Preference of A/T ending codons in mitochondrial ATP6 gene under phylum Platyhelminthes

Mazumder, Gulshana A.; Uddin, Arif; Chakraborty, Supriyo

doi:10.1016/j.molbiopara.2018.08.007

Cited by 10 publications

(6 citation statements)

References 44 publications

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“…Since the GC content is associated with the stability of mRNA secondary structure, this might play a role in determining the extent of gene expression. Similarly, the mFE value of mitochondrial ATP6 gene across the phylum Platyhelminthes also shows a significant correlation with GC content [44,45]. The mRNA stability index is another parameter that was used in our analysis to estimate mRNA stability.…”

Section: Discussionmentioning

confidence: 90%

“…Xij + T3)] on the ordinate [44,45]. In the PR2 plot, the midpoint is 0.5, which corresponds to the condition in which A = T and G = C and no bias is observed between mutation and selection pressure [46].…”

Section: Pr2 Bias Plot Analysismentioning

confidence: 99%

“…The variation in the patterns of codon usage mainly stems from two evolutionary forces, viz., mutational pressure and natural selection [44,45]. Correlation analysis of compositional constraints can identify the primary forces determining the CUB [13].…”

Section: Interrelationships Among Base Compositionsmentioning

confidence: 99%

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Codon usage pattern and its influencing factors in different genomes of hepadnaviruses

Deb

Uddin²,

Chakraborty

2020

Arch Virol

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Codon usage bias (CUB) arises from the preference for a codon over codons for the same amino acid. The major factors contributing to CUB are evolutionary forces, compositional properties, gene expression, and protein properties. The present analysis was performed to investigate the compositional properties and the extent of CUB across the genomes of members of the family Hepadnaviridae, as previously no work using bioinformatic tools has been reported. The viral genes were found to be AT rich with low CUB. Analysis of relative synonymous codon usage (RSCU) was used to identify overrepresented and underrepresented codons for each amino acid. Correlation analysis of overall nucleotide composition and its composition at the third codon position suggested that mutation pressure might influence the CUB. A highly significant correlation was observed between GC12 and GC3 (r = 0.910, p < 0.01), indicating that directional mutation affected all three codon positions across the genome. Translational selection (P2) and mutational responsive index (MRI) values of genes suggested that mutation plays a more important role than translational selection in members of the family Hepadnaviridae.Publisher's Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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Section: Discussionmentioning

confidence: 90%

Section: Pr2 Bias Plot Analysismentioning

confidence: 99%

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Codon usage pattern and its influencing factors in different genomes of hepadnaviruses

Deb

Uddin²,

Chakraborty

2020

Arch Virol

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“…The study indicated that the A- and T-ending codons were those preferentially used by the HPyVs. This result indicated that the preferred codons were influenced by compositional constraints ( Mazumder et al., 2018 ). Moreover, these results suggested that the CUB of HPyVs is shaped by the occurrence of selection constraints, as it was previously reported ( He et al., 2016 ; Majeed et al., 2020 ).…”

Section: Discussionmentioning

confidence: 90%

Human genes with relative synonymous codon usage analogous to that of polyomaviruses are involved in the mechanism of polyomavirus nephropathy

Yang

Guo

Zhao

et al. 2022

Front. Cell. Infect. Microbiol.

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Human polyomaviruses (HPyVs) can cause serious and deleterious infections in human. Yet, the molecular mechanism underlying these infections, particularly in polyomavirus nephropathy (PVAN), is not well-defined. In the present study, we aimed to identify human genes with codon usage bias (CUB) similar to that of HPyV genes and explore their potential involvement in the pathogenesis of PVAN. The relative synonymous codon usage (RSCU) values of genes of HPyVs and those of human genes were computed and used for Pearson correlation analysis. The involvement of the identified correlation genes in PVAN was analyzed by validating their differential expression in publicly available transcriptomics data. Functional enrichment was performed to uncover the role of sets of genes. The RSCU analysis indicated that the A- and T-ending codons are preferentially used in HPyV genes. In total, 5400 human genes were correlated to the HPyV genes. The protein-protein interaction (PPI) network indicated strong interactions between these proteins. Gene expression analysis indicated that 229 of these genes were consistently and differentially expressed between normal kidney tissues and kidney tissues from PVAN patients. Functional enrichment analysis indicated that these genes were involved in biological processes related to transcription and in pathways related to protein ubiquitination pathway, apoptosis, cellular response to stress, inflammation and immune system. The identified genes may serve as diagnostic biomarkers and potential therapeutic targets for HPyV associated diseases, especially PVAN.

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“…Codon usage bias ubiquitously exists in animals and has been revealed to contribute to the high expression of certain amino acids, predict the function of genes and analyze the phylogeny and evolution of species [23,24]. Relative synonymous codon usage (RSCU) reflects the ratio of the frequency of usage of a codon to the expected frequency and is a measure of nonuniform synonymous codon usage in coding sequences [22,25].…”

Section: Relative Synonymous Codon Usage (Rscu) Analysismentioning

confidence: 99%

Chromosome-Level Analysis of the Pelochelys cantorii Genome Provides Insights to Its Immunity, Growth and Longevity

Liu

Wang

et al. 2023

Biology

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The Asian giant soft-shelled turtle, Pelochelys cantorii (Trionychidae), is one of the largest aquatic turtles in China and was designated as a First-Grade Protected Animal in China in 1989. Previous investigation based on a combination of Illumina short-read, PacBio long-read and Hi-C scaffolding technologies acquired a high-quality chromosome-level genome of Pc. cantorii. In this study, comparative genomic analysis between Pc. cantorii and 16 other vertebrate genomes indicated that turtles separated from the ancestor of archosaurians approximately 256.6 (95% highest posterior density interval, 263.6–251.9) million years ago (Mya) (Upper Permian to Triassic) and that Pc. cantorii separated from the ancestor of Pd. sinensis and R. swinhoei approximately 59.3 (95% highest posterior density interval, 64.3–54.3) Mya. Moreover, several candidate genes, such as VWA5A, ABCG2, A2M and IGSF1, associated with tumor suppression, growth and age were expanded, implicating their potential roles in the exceptional longevity of turtles. This new chromosome-level assembly has important scientific value in the study of conservation of Pc. cantorii and also enriches the evolutionary investigation of turtle species.

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Preference of A/T ending codons in mitochondrial ATP6 gene under phylum Platyhelminthes

Cited by 10 publications

References 44 publications

Codon usage pattern and its influencing factors in different genomes of hepadnaviruses

Codon usage pattern and its influencing factors in different genomes of hepadnaviruses

Human genes with relative synonymous codon usage analogous to that of polyomaviruses are involved in the mechanism of polyomavirus nephropathy

Chromosome-Level Analysis of the Pelochelys cantorii Genome Provides Insights to Its Immunity, Growth and Longevity

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