Analysis of synonymous codon usage bias and phylogeny of coat protein gene in banana bract mosaic virus isolates

Patil, Atul B.; Dalvi, Vijayendra S.; Mishra, Akhilesh A.; Krishna, Bal; Azeez, Abdul

doi:10.1007/s13337-017-0380-x

Cited by 9 publications

(6 citation statements)

References 28 publications

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“…The results showed that the codons generally preferred to use the third codon position of A/U. The results are consistent with the codon usage bias of banana bract mosaic virus (BBrMV), soybean mosaic virus (SMV) and citrus tristeza virus (CTV) [ 38 , 44 , 45 ]. It is worth noting that the best optimal codon of the three narcissus viruses is CCA, which may be related to the range of the codon usage bias difference and the genetic relationship of the species.…”

Section: Discussionsupporting

confidence: 73%

Synonymous Codon Usage Analysis of Three Narcissus Potyviruses

Ding

Guo³

et al. 2022

Viruses

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Narcissus degeneration virus (NDV), narcissus late season yellows virus (NLSYV) and narcissus yellow stripe virus (NYSV), which belong to the genus Potyvirus of the family Potyviridae, cause significant losses in the ornamental value and quality of narcissus. Several previous studies have explored the genetic diversity and evolution rate of narcissus viruses, but the analysis of the synonymous codons of the narcissus viruses is still unclear. Herein, the coat protein (CP) of three viruses is used to analyze the viruses’ phylogeny and codon usage pattern. Phylogenetic analysis showed that NYSV, NDV and NLSYV isolates were divided into five, three and five clusters, respectively, and these clusters seemed to reflect the geographic distribution. The effective number of codon (ENC) values indicated a weak codon usage bias in the CP coding region of the three narcissus viruses. ENC-plot and neutrality analysis showed that the codon usage bias of the three narcissus viruses is all mainly influenced by natural selection compared with the mutation pressure. The three narcissus viruses shared the same best optimal codon (CCA) and the synonymous codon prefers to use codons ending with A/U, compared to C/G. Our study shows the codon analysis of different viruses on the same host for the first time, which indicates the importance of the evolutionary-based design to control these viruses.

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Section: Discussionsupporting

confidence: 73%

Synonymous Codon Usage Analysis of Three Narcissus Potyviruses

Ding

Guo³

et al. 2022

Viruses

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“…However FAdVs can also be isolated from healthy chickens ( 1 ). In Poland during the last decade, many adenovirus type species were isolated, examples being FAdV-1/A ( 16 , 20 ), FAdV-8a/E ( 17 , 18 , 20 ), FAdV-5/B, FAdV-6/E, FAdV-7/E, FAdV-8b/E ( 21 ), FAdV-2/11/D ( 18 – 20 ), FAdV-3/D and FAdV-10/C ( 15 , 18 ).…”

Section: Discussionmentioning

confidence: 99%

“…Relative synonymous codon usage. The relative synonymous codon usage values indicated the measure of gene expression level (16,17,21). The investigation of the synonymous codon usage in the examined region revealed differences in this region depending on the strain and adenovirus type species.…”

Section: Molecular Adenovirus Serotype Identificationmentioning

confidence: 99%

Molecular characteristics of fowl adenovirus strains detected in broiler chickens on diets without immunostimulant supplements

Niczyporuk,

Kozdruń,

Tomczyk

et al. 2024

Journal of Veterinary Research

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Introduction Outbreaks of fowl adenovirus (FAdV) infection in chicken flocks in Poland threaten birds’ health and lives and are rising in frequency. The risk of these infections in immunocompromised poultry flocks with developed clinical symptoms was analysed through virus detection in broiler chicks and correlation of cases with the birds’ immune strength. Material and Methods Samples were analysed from four broiler farms with chicks from the same hatchery in Silesia, Poland where feeding regimes were different. A normal diet was provided to birds on the control farm; a normal diet and probiotic, prebiotic, vitamin and microelement supplementation was supplied on another farm; a normal diet and antibiotics on the third; and a normal diet and both forms of supplementation were given on the fourth farm. Amplification of the virus DNA in a PCR with hexon gene L1 loop hypervariable region 1–4 primers determined the molecular characteristics of isolates of adenovirus strains obtained from necropsy tissue samples. The amplicon sequences were analysed, the pair-wise distances were determined, the maximum likelihood estimate for the gamma parameter for site rates was produced, Tajima’s D neutrality test was run and the relative synonymous codon usage and transition/transversion bias were calculated. Results Two species and two serotypes of fowl adenovirus – MW353018-FAdV-1/A-L-liver and MW353019-FAdV-5/B-I-intestine – were isolated in three-week-old broiler chicks on the control farm. Conclusion Supplementation of broiler chicken flocks with probiotics, prebiotics, vitamins and microelements may have a significant beneficial effect on immunity and can prevent virus infection. The studies provided new information on the molecular characteristics of adenovirus strains isolated from chicks with a low level of immunity.

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“…As a result of the high collinearity of genomes in the Mb-McNPV group, two isolates were selected respectively from MbMNPV (MbMNPV-CHN1 and CHb1), MacoNPV-A (MacoNPV-A-94-2 and 90/2) and MacoNPV-B clades (MacoNPV-B SK256 and 96B), for analysis. 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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Analysis of synonymous codon usage bias and phylogeny of coat protein gene in banana bract mosaic virus isolates

Cited by 9 publications

References 28 publications

Synonymous Codon Usage Analysis of Three Narcissus Potyviruses

Synonymous Codon Usage Analysis of Three Narcissus Potyviruses

Molecular characteristics of fowl adenovirus strains detected in broiler chickens on diets without immunostimulant supplements

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

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