RESUMEN
Ranaviruses, members of the genus Ranavirus within the family Iridoviridae, have become a significant concern for amphibian populations globally, along with other cold-blooded vertebrates, due to their emergence as a significant threat. We employed bioinformatics tools to examine the codon usage patterns in 61 DNA pol genes from Ranavirus, Lymphocystivirus, Megalocytivirus, and two unclassified ranaviruses, as no prior studies had been conducted on this topic. The results showed a slight or low level of codon usage bias (CUB) in the DNA pol genes of Ranavirus. Relative synonymous codon usage (RSCU) analysis indicated that the predominant codons favored in Ranavirus DNA pol genes terminate with C or G. Correlation analysis examining nucleotide content, third codon position, effective number of codons (ENC), correspondence analysis (COA), Aroma values, and GRAVY values indicated that the CUB across DNA pol genes could be influenced by both mutation pressure and natural selection. The neutrality plot indicated that natural selection is the primary factor driving codon usage. Furthermore, the analysis of the codon adaptation index (CAI) illustrated the robust adaptability of Ranavirus DNA pol genes to their hosts. Analysis of the relative codon deoptimization index (RCDI) suggested that Ranavirus DNA pol genes underwent greater selection pressure from their hosts. These findings will aid in comprehending the factors influencing the evolution and adaptation of Ranavirus to its hosts.
RESUMEN
Invertebrate iridescent viruses (IIVs) are double-stranded DNA viruses that belong to the Iridoviridae family. IIVs result diseases that vary in severity from subclinical to lethal in invertebrate hosts. Codon usage bias (CUB) analysis is a versatile method for comprehending the genetic and evolutionary aspects of species. In this study, we analyzed the CUB in 10 invertebrate iridescent viruses exonuclease genes by calculating and comparing the nucleotide contents, effective number of codons (ENC), codon adaptation index (CAI), relative synonymous codon usage (RSCU), and others. The results revealed that IIVs exonuclease genes are rich in A/T. The ENC analysis displayed a low codon usage bias in IIVs exonuclease genes. ENC-plot, neutrality plot, and parity rule 2 plot demonstrated that besides mutational pressure, other factors like natural selection, dinucleotide content, and aromaticity also contributed to CUB. The findings could enhance our understanding of the evolution of IIVs exonuclease genes.
Asunto(s)
Uso de Codones , Iridovirus , Animales , Iridovirus/genética , Codón , Invertebrados/genética , Mutación , Selección Genética , Evolución MolecularRESUMEN
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 favored 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. Additionally, the analysis of codon adaptation index demonstrated that the IIV6 DNA ligase gene is strongly adapted to its host. These 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.
Asunto(s)
Uso de Codones , Iridovirus , Iridovirus/genética , NAD , ADN Ligasas/genética , Codón/genética , Evolución MolecularRESUMEN
Cytochrome P450 monooxygenases are one of the largest heme-containing protein groups, and the majority of them catalyze hydroxylation reactions dependent on nicotinamide adenine dinucleotide phosphate and oxygen. Cytochrome P450 (CYP) enzymes function in a wide range of monooxygenation reactions essential in primary and secondary metabolism in plants. Camellia sinensis (L.) Kuntze is a commercially and economically valuable plant due to its medicinally important secondary metabolites and as a beloved beverage. Cytochrome P450 monooxygenases play a significant role in the biosynthesis of a variety of secondary metabolites in tea. Although the biosynthesis of secondary metabolites has been investigated in detail, there have been limited studies conducted on identifying the genetic mechanisms of CYP-catalyzed secondary metabolic pathways in the C. sinensis (tea) plant. In our study, we characterized a putative C. sinensis (L.) Kuntze cytochrome P450 monooxygenase gene (Csp450), which has 1759 bp full-length cDNA with 49 bp of 5' and 183 bp of 3' untranslated regions. eTh CDS of the gene is 1527 bp and 508 amino acids in length. BLAST results of the deduced amino acid sequence revealed a high similarity with the CYP704C1-like superfamily. Preharvest period gene expression analysis from May, July, and September did not show any difference.