Prediction of gene expression and codon usage in human parasitic helminths

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

doi:10.1007/s13258-015-0381-3

Cited by 8 publications

(4 citation statements)

References 25 publications

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“…9 Similarly, the studies on the mitochondrial protein-coding genes of Wuchereria bancrofti and Schistosoma haematobium revealed the mean Nc values as 46.91 and 45.17, respectively. 45 These results supported our present findings. Weak CUB might be beneficial for prompt replication of DNA with potential usage of preferred codons, 23 and it might be associated with high genetic variability in codon usage from evolutionary context.…”

Section: Discussionsupporting

confidence: 93%

“…Further study on mitochondrial DNA of B. mori revealed that the Nc values ranged from 23.14 to 44.00, with an average of 29.47 . Similarly, the studies on the mitochondrial protein‐coding genes of Wuchereria bancrofti and Schistosoma haematobium revealed the mean Nc values as 46.91 and 45.17, respectively . These results supported our present findings.…”

Section: Discussionsupporting

confidence: 89%

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Similarities and dissimilarities of codon usage in mitochondrial ATP genes among fishes, aves, and mammals

Uddin¹,

Mazumder

Barbhuiya

et al. 2020

IUBMB Life

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In this study, we used bioinformatic approach to analyze the compositional features and codon usage bias (CUB) of ATP6 and ATP8 genes among three groups, namely, fishes, aves, and mammals which thrive in three different habitats as no work was reported yet. The coding sequences of these genes were retrieved from the National Center for Biotechnology Information to explore the similarities and dissimilarities of codon usage of each gene among these groups. Low values of synonymous codon usage order in fishes, aves, and mammals for ATP6 and ATP8 genes suggested that the CUB of ATP6 and ATP8 genes was low. In ATP6 gene, overall GC contents in fishes, aves and mammals were (mean ± SD) 44.09 ± 3.10, 46.65 ± 1.90, and 39.41 ± 2.89%, respectively, whereas in ATP8 gene, the overall GC contents were 42.76 ± 4.38, 44.16 ± 2.43, and 34.19 ± 3.82% in fishes, aves, and mammals, that is, both genes were found to be AT rich. In ATP6 gene, the codon AGC was overrepresented in fishes but under‐represented in aves and mammals, whereas in ATP8 gene, the codon GCC was overrepresented in fishes but underrepresented in aves and mammals. The pattern of codon usage was different in these genes and varied among groups as evident from correspondence analysis. The slope of the regression line in neutrality plot was lower than 0.5, which revealed that the role of natural selection was higher than mutation pressure in shaping the CUB in ATP6 and ATP8 genes.

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Section: Discussionsupporting

confidence: 93%

Section: Discussionsupporting

confidence: 89%

Similarities and dissimilarities of codon usage in mitochondrial ATP genes among fishes, aves, and mammals

Uddin¹,

Mazumder

Barbhuiya

et al. 2020

IUBMB Life

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“…demonstrated that the presence of preferred codons in cds of mtprotein coding genes was largely influenced by compositional constraints, which are in conformity with the findings of Butt et al (2014). Similar to our results low CUB was observed in mt-protein coding genes of Wuchereria bancrofti and Schistosoma haematobium (Mazumder, Uddin, & Chakraborty, 2017). In the mitochondrial ND2 gene, it was reported that low CUB might be advantageous for DNA replication in vertebrates (Jenkins & Holmes, 2003).…”

Section: Rscu Analysis and Nucleotide Composition Analysis Togethersupporting

confidence: 92%

Genome‐wide comparison of codon usage dynamics in mitochondrial genes across different species of amphibian genus Bombina

Barbhuiya

Uddin²,

Chakraborty

2019

J Exp Zool Pt B

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The biological phenomenon where some synonymous codons are repeatedly preferred to others in gene transcripts is called codon usage bias (CUB). The analysis of CUB is not only helpful in evolutionary biology but also in improving the expression level of exogenous genes in the host cell by codon optimization. The overall nucleotide composition analysis demonstrated an unequal distribution of four nucleobases and T% was the highest in all seven species. The genes were AT‐rich, evident from overall low GC content. In addition, third codon position analysis indicated that in four Bombina species namely, Bombina fortinuptialis, Bombina lichuanensis, Bombina maxima, Bombina microdeladigitora, nucleobase A3/T3 was the preferred one, whereas A3/C3 was favored in Bombina bombina, Bombina orientalis, and Bombina variegata. Influence of mutation pressure on codon distribution and codon bias was evident from correlation analysis. Correspondence analysis demonstrated that compositional bias driven by mutation pressure along with natural selection acted on CUB of mitochondrial genes. Neutrality plot revealed that natural selection played a major role whereas mutation pressure had a minor but significant role. Our phylogenetic analyses showed that closely linked species belonging to the same genus were noticeably separated in different clades.

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“…The mitogenomes of higher plants exhibit distinctive expression patterns, including RNA editing and codon preference [ 28 ]. Codon usage bias is the uneven frequency of synonymous codon usage in coding DNA [ 29 ], meaning that synonymous codons are not uniformly utilized in gene transcripts to encode all amino acids, except for methionine (Met) and tryptophan (Trp) [ 30 ]. Codon usage bias is a widespread phenomenon in the natural world and represents molecular evolution [ 31 ].…”

Section: Discussionmentioning

confidence: 99%

De Novo Assembly and Comparative Analysis of Mitochondrial Genomes of Two Pueraria montana Varieties

Guo,

Lao,

et al. 2024

IJMS

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Pueraria montana is a species with important medicinal value and a complex genetic background. In this study, we sequenced and assembled the mitochondrial (mt) genomes of two varieties of P. montana. The mt genome lengths of P. montana var. thomsonii and P. montana var. montana were 457,390 bp and 456,731 bp, respectively. Both P. montana mitogenomes showed a multi-branched structure consisting of two circular molecules, with 56 genes annotated, comprising 33 protein-coding genes, 18 tRNA genes (trnC-GCA and trnM-CAU are multi-copy genes), and 3 rRNA genes. Then, 207 pairs of long repeats and 96 simple sequence repeats (SSRs) were detected in the mt genomes of P. montana, and 484 potential RNA-editing sites were found across the 33 mitochondrial protein-coding genes of each variety. Additionally, a syntenic sequence analysis showed a high collinearity between the two mt genomes. This work is the first to analyze the mt genomes of P. montana. It can provide information that can be used to analyze the structure of mt genomes of higher plants and provide a foundation for future comparative genomic studies and evolutionary biology research in related species.

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Prediction of gene expression and codon usage in human parasitic helminths

Cited by 8 publications

References 25 publications

Similarities and dissimilarities of codon usage in mitochondrial ATP genes among fishes, aves, and mammals

Similarities and dissimilarities of codon usage in mitochondrial ATP genes among fishes, aves, and mammals

Genome‐wide comparison of codon usage dynamics in mitochondrial genes across different species of amphibian genus Bombina

De Novo Assembly and Comparative Analysis of Mitochondrial Genomes of Two Pueraria montana Varieties

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