Genetic variation analysis of apple chlorotic leaf spot virus coat protein reveals a new phylogenetic type and two recombinants in China

Chen, Shanyi; Zhou, Ying; Ye, Ting; Lü, Hao; Guo, Liyun; Fan, Zaifeng; Li, Shifang; Zhou, Tao

doi:10.1007/s00705-013-1927-9

Cited by 15 publications

(16 citation statements)

References 23 publications

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“…Recombination is a powerful evolutionary driving force that results in the generation of new genotypes in RNA viruses [85,86]. Recombination events have been previously reported in RNA viruses in the family Betaflexiviridae and Closteroviridae [79,84,87,88] and in this study, multiple recombination events were identified amongst Australian isolates of ACLSV, CGRMV, CVA, LChV1, LChV2 and PBNSPaV. All the Australian recombinant isolates shared similar phylogenetic groupings with their major parental sequence which indicates close genetic connectivity within the population of these recombinants.…”

Section: Discussionmentioning

confidence: 97%

Updating the Quarantine Status of Prunus Infecting Viruses in Australia

Kinoti

Nancarrow

Dann³

et al. 2020

Viruses

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One hundred Prunus trees, including almond (P. dulcis), apricot (P. armeniaca), nectarine (P. persica var. nucipersica), peach (P. persica), plum (P. domestica), purple leaf plum (P. cerasifera) and sweet cherry (P. avium), were selected from growing regions Australia-wide and tested for the presence of 34 viruses and three viroids using species-specific reverse transcription-polymerase chain reaction (RT-PCR) or polymerase chain reaction (PCR) tests. In addition, the samples were tested using some virus family or genus-based RT-PCR tests. The following viruses were detected: Apple chlorotic leaf spot virus (ACLSV) (13/100), Apple mosaic virus (ApMV) (1/100), Cherry green ring mottle virus (CGRMV) (4/100), Cherry necrotic rusty mottle virus (CNRMV) (2/100), Cherry virus A (CVA) (14/100), Little cherry virus 2 (LChV2) (3/100), Plum bark necrosis stem pitting associated virus (PBNSPaV) (4/100), Prune dwarf virus (PDV) (3/100), Prunus necrotic ringspot virus (PNRSV) (52/100), Hop stunt viroid (HSVd) (9/100) and Peach latent mosaic viroid (PLMVd) (6/100). The results showed that PNRSV is widespread in Prunus trees in Australia. Metagenomic high-throughput sequencing (HTS) and bioinformatics analysis were used to characterise the genomes of some viruses that were detected by RT-PCR tests and Apricot latent virus (ApLV), Apricot vein clearing associated virus (AVCaV), Asian Prunus Virus 2 (APV2) and Nectarine stem pitting-associated virus (NSPaV) were also detected. This is the first report of ApLV, APV2, CGRMV, CNRNV, LChV1, LChV2, NSPaV and PBNSPaV occurring in Australia. It is also the first report of ASGV infecting Prunus species in Australia, although it is known to infect other plant species including pome fruit and citrus.

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Section: Discussionmentioning

confidence: 97%

Updating the Quarantine Status of Prunus Infecting Viruses in Australia

Kinoti

Nancarrow

Dann³

et al. 2020

Viruses

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“…These authors also showed that co-variable aa positions 40 and 75 were critical for effective viral replication. Other multiple aa alignments showed another covariation in the ACLSV CP at position 79, among 55 Chinese apple ACLSV isolates (Chen et al 2013). Brazilian isolates showed conserved signatures of type B6 isolates at positions 40, 59, 75, 130 and 184, that places them with type B6 isolates, except for isolates M220 (apple) and PR1 (plum), which appear to be variants of the type B6 isolates.…”

Section: Resultsmentioning

confidence: 93%

“…The regions of highest genetic variation in the ACLSV CP appear to vary considerably. They have been observed in the N-terminal (German et al 1990) and the middle portion of the CP gene (Rana et al 2010;Chen et al 2013). Nucleotide diversity (π) was analyzed throughout the length of the coat protein gene of ACLSV (Fig.…”

Section: Resultsmentioning

confidence: 99%

Characterization and genetic variability of coat protein genes of Apple chlorotic leaf spot virus isolates from southern Brazil

Nickel

Silva

Fajardo

et al. 2017

Trop. plant pathol.

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Apple chlorotic leaf spot virus (ACLSV) infects temperate rosaceous fruit trees worldwide and causes a wide range of diseases that are economically highly damaging. This study was carried out to analyze genetic variability of regional ACLSV isolates and compare it with ACLSV isolates from other parts of the world. Nineteen amplicons of ACLSV, corresponding to the coat protein (CP) gene of isolates from apple, plum, and nectarine, from two states in southern Brazil, have been analyzed for genetic variation and compared phylogenetically among themselves and with other sequences available in GenBank. Sequences identities among complete CP genes of these isolates ranged from 87.5 to 100% and 92.2 to 100% at the nucleotide (nt) and the deduced amino acid (daa) levels, respectively. In the comparison with isolates from Asia, Europe and North America, identities were 68.4 to 100% and 72.5 to 100% at nt and daa levels, respectively. Phylogenetic trees based on nucleotide sequences showed that these isolates grouped into two clusters, cluster 1 containing apple isolates and cluster 2 comprising apple, plum and nectarine isolates. Most Brazilian isolates showed conserved signatures (Ser 40 , Leu 59 , Tyr 75 , Thr 130 and Leu 184) in their CPs, which place them with type B6 isolates. However, some Brazilian isolates were found to be variants of type B6. These analyzes indicated that Brazilian isolates had lower genetic variability compared to isolates from China, India and Japan and that the CP genes were under negative selection. The greatest diversity of nucleotides was observed in the central portion of the CP gene, represented predominantly by synonymous substitutions. One natural recombinant was detected among ACLSV isolates from Brazil.

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“…Though no recombination hotspot was found, recombination events play an important role in ASGV evolution as reported recombination in cp gene (Negi et al, 2010). Moreover, recombination might be common in members of Betaflexiviridae as detected in a few reports (Singh et al, 2007(Singh et al, , 2008(Singh et al, , 2012Komorowska et al, 2011;Singh et al, 2012;Dhir et al, 2013;Pramesh and Baranwal, 2013;Alabi et al, 2014;Chen et al, 2014). As no vector is known for ASGV and it can be transmitted by grafting, recombinant events among isolates from different host species and countries, and phylogenetic clusters with no correlation to host or geographical origins are likely to be the result of vegetative propagation and exchanges of propagation materials between countries.…”

Section: Discussionmentioning

confidence: 92%

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

Chen¹,

Chen²,

Li³

et al. 2014

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Summary. -Apple stem grooving virus (ASGV) is one of the most important viral pathogens infecting pome and stone fruit trees worldwide. In this study, with the complete nucleotide sequence of isolate ASGV-T47, which we generated, molecular variation and recombination in ASGV full genomic sequences worldwide were analyzed. ASGV-T47 shared 79.7-97.6% nucleotide identity with the other isolates worldwide and had the highest identity with an isolate from Japan. Phylogenetic analysis based on whole genome clustered all 16 isolates from around the world into two groups with no correlation to host or geographical origin. Four isolates were detected to be recombinants. Selection pressure estimation indicated that the two codons at positions 1756 and 1798 are under positive selection, while purifying selection is the primary evolutionary dynamics for ASGV.Keywords: capillovirus; full genome sequence; recombination; variation; evolution; selection * Corresponding author. E-mail: taozhoucau@cau.edu.cn; phone: +8610-62732771. Abbreviations: ASGV = apple stem grooving virus; CP = coat protein; ORF(s) = open reading frame(s); SPMMV = sweet potato mild mottle virust

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Genetic variation analysis of apple chlorotic leaf spot virus coat protein reveals a new phylogenetic type and two recombinants in China

Cited by 15 publications

References 23 publications

Updating the Quarantine Status of Prunus Infecting Viruses in Australia

Updating the Quarantine Status of Prunus Infecting Viruses in Australia

Characterization and genetic variability of coat protein genes of Apple chlorotic leaf spot virus isolates from southern Brazil

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

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