Proposed classification of the bipartite-genomed raspberry bushy dwarf idaeovirus, with tripartite-genomed viruses in the family Bromoviridae

Genetic Characterization of Raspberry Bushy Dwarf Virus Isolated from Red Raspberry in Kazakhstan

Raspberry bushy dwarf virus (RBDV) is an economically significant pathogen of raspberry and grapevine, and it has also been found in cherry. Most of the currently available RBDV sequences are from European raspberry isolates. This study aimed to sequence genomic RNA2 of both cultivated and wild raspberry in Kazakhstan and compare them to investigate their genetic diversity and phylogenetic relationships, as well as to predict their protein structure. Phylogenetic and population diversity analyses were performed on all available RBDV RNA2, MP and CP sequences. Nine of the isolates investigated in this study formed a new, well-supported clade, while the wild isolates clustered with the European isolates. Predicted protein structure analysis revealed two regions that differed between α- and β-structures among the isolates. For the first time, the genetic composition of Kazakhstani raspberry viruses has been characterized.

Discovery of Four Novel Viruses Associated with Flower Yellowing Disease of Green Sichuan Pepper (Zanthoxylum Armatum) by Virome Analysis

An emerging virus-like flower yellowing disease (FYD) of green Sichuan pepper (Zanthoxylum armatum v. novemfolius) has been recently reported. Four new RNA viruses were discovered in the FYD-affected plant by the virome analysis using high-throughput sequencing of transcriptome and small RNAs. The complete genomes were determined, and based on the sequence and phylogenetic analysis, they are considered to be new members of the genera Nepovirus (Secoviridae), Idaeovirus (unassigned), Enamovirus (Luteoviridae), and Nucleorhabdovirus (Rhabdoviridae), respectively. Therefore, the tentative names corresponding to these viruses are green Sichuan pepper-nepovirus (GSPNeV), -idaeovirus (GSPIV), -enamovirus (GSPEV), and -nucleorhabdovirus (GSPNuV). The viral population analysis showed that GSPNeV and GSPIV were dominant in the virome. The small RNA profiles of these viruses are in accordance with the typical virus-plant interaction model for Arabidopsis thaliana. Rapid and sensitive RT-PCR assays were developed for viral detection, and used to access the geographical distributions. The results revealed a correlation between GSPNeV and the FYD. The viruses pose potential threats to the normal production of green Sichuan pepper in the affected areas due to their natural transmission and wide spread in fields. Collectively, our results provide useful information regarding taxonomy, transmission and pathogenicity of the viruses as well as management of the FYD.

The 1b gene of raspberry bushy dwarf virus is a virulence component that facilitates systemic virus infection in plants

A product translated from the 1b gene of raspberry bushy dwarf virus (RBDV) was specifically detected in RBDV-infected Nicotiana benthamiana plants by immunoblot analysis. To analyze the effects of the 1b gene on virus infection in host plants, an RBDV deletion mutant virus (RB∆1bstop), which is unable to express the 1b gene, was constructed and inoculated to N. benthamiana plants. The results showed that accumulation of the virus genomic (g) RNAs 1 and 2 decreased in inoculated leaves, and that systemic virus spread was delayed compared with wild-type RBDV. In contrast, accumulation of the viral gRNAs 1 and 2 was elevated in RB∆1bstop-infected leaf tissues during ectopic expression of the 1b gene. Furthermore, we found that the 1b has weak RNA silencing suppressor activity.

Blackcurrant Leaf Chlorosis Associated Virus: Evidence of the Presence of Circular RNA during Infections

Blackcurrant leaf chlorosis associated virus (BCLCaV) was detected recently by next-generation sequencing (NGS) and a new and distinct species in the genus Idaeovirus was proposed. Analysis of NGS-derived paired-end reads revealed the existence of bridge reads encompassing the 3′-terminus and 5′-terminus of RNA-2 or RNA-3 of BCLCaV. The full RNA-2 or RNA-3 could be amplified using outward facing or abutting primers; also, RNA-2/RNA-3 could be detected even after three consecutive RNase R enzyme treatments, with denaturation at 95 °C preceding each digestion. Evidence was obtained indicating that there are circular forms of BCLCaV RNA-2 and RNA-3.

Horizontal pollen transmission of Gentian ovary ring-spot virus is initiated during penetration of the stigma and style by infected pollen tubes

Gentian ovary ring-spot virus (GORV) infected gentian plants by pollination with GORV-infected gentian pollen grains, but the virus was not horizontally transmitted to gentian plants by transfer of pollen from GORV-infected Nicotiana benthamiana plants. However, N. benthamiana plants were infected with the virus by pollination with infected gentian pollen as well as by pollination with infected N. benthamiana pollen. When infected gentian pollen grains were placed on N. benthamiana stigmas, germinating pollen tubes penetrated into the stigmas and the styles (stigma-style). Virus infection occurred during penetration of the stigma-style, and the virus subsequently spread systemically to the mother plant. On the other hand, most infected N. benthamiana pollen grains failed to germinate on gentian stigmas, and virus infections were not detected in the stigma-style.