Analysis of factors affecting codon usage bias in human papillomavirus Creative Commons

Link for citation this article

Takaaki Kamatani,

Tatsuo Shirota

Journal of Bioinformatics and Sequence Analysis, Год журнала: 2018, Номер Vol.9(1), С. 1 - 9, https://doi.org/10.5897/JBSA2017.0106

Опубликована Янв. 31, 2018

Последнее обновление статьи Авг. 23, 2022

Indices of codon usage pattern of human papillomavirus (HPV) were analyzed to understand the key determinants of synonymous codon usage in the HPV genome. The complete sequences of 39 HPV genomes were downloaded from the website of the National Center for Biotechnology Information. The relative synonymous codon usage values, effective number of codons, GC content, percentage of GCs at the third position of synonymous codons (GC3s), codon adaptation index, hydrophobicity, aromaticity of conceptually translated gene products were calculated using the Codon W 1.4.2 program. HPV preferentially used codons ending with A/U. By comparing relative synonymous codon usage of the HPV …

Similarities and dissimilarities of codon usage in mitochondrial ATP genes among fishes, aves, and mammals DOI Open Access
Arif Uddin, Tarikul Huda Mazumder, Parvin A. Barbhuiya

и другие.

IUBMB Life, Год журнала: 2020, Номер 72(5), С. 899 - 914

Опубликована: Янв. 20, 2020

Abstract In this study, we used bioinformatic approach to analyze the compositional features and codon usage bias (CUB) of ATP6 ATP8 genes among three groups, namely, fishes, aves, mammals which thrive in different habitats as no work was reported yet. The coding sequences these were retrieved from National Center for Biotechnology Information explore similarities dissimilarities each gene groups. Low values synonymous order suggested that CUB low. ATP 6 gene, overall GC contents aves (mean ± SD ) 44.09 3.10, 46.65 1.90, 39.41 2.89%, respectively, whereas 42.76 4.38, 44.16 2.43, 34.19 3.82% mammals, is, both found be AT rich. AGC overrepresented fishes but under‐represented GCC underrepresented mammals. pattern varied groups evident correspondence analysis. slope regression line neutrality plot lower than 0.5, revealed role natural selection higher mutation pressure shaping genes.

Язык: Английский

Процитировано

32
Structural Characteristics and Phylogenetic Analysis of the Mitochondrial Genomes of Four Krisna Species (Hemiptera: Cicadellidae: Iassinae) DOI Open Access

Yanqiong Yang,

Jiajia Wang, Ren‐Huai Dai

и другие.

Genes, Год журнала: 2023, Номер 14(6), С. 1175 - 1175

Опубликована: Май 28, 2023

Krisna species are insects that have piercing–sucking mouthparts and belong to the Krisnini tribe in Iassinae subfamily of leafhoppers Cicadellidae family. In this study, we sequenced compared mitochondrial genomes (mitogenomes) four species. The results showed all mitogenomes were composed cyclic double-stranded molecules contained 13 protein-coding genes (PCGs) 22 2 coding for tRNAs rRNAs, respectively. Those exhibited similar base composition, gene size, codon usage patterns genes. analysis nonsynonymous substitution rate (Ka)/synonymous (Ks) evolution occurred fastest ND4 slowest COI. PCGs underwent purification selection suitable studying phylogenetic relationships within Krisna. ND2, ND6, ATP6 had highly variable nucleotide diversity, whereas COI ND1 lowest diversity. Genes or regions with high diversity can provide potential marker candidates population genetics delimitation Analyses parity neutral plots both natural mutation pressure affected bias. analysis, subfamilies restored a monophyletic group; is monophyletic, genus paraphyletic. Our study provides novel insights into significance background composition CDSs genome, which could enable identification different organization may be used accurate

Язык: Английский

Процитировано

10
Analysis of codon usage bias in mitochondrial CO gene among platyhelminthes DOI

Gulshana A. Mazumder,

Arif Uddin, Supriyo Chakraborty

и другие.

Molecular and Biochemical Parasitology, Год журнала: 2021, Номер 245, С. 111410 - 111410

Опубликована: Сен. 1, 2021

Язык: Английский

Процитировано

5
Description of mitochondrial genomes and phylogenetic analysis of Megophthalminae (Hemiptera: Cicadellidae) DOI Creative Commons
Sun Mingming, Jiajia Wang, Guy Smagghe

и другие.

Journal of Insect Science, Год журнала: 2024, Номер 24(6)

Опубликована: Ноя. 1, 2024

To elucidate phylogenetic relationships within the leafhopper's subfamily Megophthalminae (Hemiptera: Cicadellidae), mitogenomes of 12 species were sequenced and assembled. These added to eight other that are currently available. Mitogenome size ranged from 15,193 bp in Onukigallia onukii (Matsumura, 1912) 15,986 Multinervis guangxiensis (Li Li, 2013), they all contained 37 genes, gene order was similar leafhoppers. Nucleotide composition analysis showed AT content higher than GC, protein-coding genes usually ended with A/T at 3rd codon position. The Ka/Ks ratio CYTB has slowest evolutionary rate, while ND4 is fastest rate. Relative synonymous usage revealed most frequently used UUA (L), followed by CGA (R), least CCG (P). Parity plot neutrality analyses bias mitochondrial influenced natural selection mutation pressure. However, plays a major role, effect pressure small. Effective number codons values 40.15-49.17, which represented relatively low bias. Phylogenetic based on three datasets (AA, 13PCG, 13PCG_2rRNA) using two methods (maximum likelihood Bayesian inference). In obtained topology, clustered into monophyletic group. conclusion, our results clarify structural modules confirm monophyly Cicadellidae.

Язык: Английский

Процитировано

0