Complete genome sequence of a new isolate of potato virus M in Yunnan, China

Su, Xiaoxia; Wu, Kai; Zhang, Li Zhen; Rahman, Mohammad Siddiqur; Zheng, Kuanyu; T, Li; Zhang, Zhongkai; Dong, Jiahong

doi:10.1007/s00705-017-3380-7

Cited by 7 publications

(5 citation statements)

References 11 publications

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“…Low codon usage bias and higher genomic stability were observed from CTV, PRSV and RSV [60,61,62]. PVM, a carlavirus belonging to the family of Betaflexviridae , is an economically important pathogen of potato and pepino worldwide [3,4,5,6]. In the present study, comprehensive analyses of codon usage of PVM based on the CP and NABP coding sequences were performed.…”

Section: Discussionmentioning

confidence: 99%

“…PVM was first isolated from potato ( Solanum tuberosum ) in the United States in 1923 [1], and then isolated from pepino ( Solanum muricatum ), tomato and tobacco [2,3]. PVM is transmitted in a non-persistent manner by aphid and causes large economic losses of nightshade crops worldwide [2,3,4,5,6,7]. PVM contains a single stranded positive-sense RNA molecule that is approximately 8.5 kb in length and is enveloped by flexuous filamentous virions [8].…”

Section: Introductionmentioning

confidence: 99%

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Analysis of Synonymous Codon Usage Bias in Potato Virus M and Its Adaption to Hosts

Gan

Liang

2019

Viruses

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Potato virus M (PVM) is a member of the genus Carlavirus of the family Betaflexviridae and causes large economic losses of nightshade crops. Several previous studies have elucidated the population structure, evolutionary timescale and adaptive evolution of PVM. However, the synonymous codon usage pattern of PVM remains unclear. In this study, we performed comprehensive analyses of the codon usage and composition of PVM based on 152 nucleotide sequences of the coat protein (CP) gene and 125 sequences of the cysteine-rich nucleic acid binding protein (NABP) gene. We observed that the PVM CP and NABP coding sequences were GC-and AU-rich, respectively, whereas U- and G-ending codons were preferred in the PVM CP and NABP coding sequences. The lower codon usage of the PVM CP and NABP coding sequences indicated a relatively stable and conserved genomic composition. Natural selection and mutation pressure shaped the codon usage patterns of PVM, with natural selection being the most important factor. The codon adaptation index (CAI) and relative codon deoptimization index (RCDI) analysis revealed that the greatest adaption of PVM was to pepino, followed by tomato and potato. Moreover, similarity Index (SiD) analysis showed that pepino had a greater impact on PVM than tomato and potato. Our study is the first attempt to evaluate the codon usage pattern of the PVM CP and NABP genes to better understand the evolutionary changes of a carlavirus.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Analysis of Synonymous Codon Usage Bias in Potato Virus M and Its Adaption to Hosts

Gan

Liang

2019

Viruses

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“…T40 and T50 isolates, originally collected from unrelated private gardens located in the same village (Plavecký Mikuláš), are phylogenetically related and fell into the major phylogenetic PVM group, together with potato and tomato isolates from Europe and Asia. Isolate YN (KY364848), reported recently as a divergent PVM variant (Su et al 2017) is included in a well-supported phylogenetic group with Bangladesh isolates (MF133528-MF133530). Interestingly, the Slovak T20 isolate did not cluster together with any of the isolates analysed, either with the major group including T40 and T50 or with the one represented by Chinese and Bangladesh isolates.…”

Section: Resultsmentioning

confidence: 96%

“…The relatively high intraspecies variability detected for PVM (17.3%) is mainly due to the recent characterisation of a divergent Chinese isolate YN (KY364848; Su et al 2017) and isolates from Bangladesh (MF133528-MF133530; Xu H., direct submission). Interestingly, these divergent PVM isolates were characterised using HTS, further confirming the potential of this approach for characterisation of isolates escaping standard detection methods.…”

Section: Discussionmentioning

confidence: 99%

High-throughput sequencing of Potato virus M from tomato in Slovakia reveals a divergent variant of the virus

Glasa¹,

Šoltýs²,

Predajňa³

et al. 2019

Plant Prot. Sci.

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High-throughput sequencing (HTS) analysis of tomato (Solanum lycopersicum) samples revealed the presence of Potato virus M (PVM) in this crop in Slovakia. Full-length genomes of three PVM isolates were obtained using both HTS and Sanger sequencing validation. While two isolates (T40 and T50) were shown to belong to major Group I, a divergent T20 isolate was phylogenetically unrelated to any known PVM variant, potentially representing a new phylogenetic group. Despite a relatively high intraspecies diversity (17.3 ± 0.3%), no evidence of recombination was detected in the dataset of available complete PVM sequences. Conventional screening of tomato plants in Slovakia using ELISA and RT-PCR further confirmed a frequent occurrence of PVM in this host. Developed RT-PCR showed its polyvalence to detect the PVM Group I isolates, however, in silico analysis of primer binding sites indicated its compromised use for Group II isolates. Our results further pinpoint the significance of HTS for unbiased unveiling of virus diversity and a need for continual optimisation of molecular detection tools.

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“…Unlike many other viruses, these two strains have recently been distinguished and there was no prior discrimination of these strains based on biological properties. There is evidence for the existence of genetic variation within these strains, in particular within PVM-D (Cavileer et al, 1998;Xu et al, 2010;Tabasinejad et al, 2014;Plchova et al, 2015;Su et al, 2017;He et al, 2019).…”

Section: Intraspecific Diversitymentioning

confidence: 99%

Pest categorisation of potato virus M (non‐EU isolates)

Bragard¹,

Dehnen‐Schmutz²,

Gonthier³

et al. 2020

EFS2

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Following a request from the EU Commission, the Panel on Plant Health has addressed the pest categorisation of non-EU isolates of potato virus M (PVM). The information currently available on geographical distribution, biology, epidemiology, potential entry pathways, potential additional impact compared to the current situation in the EU and availability of control measures of non-EU isolates of PVM has been evaluated with regard to the criteria to qualify as a potential Union quarantine pest. Because non-EU isolates of PVM are absent from the EU, they do not meet one of the requirements to be regulated as a regulated non-quarantine pest (RNQP) (presence in the EU); as a consequence, the Panel decided not to evaluate the other RNQP criteria for these isolates. Populations of PVM can be subdivided into two strains: the ordinary strain (PVM-O) is present in the EU, while the divergent strain (PVM-D) is absent from the EU or considered to have at most a limited distribution in the EU. Non-EU isolates of PVM-O are not expected to have an additional impact in the EU compared to EU isolates and therefore do not meet the corresponding criterion to qualify as a potential Union quarantine pest. The Panel is unable to conclude on the potential impact of non-EU PVM-D isolates in the EU territory, but PVM-D isolates meet all the other criteria to qualify as a potential Union quarantine pest.

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Complete genome sequence of a new isolate of potato virus M in Yunnan, China

Cited by 7 publications

References 11 publications

Analysis of Synonymous Codon Usage Bias in Potato Virus M and Its Adaption to Hosts

Analysis of Synonymous Codon Usage Bias in Potato Virus M and Its Adaption to Hosts

High-throughput sequencing of Potato virus M from tomato in Slovakia reveals a divergent variant of the virus

Pest categorisation of potato virus M (non‐EU isolates)

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