Mutation and Selection Cause Codon Usage and Bias in Mitochondrial Genomes of Ribbon Worms (Nemertea)

Chen, Hạixia; Sun, Shichun; Norenburg, Jon L.; Sundberg, Per

doi:10.1371/journal.pone.0085631

Cited by 64 publications

(56 citation statements)

References 49 publications

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“…Had mutation pressure alone acted on these species, then we could have expected equal usage of AT and GC bases. Hence, our finding demonstrated that both natural selection and mutation might have influenced the codon pattern in mt‐protein coding genes of Bombina species, which supports the result of H. Chen, Sun, Norenburg, and Sundberg () in mtDNA of ribbon worm.…”

Section: Discussionsupporting

confidence: 86%

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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Section: Discussionsupporting

confidence: 86%

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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“…AT‐rich genome was also found in Plasmodium falciparum , Tetraphalerus bruchi , and Paranemertes cf. peregrine and Cephalothrix hongkongiensis …”

Section: Discussionmentioning

confidence: 99%

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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“…It is found to be endemic in some countries. Several surveys state that in Africa, urogenital schistosomiasis is due to the infection with S. haematobium (Chen et al 2014). In human it is caused by the penetration of infectious larvae (cercariae) through the skin of people.…”

Section: Introductionmentioning

confidence: 99%

“…Then in the body, adult schistosomes are developed from the larvae. For acute schistosomiasis (Katayama syndrome), the incubation period is found to be 14-84 days and characterized by headache, myalgia, diarrhea, fever and respiratory symptoms, but the chronic infection is thought to remain asymptomatic for many years (Chen et al 2014). For the standard diagnostics of urogenital schistosomiasis, a filtration technique is typically used.…”

Section: Introductionmentioning

confidence: 99%

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Prediction of gene expression and codon usage in human parasitic helminths

2015

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Codon usage bias refers to the differences in the occurrence frequency of synonymous codons. To understand the patterns of codon usage in mitochondrial genes we used bioinformatic approaches to analyze the protein coding sequences of W. bancrofti and S. haematobium as no work was reported earlier. It was found that the ENC value ranged from 43 to 60 with a mean of 46.91 in W. bancrofti but varied from 49 to 60 with a mean of 45.17 in S. haematobium, respectively. In W. bancrofti a significant positive correlation was found between ENC and GC3% (r = 0.826**, p \ 0.01), but in S. haematobium significant correlation was found between ENC and GC3% (r = 0.983**, p \ 0.01). Principal component analysis suggests that the pattern of codon usage significantly differed between W. bancrofti and S. haematobium. Neutrality plot reveals that natural selection played a major role while mutation pressure played a minor role in codon usage pattern in the mitochondrial protein coding genes of W. bancrofti and S. haematobium. Various factors namely nucleotide composition, natural selection and mutation pressure affected the codon usage pattern.

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Mutation and Selection Cause Codon Usage and Bias in Mitochondrial Genomes of Ribbon Worms (Nemertea)

Cited by 64 publications

References 49 publications

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

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

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

Prediction of gene expression and codon usage in human parasitic helminths

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