to UGC, GoI New Delhi for the JRF. P.K.B. is thankful to Tezpur University for the Institutional fellowship. S.D. is thankful for DBT, GoI, for the MSc fellowship. S.S.S. and S.K.R. are thankful to DBT, GoI for the twinning grant (BT/PR16361/NER/95/192/2015 date 18 October 2016) to them. S.K.R. and R.C.D. are thankful to DBT, GoI for the twinning grant BT/PR16182/NER/95/92/2015. S.S.S. is thankful to DBT for the NE Overseas Associateship, which helped him to work in University of Bath. EF, S.S.S., R.C.D., and S.K.R. are thankful to the society for Molecular Biology and Evolution (SMBE) for holding the satellite meeting at Kaziranga, Assam, India on 14–17 December 2017, which helped the authors to have collaboration on this work. N.D.N., R.C.D., S.K.R., and S.S.S. thankfully acknowledge the DBT funded Bioinformatics and Computational Biology Centre at Tezpur University.

Keywords

Pretermination codon
Synonymous/non-synonymous sites
Transition
Transversion
dN/dS

ASJC Scopus subject areas

Molecular Biology
Genetics

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10.1093/dnares/dsac023Licence: CC BY

Cite this

Aziz, R., Sen, P., Beura, P. K., Das, S., Tula, D., Dash, M., Namsa, N. D., Deka, R. C., Feil, E. J., Satapathy, S. S., & Ray, S. K. (2022). Incorporation of transition to transversion ratio and nonsense mutations, improves the estimation of the number of synonymous and non-synonymous sites in codons. DNA research : an international journal for rapid publication of reports on genes and genomes, 29(4), Article dsac023. https://doi.org/10.1093/dnares/dsac023

Incorporation of transition to transversion ratio and nonsense mutations, improves the estimation of the number of synonymous and non-synonymous sites in codons. / Aziz, Ruksana; Sen, Piyali; Beura, Pratyush Kumar et al.
In: DNA research : an international journal for rapid publication of reports on genes and genomes, Vol. 29, No. 4, dsac023, 03.08.2022.

Research output: Contribution to journal › Article › peer-review

Aziz, R, Sen, P, Beura, PK, Das, S, Tula, D, Dash, M, Namsa, ND, Deka, RC, Feil, EJ, Satapathy, SS & Ray, SK 2022, 'Incorporation of transition to transversion ratio and nonsense mutations, improves the estimation of the number of synonymous and non-synonymous sites in codons', DNA research : an international journal for rapid publication of reports on genes and genomes, vol. 29, no. 4, dsac023. https://doi.org/10.1093/dnares/dsac023

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abstract = "A common approach to estimate the strength and direction of selection acting on protein coding sequences is to calculate the dN/dS ratio. The method to calculate dN/dS has been widely used by many researchers and many critical reviews have been made on its application after the proposition by Nei and Gojobori in 1986. However, the method is still evolving considering the non-uniform substitution rates and pretermination codons. In our study of SNPs in 586 genes across 156 Escherichia coli strains, synonymous polymorphism in 2-fold degenerate codons were higher in comparison to that in 4-fold degenerate codons, which could be attributed to the difference between transition (Ti) and transversion (Tv) substitution rates where the average rate of a transition is four times more than that of a transversion in general. We considered both the Ti/Tv ratio, and nonsense mutation in pretermination codons, to improve estimates of synonymous (S) and non-synonymous (NS) sites. The accuracy of estimating dN/dS has been improved by considering the Ti/Tv ratio and nonsense substitutions in pretermination codons. We showed that applying the modified approach based on Ti/Tv ratio and pretermination codons results in higher values of dN/dS in 29 common genes of equal reading-frames between E. coli and Salmonella enterica. This study emphasizes the robustness of amino acid composition with varying codon degeneracy, as well as the pretermination codons when calculating dN/dS values.",

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note = "We are very much thankful to the anonymous reviewers for their critical comments that helped us to revise the article and improve its quality. R.A. is thankful for the JRF fellowship from the DBT grant (BT/511/NE/TBP/2013) and (BT/403/NE/U-Excel/2013). P.S. is thankful to UGC, GoI New Delhi for the JRF. P.K.B. is thankful to Tezpur University for the Institutional fellowship. S.D. is thankful for DBT, GoI, for the MSc fellowship. S.S.S. and S.K.R. are thankful to DBT, GoI for the twinning grant (BT/PR16361/NER/95/192/2015 date 18 October 2016) to them. S.K.R. and R.C.D. are thankful to DBT, GoI for the twinning grant BT/PR16182/NER/95/92/2015. S.S.S. is thankful to DBT for the NE Overseas Associateship, which helped him to work in University of Bath. EF, S.S.S., R.C.D., and S.K.R. are thankful to the society for Molecular Biology and Evolution (SMBE) for holding the satellite meeting at Kaziranga, Assam, India on 14–17 December 2017, which helped the authors to have collaboration on this work. N.D.N., R.C.D., S.K.R., and S.S.S. thankfully acknowledge the DBT funded Bioinformatics and Computational Biology Centre at Tezpur University.",

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AU - Das, Saurav

AU - Tula, Debapriya

AU - Dash, Madhusmita

AU - Namsa, Nima Dondu

AU - Deka, Ramesh Chandra

AU - Feil, Edward J.

AU - Satapathy, Siddhartha Sankar

AU - Ray, Suvendra Kumar

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Incorporation of transition to transversion ratio and nonsense mutations, improves the estimation of the number of synonymous and non-synonymous sites in codons

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

Access to Document

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