Fang Ren

Occurrence and genetic diversity analysis of apple stem pitting virus isolated from apples in China.

Two primer pairs were used to detect apple stem pitting virus (ASPV) using a reverse transcription (RT)-PCR test. 82 out of the 141 randomly collected samples, from ten orchards in five provinces and regions of China, tested positive. In the positive samples forty-five (55%) were infected by ASPV and two other viruses. The full coat protein (CP) and the triple gene block (TGB) gene 1, 2 and 3 of partial ASPV isolates were subsequently cloned. The nucleotide and amino acid identities of 39 CP sequence variants from 31 Chinese apple samples were compared with that of previously reported ASPV isolates and were 67.4–96.0% and 68.4–97.7%, respectively. All ASPV sequence variants from Chinese apples separated into two clades with CP- and TGB-based phylogenetic trees, whilst the grouping of TGB2 and TGB3 trees was the same. Three recombinants (FS06-2, X5-2, and XLF-C-2) for CP and six (TH2-5, X8-2, FS05-2, X6-2 and XLF-A-1) recombinants for TGB were identified from the Chinese apple isolates. Two recombinants were found in the TGB sequence of isolate XLF-A-1. The results presented here may assist in the development of a more comprehensive screening tool for apple viruses.

Identification of a divergent variant of grapevine berry inner necrosis virus in grapevines showing chlorotic mottling and ring spot symptoms

A new variant of grapevine berry inner necrosis virus (GINV) was identified by sequencing of small RNA extracted from ‘Beta’ and Thompson seedless grapevines showing leaf mottle and ring spot symptoms. However, GINV was not found in symptomless samples used as a control. The complete genome sequences of two GINV isolates (KU234316-17) were determined, and these showed 75.76–89.74% sequence identity to the genome of a previously reported Japanese GINV isolate. The new variants appear to be evolutionarily distinct from the original GINV isolate. This is the first report of GINV outside of Japan.

Analysis of virus structure variants in before- and after-thermotherapy-treated apple plants

ABSTRACT Pre-thermotherapy apple plants and their homologous regenerated virus-infected apple plants were used to analyze the effect of high temperature on the structure of plant virus variants. The target bands of apple chlorotic leaf spot virus (ACLSV), apple stem grooving virus (ASGV), and apple mosaic virus (ApMV) in the plants of the two populations were purified and cloned, and 16 positive clones of each sample were randomly selected for single-strand conformation polymorphism (SSCP) analysis. The results showed that a predominant haplotype could be found in the two populations. The main variant was the same both in the regenerated and homologous treated plants, but the percentages in regenerated plants could be lower than, the same as, or higher than that in pre-thermotherapy plants. Two types could be divided depending on the percentage of the predominant haplotype in the treated plants, diversity (less 70%) and simple (more 80%), respectively. The clones of different haplotype in each isolates were sent to sequence, and the alignment results in accordance with that of the SSCP analysis. All the results indicated that thermotherapy could not affect the predominant variants of virus in treated plants, just change its percentage.