Transcribed intergenic regions exhibit a lower frequency of nucleotide polymorphism than the untranscribed intergenic regions in the genomes of Escherichia coli and Salmonella enterica

Beura, Pratyush Kumar; Sen, Piyali; Aziz, Ruksana; Satapathy, Siddhartha Shankar; Ray, Suvendra Kumar

doi:10.1007/s12041-023-01418-w

Cited by 2 publications

(6 citation statements)

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“…Susceptibility of different sites for ti and tv are not same as evident by C→T ti and G→T tv are more frequent than the other ti and tv , respectively (Sen et al . 2022; Beura et al . 2023).…”

Section: Discussionmentioning

confidence: 99%

“…The logic is that the most abundant nucleotide in a species is the ancestral nucleotide in the species (Sen et al 2022; Aziz et al . 2022; Sen 2022, Beura et al . 2023).…”

Section: Methodsmentioning

confidence: 99%

“…The logic behind the derivation of the reference sequence is that the most abundant nucleotide in a position is considered as the ancestral nucleotide for the position (Sen et al 2022; Aziz et al . 2022; Sen 2022, Beura et al . 2023).…”

Section: Methodsmentioning

confidence: 99%

“…In case of improved Sti and improved Stv cases the possible sites have been normalized respectively. Susceptibility of different sites for ti and tv are not same as evident by C T ti and G T tv are more frequent than the other ti and tv, respectively(Sen et al 2022;Beura et al 2023). Therefore, the correlation value between improved Sti and improved Stv is likely to be weaker than the same between Sti and Stv values.As transitions are more frequent events than transversion, transition can be consideredalone to understand the selection on coding sequences.…”

mentioning

confidence: 94%

“…Accordingly, it has been recently reported that the synonymous variation in TFD codons is relatively higher than the FFD codons in Escherichia coli (Aziz et al 2022). Therefore, in any organism, the ratio is likely to vary across the coding sequences having differences in degenerate codon composition (Beura et al 2023). Hence, an estimation of ௧ ௧௩ ratio in a coding sequence by accounting codon degeneracy and PTC compositions will be important to further carrying out comparative analysis of this value among coding sequences in a genome.…”

Section: Introductionmentioning

confidence: 99%

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Synonymous and non-synonymous transitions/transversions vividly disclose purifying selection inEscherichia colicoding sequences

Beura

Aziz

Sen

et al. 2022

Preprint

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Transition to transversion ratio (ti/tv) is important in the study of molecular evolution, which provides the understanding of mutational bias in an organism. Since, synonymous polymorphism for two-fold degenerate codons depends only on transitions, two-fold degenerate codons and four-fold degenerate codons are different regarding (Ti/Tv) ratios both for synonymous as well as non-synonymous mutations. Therefore, various coding sequences in any organism having difference in degenerate codon composition is likely to affects the ti/tv ratio. In addition to the above, compositional differences among the coding sequences regarding pretermination codon is also likely to influence the ti/tv ratio because purifying selection is stronger on non-synonymous substitutions leading to termination codons. In this study we have improve the method of finding the ratio between transition to transversion, synonymous transition to synonymous transversion and non-synonymous transition to non-synonymous transversion and also developed a computer program to calculate the values. Our analyses in 2516 coding sequences in the E. coli genome suggested a strong correlation between codon degeneracy with synonymous transition to transversion ratio, also we have observed a moderate correlation between pretermination codons and non-synonymous transition to transversion. The percentage change between the conventional and improved method was the most striking part of our observation.

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Section: Discussionmentioning

confidence: 99%

“…The logic is that the most abundant nucleotide in a species is the ancestral nucleotide in the species (Sen et al 2022; Aziz et al . 2022; Sen 2022, Beura et al . 2023).…”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 94%

Section: Introductionmentioning

confidence: 99%

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Synonymous and non-synonymous transitions/transversions vividly disclose purifying selection inEscherichia colicoding sequences

Beura

Aziz

Sen

et al. 2022

Preprint

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High frequency of transition to transversion ratio in the stem region of RNA secondary structure of untranslated region of SARS-CoV-2

Dash,

Meher,

Aditya Kumar

et al. 2024

PeerJ

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Introduction The propensity of nucleotide bases to form pairs, causes folding and the formation of secondary structure in the RNA. Therefore, purine (R): pyrimidine (Y) base-pairing is vital to maintain uniform lateral dimension in RNA secondary structure. Transversions or base substitutions between R and Y bases, are more detrimental to the stability of RNA secondary structure, than transitions derived from substitutions between A and G or C and T. The study of transversion and transition base substitutions is important to understand evolutionary mechanisms of RNA secondary structure in the 5′ and 3′ untranslated (UTR) regions of SARS-CoV-2. In this work, we carried out comparative analysis of transition and transversion base substitutions in the stem and loop regions of RNA secondary structure of SARS-CoV-2. Methods We have considered the experimentally determined and well documented stem and loop regions of 5′ and 3′ UTR regions of SARS-CoV-2 for base substitution analysis. The secondary structure comprising of stem and loop regions were visualized using the RNAfold web server. The GISAID repository was used to extract base sequence alignment of the UTR regions. Python scripts were developed for comparative analysis of transversion and transition frequencies in the stem and the loop regions. Results The results of base substitution analysis revealed a higher transition (ti) to transversion (tv) ratio (ti/tv) in the stem region of UTR of RNA secondary structure of SARS-CoV-2 reported during the early stage of the pandemic. The higher ti/tv ratio in the stem region suggested the influence of secondary structure in selecting the pattern of base substitutions. This differential pattern of ti/tv values between stem and loop regions was not observed among the Delta and Omicron variants that dominated the later stage of the pandemic. It is noteworthy that the ti/tv values in the stem and loop regions were similar among the later dominant Delta and Omicron variant strains which is to be investigated to understand the rapid evolution and global adaptation of SARS-CoV-2. Conclusion Our findings implicate the lower frequency of transversions than the transitions in the stem regions of UTRs of SARS-CoV-2. The RNA secondary structures are associated with replication, translation, and packaging, further investigations are needed to understand these base substitutions across different variants of SARS-CoV-2.

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Transcribed intergenic regions exhibit a lower frequency of nucleotide polymorphism than the untranscribed intergenic regions in the genomes of Escherichia coli and Salmonella enterica

Cited by 2 publications

References 15 publications

Synonymous and non-synonymous transitions/transversions vividly disclose purifying selection inEscherichia colicoding sequences

Synonymous and non-synonymous transitions/transversions vividly disclose purifying selection inEscherichia colicoding sequences

High frequency of transition to transversion ratio in the stem region of RNA secondary structure of untranslated region of SARS-CoV-2

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