Complete sequence analysis of rice transitory yellowing virus and its comparison to rice yellow stunt virus

Symptoms and yield loss caused by rice stripe mosaic virus

Background

Rice stripe mosaic virus (RSMV) is a tentative new Cytorhabdovirus species in family Rhabdoviridae transmitted by the leafhopper Recilia dorsalis. Although the virus was first detected in southern China in 2015, few studies have investigated rice symptoms and yield losses caused by RSMV infection.

Methods

In this study, we observed and systematically compared symptoms of three virally infected, representative varieties of indica, hybrid and japonica rice and determined the yield parameters of the artificially inoculated plants.

Results

The three RSMV-infected cultivated rice varieties exhibited slight dwarfing, striped mosaicism, stiff, crinkled or even twisted leaves, an increased number of tillers, delayed heading, cluster-shaped shortening of panicles and mostly unfilled grains. Slight differences in symptom occurrence time were observed under different environmental conditions. For example, mosaic symptoms appeared earlier and crinkling symptoms appeared later, with both symptoms later receding in some infected plants. Yield losses due to RSMV also differed among varieties. The most serious yield reduction was experienced by indica rice (cv. Meixiangzhan), followed by hybrid indica rice (cv. Wuyou 1179) and then japonica (cv. Nipponbare). Single panicle weight, seed setting rate and 1000-kernel weight were reduced in the three infected varieties compared with healthy plants—by 85.42, 94.85 and 31.56% in Meixiangzhan; 52.43, 53.06 and 25.65% in Wuyou 1179 and 25.53, 49.32 and 23.86% in Nipponbare, respectively.

Conclusions

Our findings contribute basic data for field investigations, formulation of prevention and control strategies and further study of the pathogenesis of RSMV.

Identification and Characterization of Wheat Yellow Striate Virus, a Novel Leafhopper-Transmitted Nucleorhabdovirus Infecting Wheat

A new wheat viral disease was found in China. Bullet-shaped viral particles within the nucleus of the infected wheat leave cells, which possessed 180-210 nm length and 35-40 nm width, were observed under transmission electron microscopy. A putative wheat-infecting rhabdovirus vectored by the leafhopper Psammotettix alienus was identified and tentatively named wheat yellow striate virus (WYSV). The full-length nucleotide sequence of WYSV was determined using transcriptome sequencing and RACE analysis of both wheat samples and leafhoppers P. alienus. The negative-sense RNA genome of WYSV contains 14,486 nucleotides (nt) and seven open reading frames (ORFs) encode deduced proteins in the order N-P-P3-M-P6-G-L on the antisense strand. In addition, WYSV genome has a 76-nt 3' leader RNA and a 258-nt 5' trailer, and the ORFs are separated by conserved intergenic sequences. The entire genome sequence shares 58.1 and 57.7% nucleotide sequence identity with two strains of rice yellow stunt virus (RYSV-A and RYSV-B) genomes, respectively. The highest amino acid sequence identity was 63.8% between the L proteins of the WYSV and RYSV-B, but the lowest was 29.5% between the P6 proteins of these viruses. Phylogenetic analysis firmly established WYSV as a new member of the genus Nucleorhabdovirus. Collectively, this study provided evidence that WYSV is likely the first nucleorhabdovirus described infecting wheat via leafhopper P. alienus transmission.

Cytorhabdovirus P3 genes encode 30K-like cell-to-cell movement proteins

Plant viruses encode movement proteins (MP) to facilitate cell-to-cell transport through plasmodesmata. In this study, using trans-complementation of a movement-defective turnip vein-clearing tobamovirus (TVCV) replicon, we show for the first time for cytorhabdoviruses (lettuce necrotic yellows virus (LNYV) and alfalfa dwarf virus (ADV)) that their P3 proteins function as MP similar to the TVCV P30 protein. All three MP localized to plasmodesmata when ectopically expressed. In addition, we show that these MP belong to the 30K superfamily since movement was inhibited by mutation of an aspartic acid residue in the critical 30K-specific LxD/N50-70G motif. We also report that Nicotiana benthamiana microtubule-associated VOZ1-like transcriptional activator interacts with LNYV P3 and TVCV P30 but not with ADV P3 or any of the MP point mutants. This host protein, which is known to interact with P3 of sonchus yellow net nucleorhabdovirus, may be involved in aiding the cell-to-cell movement of LNYV and TVCV.

Occurrence and Identification of a New Vector of Rice Orange Leaf Phytoplasma in South China

Rice orange leaf disease (ROLD) is caused by rice orange leaf phytoplasma (ROLP) and occurs sporadically in rice-growing areas in countries of eastern and southeastern Asia. ROLD caused severe damage to rice production in South China in the 1980s. Although its impact subsequently declined in South China, it has reemerged as a serious threat recently. Our study showed that ROLD occurrence varies in different seasons and fields. It was more severe in summer-grown crops (from July to October) than in spring-grown crops (from March to July). In most fields, the incidence was less than 10%, and diseased plants were scattered throughout the fields. In 20% of fields, the incidence was between 10 and 30%. In some fields, over 90% of plants were affected, causing crop failure. Typical symptoms of ROLD include orange-colored leaves and poor growth. Diseased plants were determined as positive for ROLP but negative for Rice tungro bacilliform virus, Rice tungro spherical virus, and Rice transitory yellowing virus through polymerase chain reaction and reverse-transcription polymerase chain reaction. Phytoplasma bodies but not virus-like particles were observed by electron microscopy in phloem tissue of diseased leaves. The leafhopper Inazuma dorsalis, previously identified as the unique vector for ROLP, was rare in the affected fields. Another leafhopper, Nephotettix cincticeps, previously considered a nonvector for this phytoplasma, was very common. Transmission tests revealed that this insect could also transmit ROLP; therefore, it might represent a new vector responsible for the recent incidence of ROLD.

Recent progress in research on cell-to-cell movement of rice viruses

To adapt to plants as hosts, plant viruses have evolutionally needed the capacity to modify the host plasmodesmata (PD) that connect adjacent cells. Plant viruses have acquired one or more genes that encode movement proteins (MPs), which facilitate the cell-to-cell movement of infectious virus entities through PD to adjacent cells. Because of the diversity in their genome organization and in their coding sequences, rice viruses may each have a distinct cell-to-cell movement strategy. The complexity of their unusual genome organizations and replication strategies has so far hampered reverse genetic research on their genome in efforts to investigate virally encoded proteins that are involved in viral movement. However, the MP of a particular virus can complement defects in cell-to-cell movement of other distantly related or even unrelated viruses. Trans-complementation experiments using a combination of a movement-defective virus and viral proteins of interest to identify MPs of several rice viruses have recently been successful. In this article, we reviewed recent research that has advanced our understanding of cell-to-cell movement of rice viruses.

Detection and diagnosis of rice-infecting viruses

Rice-infecting viruses have caused serious damage to rice production in Asian, American, and African countries, where about 30 rice viruses and diseases have been reported. To control these diseases, developing accurate, quick methods to detect and diagnose the viruses in the host plants and any insect vectors of the viruses is very important. Based on an antigen-antibody reaction, serological methods such as latex agglutination reaction and enzyme-linked immunosorbent assay have advanced to detect viral particles or major proteins derived from viruses. They aid in forecasting disease and surveying disease spread and are widely used for virus detection at plant protection stations and research laboratories. From the early 2000s, based on sequence information for the target virus, several other methods such as reverse transcription-polymerase chain reaction (RT-PCR) and reverse transcription-loop-mediated isothermal amplification have been developed that are sensitive, rapid, and able to differentiate closely related viruses. Recent techniques such as real-time RT-PCR can be used to quantify the pathogen in target samples and monitor population dynamics of a virus, and metagenomic analyses using next-generation sequencing and microarrays show potential for use in the diagnosis of rice diseases.

The movement protein encoded by gene 3 of rice transitory yellowing virus is associated with virus particles

Gene 3 in the genomes of several plant-infecting rhabdoviruses, including rice transitory yellowing virus (RTYV), has been postulated to encode a cell-to-cell movement protein (MP). Trans-complementation experiments using a movement-defective tomato mosaic virus and the P3 protein of RTYV, encoded by gene 3, facilitated intercellular transport of the mutant virus. In transient-expression experiments with the GFP-fused P3 protein in epidermal leaf cells of Nicotiana benthamiana, the P3 protein was associated with the nucleus and plasmodesmata. Immunogold-labelling studies of thin sections of RTYV-infected rice plants using an antiserum against Escherichia coli-expressed His(6)-tagged P3 protein indicated that the P3 protein was located in cell walls and on virus particles. In Western blots using antisera against E. coli-expressed P3 protein and purified RTYV, the P3 protein was detected in purified RTYV, whilst antiserum against purified RTYV reacted with the E. coli-expressed P3 protein. After immunogold labelling of crude sap from RTYV-infected rice leaves, the P3 protein, as well as the N protein, was detected on the ribonucleocapsid core that emerged from partially disrupted virus particles. These results provide evidence that the P3 protein of RTYV, which functions as a viral MP, is a viral structural protein and seems to be associated with the ribonucleocapsid core of virus particles.

Rhabdovirus accessory genes

The Rhabdoviridae is one of the most ecologically diverse families of RNA viruses with members infecting a wide range of organisms including placental mammals, marsupials, birds, reptiles, fish, insects and plants. The availability of complete nucleotide sequences for an increasing number of rhabdoviruses has revealed that their ecological diversity is reflected in the diversity and complexity of their genomes. The five canonical rhabdovirus structural protein genes (N, P, M, G and L) that are shared by all rhabdoviruses are overprinted, overlapped and interspersed with a multitude of novel and diverse accessory genes. Although not essential for replication in cell culture, several of these genes have been shown to have roles associated with pathogenesis and apoptosis in animals, and cell-to-cell movement in plants. Others appear to be secreted or have the characteristics of membrane-anchored glycoproteins or viroporins. However, most encode proteins of unknown function that are unrelated to any other known proteins. Understanding the roles of these accessory genes and the strategies by which rhabdoviruses use them to engage, divert and re-direct cellular processes will not only present opportunities to develop new anti-viral therapies but may also reveal aspects of cellar function that have broader significance in biology, agriculture and medicine.