Evolutionary Rates and Phylogeographical Analysis of Odontoglossum Ringspot Virus Based on the 166 Coat Protein Gene Sequences

He, Zhen; Dong, Tingting; Wu, Weiwen; Chen, Wen; Liu, Xian; Li, Liangjun

doi:10.5423/ppj.oa.04.2019.0113

Cited by 4 publications

(4 citation statements)

References 45 publications

(62 reference statements)

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“…In the present study, our phylogenetic analysis based on ML and MCC found three and four lineages based on the ORF1 and ORF2 protein coding sequences, respectively. The evolutionary rates of the two BBWV-2 ORF coding sequences were 8.895 × 10 −4 and 4.560 × 10 −4 subs/site/year, respectively, similar to tobacco mosaic virus (TMV) [ 60 ] but slightly slower than the previously reported plant RNA viruses such as PVM [ 61 ], turnip mosaic virus [ 62 ], odontoglossum ringspot virus (ORSV) [ 63 ], and potato virus Y [ 64 ].…”

Section: Discussionmentioning

confidence: 75%

Phylodynamics and Codon Usage Pattern Analysis of Broad Bean Wilt Virus 2

Dong

Qin

et al. 2021

Viruses

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Broad bean wilt virus 2 (BBWV-2), which belongs to the genus Fabavirus of the family Secoviridae, is an important pathogen that causes damage to broad bean, pepper, yam, spinach and other economically important ornamental and horticultural crops worldwide. Previously, only limited reports have shown the genetic variation of BBWV2. Meanwhile, the detailed evolutionary changes, synonymous codon usage bias and host adaptation of this virus are largely unclear. Here, we performed comprehensive analyses of the phylodynamics, reassortment, composition bias and codon usage pattern of BBWV2 using forty-two complete genome sequences of BBWV-2 isolates together with two other full-length RNA1 sequences and six full-length RNA2 sequences. Both recombination and reassortment had a significant influence on the genomic evolution of BBWV2. Through phylogenetic analysis we detected three and four lineages based on the ORF1 and ORF2 nonrecombinant sequences, respectively. The evolutionary rates of the two BBWV2 ORF coding sequences were 8.895 × 10−4 and 4.560 × 10−4 subs/site/year, respectively. We found a relatively conserved and stable genomic composition with a lower codon usage choice in the two BBWV2 protein coding sequences. ENC-plot and neutrality plot analyses showed that natural selection is the key factor shaping the codon usage pattern of BBWV2. Strong correlations between BBWV2 and broad bean and pepper were observed from similarity index (SiD), codon adaptation index (CAI) and relative codon deoptimization index (RCDI) analyses. Our study is the first to evaluate the phylodynamics, codon usage patterns and adaptive evolution of a fabavirus, and our results may be useful for the understanding of the origin of this virus.

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Section: Discussionmentioning

confidence: 75%

Phylodynamics and Codon Usage Pattern Analysis of Broad Bean Wilt Virus 2

Dong

Qin

et al. 2021

Viruses

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“…Alkyl halides --480 cm -1 carbohydrates, and other cellular materials. However, they could not be kept in a vacuum under an electron beam as it can also be associated with the consistency of biosynthesis (Liu et al, 2019). The DLS graph of synthesized AgNPs showed two peaks, a strong peak at 480.7 nm with 98% intensity area and a weak peak at 5256 nm with 2% intensity area.…”

Section: Dlsmentioning

confidence: 99%

“…One of the obstacles in cultivating orchids is infectious diseases that affect flower quality. Orchids can be infected with 50 types of viruses (He et al, 2019), including Odontoglossum ringspot virus (ORSV) (Pai et al, 2019). The virus is an important type that attacks orchids and is popular in the world.…”

Section: Introductionmentioning

confidence: 99%

Untitled

2021

JJBS

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Instructions to AuthorsScopes Study areas include cell biology, genomics, microbiology, immunology, molecular biology, biochemistry, embryology, immunogenetics, cell and tissue culture, molecular ecology, genetic engineering and biological engineering, bioremediation and biodegradation, bioinformatics, biotechnology regulations, gene therapy, organismal biology, microbial and environmental biotechnology, marine sciences. The JJBS welcomes the submission of manuscript that meets the general criteria of significance and academic excellence. All articles published in JJBS are peerreviewed. Papers will be published approximately one to two months after acceptance.

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Section: Introductionmentioning

confidence: 99%

Physiological Analysis of Orchid Chlorophyll against Odontoglossum ringspot virus Infection

2021

JJBS

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Orchids (Orchidaceae) are one of the most popular ornamental plants having diverse flower shapes and colors. They are vastly applied as cut flowers, potted plants, and garden elements. Infectious diseases are still a major obstacle in the cultivation of orchids in Indonesia. Odontoglossum ringspot virus (ORSV) is one of the most widely reported viruses that infect orchids worldwide, including Indonesia. This research was done by mechanically injecting the virus on Phalaenopsis amabilis and Dendrobium Salaya Fancy. This study aimed to determine the symptoms of the disease, plant resistance, and chlorophyll content. The results showed that each orchid had severe disease symptoms, the incidence of both orchids was 80%, and Phalaenopsis amabilis reaction was more susceptible than Dendrobium Salaya Fancy that showed tolerant response to ORSV. Physiological response analysis also showed that the content of chlorophyll A,B, and total Dendrobium Salaya Fancy was higher (0.35 ± 0.02; 0.29 ± 0.05; 0.63 ± 0.05) than Phalaenopsis amabilis (0, 18 ± 0.0; 0.31 ± 0.06; 0.48 ± 0.04) respectively, after viral infection. This proves that Phalaenopsis is the most susceptible type of orchid virus compared to Dendrobium.

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Evolutionary Rates and Phylogeographical Analysis of Odontoglossum Ringspot Virus Based on the 166 Coat Protein Gene Sequences

Cited by 4 publications

References 45 publications

Phylodynamics and Codon Usage Pattern Analysis of Broad Bean Wilt Virus 2

Phylodynamics and Codon Usage Pattern Analysis of Broad Bean Wilt Virus 2

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Physiological Analysis of Orchid Chlorophyll against Odontoglossum ringspot virus Infection

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