Codon usage bias of Venezuelan equine encephalitis virus and its host adaption

Wang, Hongju; Liu, Shijie; Lv, Yao; Wei, Wenqiang

doi:10.1016/j.virusres.2023.199081

Cited by 12 publications

(9 citation statements)

References 59 publications

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“…Consistent with these previous studies, our results show that the patterns of codon usage in IIV6 exhibit a high degree of similarity to its host, Chilo suppressalis [70,80,81]. Furthermore, prior works have reported signi cant variations in the codon usage patterns between viruses and their respective hosts [82-84].…”

Section: Discussionsupporting

confidence: 90%

“…In order to delve deeper into the factors shaping codon usage patterns, neutrality plot analysis and PR2 plot analysis were conducted. The results of these analyses suggest that translational selection may have a signi cant in uence on CUB, which are consistent with prior studies [43,70,93]. However, the in uence of mutation pressure on CUB in some viruses seems to be greater than that of translational selection [85,94].…”

Section: Discussionsupporting

confidence: 88%

“…The CUB of a gene can be affected by the nucleotide composition within that gene [69]. The analysis of nucleotide content in IIVs DNA ligase genes demonstrated that A is the most prevalent nucleotide, followed by T. This nding aligns with previous studies conducted on other viruses such as Venezuelan equine encephalitis virus [70], Crimean-Congo hemorrhagic fever virus [71], Lumpy skin disease virus [72], Rice tungro bacilliform virus [73] and Canine distemper virus [74].…”

Section: Discussionsupporting

confidence: 84%

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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: 90%

Section: Discussionsupporting

confidence: 88%

Section: Discussionsupporting

confidence: 84%

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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 RSCU value serves as a measure of the disparity between observed and expected usage of codons. A value of RSCU greater than 1 suggests that the frequency of codon usage exceeds the predicted level (Desingu et al 2022;Li et al 2023b;Tang et al 2022;Wang et al 2023b). VMATCH was used to nd dispersed repeat sequences, and PREPuter was used to predict the four kinds of repeat sequences: the forward (F), palindromic (P), reverse (R), and complement (C).…”

Section: Codon Usage and Repeat Sequencesmentioning

confidence: 99%

A species unique to China—The complete chloroplast genome sequence of Eomecon chionantha Hance and phylogenetic relationships analysis

Huang

Miao

Zhang

et al. 2023

Preprint

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Eomecon chionantha Hance (EC) is a unique species in China with high medicinal value. Ethnic minorities in China, such as the Miao and Tujia ethnic groups, have a long history of using blood herbs for treatment, and EC has been used for this purpose for centuries. However, despite its long history of use, we have no knowledge of the chloroplast genome of EC Therefore, this study reports EC's complete chloroplast genome information to better develop and protect this unique plant species in China. The complete chloroplast genomic information indicates that EC's chloroplast DNA (CPDNA) (178,808 bp) contains 99 protein-coding genes, including 8 rRNAs, 37 tRNAs. We have discovered 54 SSRs, most of which are single nucleotide adenine-thymidine (A-T) repeats. Comparative analysis of codons, repeats, and genomic sequences have found that the CPDNA of EC is highly conserved. According to our phylogenetic tree results, EC is closely related to four species. Through K2-P analysis, we have identified five hypervariable regions, including ycf4-cemA, ycf3-trnS-GGA, trnC-GCA-petN, rpl32-trnL-UAG, and psbI-trnS-UGA. In summary, this study has reported, for the first time, the complete chloroplast genome of the unique single genus plant EC in China. This provides a more scientific basis for further development and utilization of this species and is conducive to an in-depth understanding of plant species diversity from a genomic perspective.

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“…Codon bias was analysed by CodonW 1.4.2 [40,41] and EMBOSS (https://link.zhihu.com/?target=http%3A// https://www.bioinformatics.nl/cgi-bin/emboss/). The main parameters were as follows: GC 12 (GC content of first and second position), GC 3 (GC content of the third position), GC 3s (GC content of the third position of the synonymous codons), T 3 , C 3 , A 3 , G 3 (usage frequency of the third base), ENC (number of effective codons, ENC<35 indicates strong codon usage bias; 35<ENC<50 indicates moderate codon usage bias; ENC>50 represents low codon usage bias [42]), and RSCU value (relative synonymous codon usage, RSCU <1 indicates that the codon is a high-frequency codon; RSCU=1 indicates there is no bias for the codon; RSCU >1 indicates that the codon is a low-frequency codon [43], when RSCU is greater than 1.6 or less than 0.6, it indicates that the codon is over-represented or under-represented [44]).…”

Section: Codon Usage Analysismentioning

confidence: 99%

Evolutionary analysis and biological characterization of a novel alphabaculovirus isolated from Mythimna separata

Dou,

Gao,

Zhu

et al. 2024

Journal of General Virology

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Baculoviruses are insect-specific pathogens. Novel baculovirus isolates provide new options for the biological control of pests. Therefore, research into the biological characteristics of newly isolated baculoviruses, including accurate classification and nomenclature, is important. In this study, a baculovirus was isolated from Mythimna separata and its complete genome sequence was determined by next-generation sequencing. The double-stranded DNA genome was 153 882 bp in length, encoding 163 open reading frames. The virus was identified as a variant of Mamestra brassicae multiple nucleopolyhedrovirus (MbMNPV) and designated Mamestra brassicae multiple nucleopolyhedrovirus CHN1 (MbMNPV-CHN1) according to ultrastructural analysis, genome comparison and phylogenetic analysis. Phylogenetic inference placed MbMNPV-CHN1 in a clade containing isolates of MacoNPV-A, MacoNPV-B and MbMNPV, which we have designated the Mb-McNPV group. The genomes of isolates in the Mb-McNPV group exhibited a high degree of collinearity with relatively minor differences in the content of annotated open reading frames. The development of codon usage bias in the Mb-McNPV group was affected mainly by natural selection. MbMNPV-CHN1 shows high infectivity against seven species of Lepidoptera. The yield of MbMNPV-CHN1 in the fourth- and fifth-instar M. separata larvae was 6.25×109–1.23×1010 OBs/cadaver. Our data provide insights into the classification, host range and virulence differences among baculoviruses of the Mb-McNPV group, as well as a promising potential new baculoviral insecticide.

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Codon usage bias of Venezuelan equine encephalitis virus and its host adaption

Cited by 12 publications

References 59 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

A species unique to China—The complete chloroplast genome sequence of Eomecon chionantha Hance and phylogenetic relationships analysis

Evolutionary analysis and biological characterization of a novel alphabaculovirus isolated from Mythimna separata

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