Genome Heterogeneity of Apple Stem Pitting Virus in Apple Trees

Yoshikawa, Nobuyuki; Matsuda, Haruo; Oda, Yoshiki; Isogai, Masamichi; Takahashi, Tohru; Ito, Takumi; Yoshida, Kandai

doi:10.17660/actahortic.2001.550.41

Cited by 28 publications

(16 citation statements)

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“…Sequences at 3 0 end of the genome, included the coat protein gene, and were highly variable among isolates [8][9][10]. Advances in the molecular biology of Foveaviruses have been intensively reviewed recently.…”

Section: Introductionmentioning

confidence: 99%

Complete genomic sequence analyses of Apple stem pitting virus isolates from China

2011

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The complete genomic sequences of a Chinese ASPV isolates KL1 and KL9 were determined from ten overlapping cDNA clones. The genomes of both isolates were 9265 nucleotides excluding the poly (A) tail and contained five open reading frames (ORFs). The identities between two complete genomes were 92.5% at nt level. Multiple alignment of the amino acid sequences showed that 110 aa variations between two genomic sequences and the variable domains mainly distributed in 5'-terminal of ORF1, ORF3, and ORF5, respectively. Two complete genomic sequences shared 71.4-77.3% identities with other ASPV isolates at nt level. Phylogenetic relationship analysis of the coat protein genes revealed that ASPV isolates had high variables and formed three groups. All ASPV isolates from apples were clustered to group I, whereas pear were clustered to groups II (except NC_003462) and both KL1 and KL9 were clustered to group III. Nucleotide sequences diversity analysis showed that the between-population d(NS)/d(S) ratio 0.092 was similar to these for within-group (0.092-0.095); there was no geographic differentiation between ASPV isolates.

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Section: Introductionmentioning

confidence: 99%

Complete genomic sequence analyses of Apple stem pitting virus isolates from China

2011

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“…Sequencing of the ASPV‐specific nested PCR products from three isolates (GT11, AFT5 and QK4), originating from apple, pear and quince, respectively, revealed their viral origin. Comparison of the sequences obtained with the corresponding region of the two published ASPV sequences showed 81% and 79% nucleotide identity, for apple and pear isolates respectively, with D21829 (Jelkmann, 1994) and 83% identity for the quince isolate with AB045371 (Yoshikawa et al ., 2001). Sequences from QK4, GT11 and AFT5 isolates were deposited in the EMBL‐EBI database under accession numbers AM746061, AM746059 and AM746060, respectively.…”

Section: Resultsmentioning

confidence: 99%

“…Numerous RT‐PCR assays, varying mainly on the target sequence, have been reported for the detection of ASPV (MacKenzie et al ., 1997; Kummert et al ., 1998; Malinowski et al ., 1998; Yoshikawa et al ., 2001; Menzel et al ., 2002; Hassan et al ., 2006). However, the detection range of these techniques is limited by the high genetic variability of the virus, which ranges up to 23% in the amino acid sequence of the coat protein (CP) gene (Nemchinov et al ., 1998; Schwarz & Jelkmann, 1998; Paunović et al ., 1999; Yoshikawa et al ., 2001). The development of reliable and sensitive assays using rapid and simple sample preparation techniques is necessary for successful screening of propagating material in certification schemes.…”

Section: Introductionmentioning

confidence: 99%

Reliable RT‐PCR detection of Apple stem pitting virus in pome fruits and its association with quince fruit deformation disease

Mathioudakis¹,

Maliogka²,

Dovas³

et al. 2009

Plant Pathology

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In this study a spot nested RT-PCR assay was developed for the detection of Apple stem pitting virus (ASPV). A one step RT-PCR for the generic detection of foveaviruses using degenerate primers that target a conserved region of the RNA-dependent RNA polymerase (RdRp) gene was followed by a nested PCR that amplifies a 312 bp ASPV specific product. The method is rapid, simple and displays high sensitivity and broad detection range, overcoming the virus molecular variability. The optimum sampling conditions for reliable virus detection were also investigated. ASPV was detected throughout the year in different plant tissues of affected trees, thus the method could be used for routine screening and in certification schemes of pome fruits. ASPV was detected in quince orchards in Greece in all trees that were tested, showing a fruit deformation disorder. Sequencing and phylogenetic analysis of amplicons generated by RT-PCR from plant tissue affected with the deformation disease indicated that the agent responsible was a variant of ASPV.

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“…Most recently, there were only four complete genomic sequences of ASPV isolates had been deposited in GenBank, the accession numbers were NC_003462 (Jelkmann, 1994), AB045371 (Yoshikawa et al, 2001), EU095327 and FR694186, respectively. Many ASPV CP gene sequences from different regions have been reported and the analyses have been demonstrated that the sequences of CP gene were highly variable amongst isolates (Schwarz and Jelkmann, 1998;Nechinov et al, 1997;Li et al, 2010a).…”

Section: Introductionmentioning

confidence: 99%

Cloning and Prokaryotic Expression of <i>Apple Stem Pitting Virus</i> CP Gene in Ya Pear in <i>E. coli</i>

Niu¹

2011

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In order to clarify evolutionary relationship and genetic diversity of apple stem pitting virus (ASPV), and preparation the corresponding special antiserum. In this study, total RNA was extracted from phloem tissue of Ya (Y) pear which infected by ASPV and used as template for cDNA synthesis. The coat protein (CP) gene of ASPV was cloned and sequenced. The CP gene of Ya pear was cloned into expression vector PET-28a, and transformed into E. coli BL21 (DE3), and SDS-PAGE electrophoresis analysis. The results showed that the complete CP gene consisted of 1 194 nucleotides and encodes a polypeptide of 397 amino acid (aa).Comparison of the amino acid sequences of Ya pear CP gene with other ASPV isolates showed approximately 70% similarity. Phylogenetic tree showed that all isolates of the coat protein (CP) genes of ASPV isolates at AA sequence revealed three groups. All ASPV isolates from apple were clustered to group I, whereas pear were clustered to groups Ⅱ (except NC_003462) and the Ya pear were clustered into group Ⅲ. Results of SDS-PAGE showed that specific expression of a 42 kD fusion protein was achieved by the inducing of 1 mmol/L IPTG. The complete CP gene and prokaryotic expression vector of Ya pear provided additional baseline data for preparation recombinant polyclonal antibody of ASPV and further study of ASPV molecular biology.

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Genome Heterogeneity of Apple Stem Pitting Virus in Apple Trees

Cited by 28 publications

References 0 publications

Complete genomic sequence analyses of Apple stem pitting virus isolates from China

Complete genomic sequence analyses of Apple stem pitting virus isolates from China

Reliable RT‐PCR detection of Apple stem pitting virus in pome fruits and its association with quince fruit deformation disease

Cloning and Prokaryotic Expression of <i>Apple Stem Pitting Virus</i> CP Gene in Ya Pear in <i>E. coli</i>

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