Evaluation of codon usage patterns and molecular evolution dynamics in Japanese encephalitis virus: An integrated bioinformatics approach

Suresh, Kuralayanapalya Puttahonnappa; Indrabalan, Uma Bharathi; Shreevatsa, Bhargav; Dharmashekar, Chandan; Singh, Pranav Kumar; Patil, Sharanagouda S.; Syed, Asad; Elgorban, Abdallah M.; Eswaramoorthy, Rajalakshmanan; Amachawadi, Raghavendra G.; Shivamallu, Chandan; Kollur, Shiva Prasad

doi:10.1016/j.meegid.2023.105410

Cited by 2 publications

(1 citation statement)

References 31 publications

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“…In this paper, CAI analysis revealed that IIVs DNA ligase genes show signi cant adaptation to their hosts, which implying that natural selection contributed to CUB the IIVs DNA ligase genes. These ndings are consistent with previous studies that have also reported similar results, highlighting the signi cance of natural selection in in uencing the codon usage patterns of viral genes [97,98].…”

Section: Discussionsupporting

confidence: 93%

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

Dizman

2023

Preprint

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The genome of Invertebrate iridescent virus 6 (IIV6) contains a sequence that shows similarity to eubacterial NAD+-dependent DNA ligases. The 615-amino acid open reading frame (ORF 205R) consists of several domains, including an N-terminal domain Ia, followed by an adenylation domain, an OB-fold domain, a helix-hairpin-helix (HhH) domain, and a BRCT domain. Notably, the zinc-finger domain, typically present in NAD+-dependent DNA ligases, is absent in ORF 205R. Since the protein encoded by ORF 205R (IIV6 DNA ligase gene) is involved in critical functions such as DNA replication, modification, and repair, it is crucial to comprehend the codon usage associated with this gene. In this paper, the codon usage bias (CUB) in DNA ligase gene of IIV6 and 11 reference iridoviruses was analyzed by comparing the nucleotide contents, relative synonymous codon usage (RSCU), effective number of codons (ENC), codon adaptation index (CAI), relative abundance of dinucleotides and other indices. Both the base content and the RCSU analysis indicated that the A- and T-ending codons were mostly favoured in the DNA ligase gene of IIV6. The ENC value of 35.64 implied a high CUB in the IIV6 DNA ligase gene. The ENC plot, neutrality plot, parity rule 2 plot, correspondence analysis revealed that mutation pressure and natural selection had an impact on the CUB of the IIVs DNA ligase genes. This findings will improve our comprehension of the CUB of IIV6 DNA ligase and reference genes, which may provide the required information for a fundamental evolutionary analysis of these genes.

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Section: Discussionsupporting

confidence: 93%

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

Dizman

2023

Preprint

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

Aktürk Dizman

2023

Arch Microbiol

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Evaluation of codon usage patterns and molecular evolution dynamics in Japanese encephalitis virus: An integrated bioinformatics approach

Cited by 2 publications

References 31 publications

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

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

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

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