Codon usage bias analysis of the gene encoding NAD+-dependent DNA ligase protein of Invertebrate iridescent virus 6

Aktürk Dizman, Yeşim

doi:10.1007/s00203-023-03688-5

Cited by 2 publications

(1 citation statement)

References 106 publications

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“…To discern which factor was more influential, a neutrality plot was generated using Origin, with the GC3 on the x-axis against GC12 (the average value of GC1 and GC2) on the y-axis [ 7 ]. The slope of the regression line ranged from 0 to 1; 0 represents no difference in codon base usage across the 1st, 2nd, and 3rd positions of codons, while 1 means a predominant role of mutation pressure [ 62 ].…”

Section: Methodsmentioning

confidence: 99%

Bioinformatic Analysis of Codon Usage Bias of HSP20 Genes in Four Cruciferous Species

Ji,

Liu,

Chen

et al. 2024

Plants

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Heat shock protein 20 (HSP20) serves as a chaperone and plays roles in numerous biological processes, but the codon usage bias (CUB) of its genes has remained unexplored. This study identified 140 HSP20 genes from four cruciferous species, Arabidopsis thaliana, Brassica napus, Brassica rapa, and Camelina sativa, that were identified from the Ensembl plants database, and we subsequently investigated their CUB. As a result, the base composition analysis revealed that the overall GC content of HSP20 genes was below 50%. The overall GC content significantly correlated with the constituents at three codon positions, implying that both mutation pressure and natural selection might contribute to the CUB. The relatively high ENc values suggested that the CUB of the HSP20 genes in four cruciferous species was relatively weak. Subsequently, ENc exhibited a negative correlation with gene expression levels. Analyses, including ENc-plot analysis, neutral analysis, and PR2 bias, revealed that natural selection mainly shaped the CUB patterns of HSP20 genes in these species. In addition, a total of 12 optimal codons (ΔRSCU > 0.08 and RSCU > 1) were identified across the four species. A neighbor-joining phylogenetic analysis based on coding sequences (CDS) showed that the 140 HSP20 genes were strictly and distinctly clustered into 12 subfamilies. Principal component analysis and cluster analysis based on relative synonymous codon usage (RSCU) values supported the fact that the CUB pattern was consistent with the genetic relationship at the gene level and (or) species levels. These results will not only enrich the HSP20 gene resource but also advance our understanding of the CUB of HSP20 genes, which may underlie the theoretical basis for exploration of their genetic and evolutionary pattern.

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Section: Methodsmentioning

confidence: 99%

Bioinformatic Analysis of Codon Usage Bias of HSP20 Genes in Four Cruciferous Species

Ji,

Liu,

Chen

et al. 2024

Plants

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A Comprehensive Comparative Analysis on the Codon Usage Bias of DNA Polymerase Genes in Invertebrate Iridescent Viruses

Aktürk Dizman

2024

Recep Tayyip Erdoğan Üniversitesi Fen Ve Mühendislik Bilimleri Dergisi

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Invertebrate iridescent viruses (IIVs) are classified as double-stranded DNA viruses within the Iridoviridae family. IIVs are viruses that infect invertebrate hosts, causing symptoms that vary in intensity from slight reductions in host fitness to systemic disease. Numerous earlier investigations have provided insights into the genomic, proteomic, and transcriptional analyses of invertebrate iridescent viruses. However, the codon usage bias (CUB) of IIVs has yet to be fully understood. In order to gain a more profound insight into the evolutionary features of IIVs, we conducted an extensive analysis of the codon usage patterns in the DNA polymerase genes (DNA pol genes) of 12 invertebrate iridescent viruses. The analysis of both nucleotide composition and relative synonymous codon usage (RSCU) indicated a higher prevalence of AT-ended codons in the DNA pol genes of IIVs. Additionally, a low codon usage bias was determined from the effective number of codons (ENC) value. Analyses of ENC-GC3s plot, neutrality plot, and parity rule 2 plot illustrated that the codon usage patterns in IIVs DNA pol genes were influenced by both natural selection and mutational pressure. This investigation holds significance as it has delineated the codon usage patterns within the DNA pol genes of IIVs and has furnished crucial data for a foundational study of their evolutionary aspects.

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Codon usage bias analysis of the gene encoding NAD+-dependent DNA ligase protein of Invertebrate iridescent virus 6

Cited by 2 publications

References 106 publications

Bioinformatic Analysis of Codon Usage Bias of HSP20 Genes in Four Cruciferous Species

Bioinformatic Analysis of Codon Usage Bias of HSP20 Genes in Four Cruciferous Species

A Comprehensive Comparative Analysis on the Codon Usage Bias of DNA Polymerase Genes in Invertebrate Iridescent Viruses

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