Phylogenetic analysis and recombination events in full genome sequences of apple stem grooving virus

Chen, H; Chen, S; Li, Y; Ye, T; Lü, Hao; Fan, Zaifeng; Guo, Liyun; Zhou, Tao

doi:10.4149/av_2014_04_309

Cited by 7 publications

(4 citation statements)

References 40 publications

(48 reference statements)

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“…Molecular evolution studies can help us to understand the important features of RNA viruses, such as population structure, adaptation to new hosts, and the underlying evolutionary mechanisms [ 35 ]. Several such studies on viruses in the family Betaflexiviridae , such as ASGV [ 36 ], Grapevine virus A (GVA) [ 37 ] and ACLSV [ 38 – 39 ] have recently been published. To date, there have only been limited efforts in the case of CVA, a virus of very broad geographical distribution [ 14 , 20 – 21 ].…”

Section: Discussionmentioning

confidence: 99%

Further insight into genetic variation and haplotype diversity of Cherry virus A from China

Gao

Candresse

et al. 2017

PLoS ONE

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Cherry virus A (CVA) infection appears to be prevalent in cherry plantations worldwide. In this study, the diversity of CVA isolates from 31 cherry samples collected from different orchards around Bohai Bay in northeastern China was analyzed. The complete genome of one of these isolates, ChYT52, was found to be 7,434 nt in length excluding the poly (A) tail. It shares between 79.9–98.7% identity with CVA genome sequences in GenBank, while its RdRp core is more divergent (79.1–90.7% nt identity), likely as a consequence of a recombination event. Phylogenetic analysis of ChYT52 genome with CVA genomes in Genbank resulted in at least 7 major clusters plus additional 5 isolates alone at the end of long branches suggesting the existence of further phylogroups diversity in CVA. The genetic diversity of Chinese CVA isolates from 31 samples and GenBank sequences were analyzed in three genomic regions that correspond to the coat protein, the RNA-dependent RNA polymerase core region, and the movement protein genes. With few exceptions likely representing further recombination impact, the trees various trees are largely congruent, indicating that each region provides valuable phylogenetic information. In all cases, the majority of the Chinese CVA isolates clustering in phylogroup I, together with the X82547 reference sequence from Germany. Statistically significant negative values were obtained for Tajima’s D in the three genes for phylogroup I, suggesting that it may be undergoing a period of expansion. There was considerable haplotype diversity in the individual samples and more than half samples contained genetically diverse haplotypes belonging to different phylogroups. In addition, a number of statistically significant recombination events were detected in CVA genomes or in the partial genomic sequences indicating an important contribution of recombination to CVA evolution. This work provides a foundation for elucidation of the epidemiological characteristics and evolutionary history of CVA populations.

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Section: Discussionmentioning

confidence: 99%

Further insight into genetic variation and haplotype diversity of Cherry virus A from China

Gao

Candresse

et al. 2017

PLoS ONE

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“…Several approaches to detect ASGV have been developed, such as long-distance PCR (LD PCR) to amplify the complete genome of ASGV [ 16 ], multiplex reverse transcriptase (RT)-PCR for major apple viruses [ 17 – 19 ] and pear viruses [ 20 ], and immunochromatographic assays by monoclonal antibodies specific for CP [ 21 ]. Moreover, using available genome sequences for ASGV, two phylogenetic groups and four recombinants of 16 ASGV isolates have been identified [ 22 ], and the molecular evolution of subgenomic RNA of ASGV has been studied [ 1 ].…”

Section: Introductionmentioning

confidence: 99%

Integrated analyses using RNA-Seq data reveal viral genomes, single nucleotide variations, the phylogenetic relationship, and recombination for Apple stem grooving virus

Choi

Kim

et al. 2016

BMC Genomics

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BackgroundNext-generation sequencing (NGS) provides many possibilities for plant virology research. In this study, we performed integrated analyses using plant transcriptome data for plant virus identification using Apple stem grooving virus (ASGV) as an exemplar virus. We used 15 publicly available transcriptome libraries from three different studies, two mRNA-Seq studies and a small RNA-Seq study.ResultsWe de novo assembled nearly complete genomes of ASGV isolates Fuji and Cuiguan from apple and pear transcriptomes, respectively, and identified single nucleotide variations (SNVs) of ASGV within the transcriptomes. We demonstrated the application of NGS raw data to confirm viral infections in the plant transcriptomes. In addition, we compared the usability of two de novo assemblers, Trinity and Velvet, for virus identification and genome assembly. A phylogenetic tree revealed that ASGV and Citrus tatter leaf virus (CTLV) are the same virus, which was divided into two clades. Recombination analyses identified six recombination events from 21 viral genomes.ConclusionsTaken together, our in silico analyses using NGS data provide a successful application of plant transcriptomes to reveal extensive information associated with viral genome assembly, SNVs, phylogenetic relationships, and genetic recombination.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2994-6) contains supplementary material, which is available to authorized users.

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“…MP and CP may be produced through the 3′-coterminal subgenomic RNAs (sgRNAs), and CP expression from sgRNA is essential for ASGV systemic infection in the host [ 28 , 29 ]. Phylogenetic analysis of 16 ASGV full-length genomic sequences clusters them into two groups with no correlations to host and geographical origins [ 30 , 31 ]. ASGV infection is symptomless on most commercial cultivars of apple and pear, but does induce the typical symptoms of stem pitting and grooving on some cultivars of citrus, lily, kiwifruit, and pear [ 32 – 35 ].…”

Section: Introductionmentioning

confidence: 99%

Characterization of virus-derived small interfering RNAs in Apple stem grooving virus-infected in vitro-cultured Pyrus pyrifolia shoot tips in response to high temperature treatment

Liu

Zhang

Yang

et al. 2016

Virol J

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BackgroundHeat treatment (known as thermotherapy) together with in vitro culture of shoot meristem tips is a commonly used technology to obtain virus-free germplasm for the effective control of virus diseases in fruit trees. RNA silencing as an antiviral defense mechanism has been implicated in this process. To understand if high temperature-mediated acceleration of the host antiviral gene silencing system in the meristem tip facilitates virus-derived small interfering RNAs (vsiRNA) accumulation to reduce the viral RNA titer in the fruit tree meristem tip cells, we used the Apple stem grooving virus (ASGV)–Pyrus pyrifolia pathosystem to explore the possible roles of vsiRNA in thermotherapy.ResultsAt first we determined the full-length genome sequence of the ASGV-Js2 isolate and then profiled vsiRNAs in the meristem tip of in vitro-grown pear (cv. ‘Jinshui no. 2’) shoots infected by ASGV-Js2 and cultured at 24 and 37 °C. A total of 7,495 and 7,949 small RNA reads were obtained from the tips of pear shoots cultured at 24 and 37 °C, respectively. Mapping of the vsiRNAs to the ASGV-Js2 genome revealed that they were unevenly distributed along the ASGV-Js2 genome, and that 21- and 22-nt vsiRNAs preferentially accumulated at both temperatures. The 5′-terminal nucleotides of ASGV-specific siRNAs in the tips cultured under different temperatures had a similar distribution pattern, and the nucleotide U was the most frequent. RT-qPCR analyses suggested that viral genome accumulation was drastically compromised at 37 °C compared to 24 °C, which was accompanied with the elevated levels of vsiRNAs at 37 °C. As plant Dicer-like proteins (DCLs), Argonaute proteins (AGOs), and RNA-dependent RNA polymerases (RDRs) are implicated in vsiRNA biogenesis, we also cloned the partial sequences of PpDCL2,4, PpAGO1,2,4 and PpRDR1 genes, and found their expression levels were up-regulated in the ASGV-infected pear shoots at 37 °C.ConclusionsCollectively, these results showed that upon high temperature treatment, the ASGV-infected meristem shoot tips up-regulated the expression of key genes in the RNA silencing pathway, induced the biogenesis of vsiRNAs and inhibited viral RNA accumulation. This study represents the first report on the characterization of the vsiRNA population in pear plants infected by ASGV-Js2, in response to high temperature treatment.Electronic supplementary materialThe online version of this article (doi:10.1186/s12985-016-0625-0) contains supplementary material, which is available to authorized users.

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Phylogenetic analysis and recombination events in full genome sequences of apple stem grooving virus

Cited by 7 publications

References 40 publications

Further insight into genetic variation and haplotype diversity of Cherry virus A from China

Further insight into genetic variation and haplotype diversity of Cherry virus A from China

Integrated analyses using RNA-Seq data reveal viral genomes, single nucleotide variations, the phylogenetic relationship, and recombination for Apple stem grooving virus

Characterization of virus-derived small interfering RNAs in Apple stem grooving virus-infected in vitro-cultured Pyrus pyrifolia shoot tips in response to high temperature treatment

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