Molecular analysis of a California strain of Rupestris stem pitting-associated virus isolated from declining Syrah grapevines

The sequence of the genome of a Rupestris stem pitting-associated virus (RSPaV) isolated from a declining Syrah grapevine in California, designated the Syrah strain (RSPaV-SY) was determined. The genome of this strain had an overall nucleotide identity os 77% in comparison with RSPaV sequences in GenBank; the coat protein was the most conservd gene among RSPaV sequences among replicase was the least conserved gene. Phylogenetic analysis of partial coat protein and replicase gene sequences showed RSPaV-SY clustrd independently from the majority of RSPaV isolates

Metagenomic analysis of viruses associated with maize lethal necrosis in Kenya

Background: Maize lethal necrosis is caused by a synergistic co-infection of Maize chlorotic mottle virus (MCMV) and a specific member of the Potyviridae, such as Sugarcane mosaic virus (SCMV), Wheat streak mosaic virus (WSMV) or Johnson grass mosaic virus (JGMV). Typical maize lethal necrosis symptoms include severe yellowing and leaf drying from the edges. In Kenya, we detected plants showing typical and atypical symptoms. Both groups of plants often tested negative for SCMV by ELISA. Methods: We used next-generation sequencing to identify viruses associated to maize lethal necrosis in Kenya through a metagenomics analysis. Symptomatic and asymptomatic leaf samples were collected from maize and sorghum representing sixteen counties. Results: Complete and partial genomes were assembled for MCMV, SCMV, Maize streak virus (MSV) and Maize yellow dwarf virus-RMV (MYDV-RMV). These four viruses (MCMV, SCMV, MSV and MYDV-RMV) were found together in 30 of 68 samples. A geographic analysis showed that these viruses are widely distributed in Kenya. Phylogenetic analyses of nucleotide sequences showed that MCMV, MYDV-RMV and MSV are similar to isolates from East Africa and other parts of the world. Single nucleotide polymorphism, nucleotide and polyprotein sequence alignments identified three genetically distinct groups of SCMV in Kenya. Variation mapped to sequences at the border of NIb and the coat protein. Partial genome sequences were obtained for other four potyviruses and one polerovirus. Conclusion: Our results uncover the complexity of the maize lethal necrosis epidemic in Kenya. MCMV, SCMV, MSV and MYDV-RMV are widely distributed and infect both maize and sorghum. SCMV population in Kenya is diverse and consists of numerous strains that are genetically different to isolates from other parts of the world. Several potyviruses, and possibly poleroviruses, are also involved

A remarkable synergistic effect at the transcriptomic level in peach fruits doubly infected by Prunus necrotic ringspot virus and Peach latent mosaic viroid

[EN] Background: Microarray profiling is a powerful technique to investigate expression changes of large amounts of genes in response to specific environmental conditions. The majority of the studies investigating gene expression changes in virus-infected plants are limited to interactions between a virus and a model host plant, which usually is Arabidopsis thaliana or Nicotiana benthamiana. In the present work, we performed microarray profiling to explore changes in the expression profile of field-grown Prunus persica (peach) originating from Chile upon single and double infection with Prunus necrotic ringspot virus (PNRSV) and Peach latent mosaic viroid (PLMVd), worldwide natural pathogens of peach trees. Results: Upon single PLMVd or PNRSV infection, the number of statistically significant gene expression changes was relatively low. By contrast, doubly-infected fruits presented a high number of differentially regulated genes. Among these, down-regulated genes were prevalent. Functional categorization of the gene expression changes upon double PLMVd and PNRSV infection revealed protein modification and degradation as the functional category with the highest percentage of repressed genes whereas induced genes encoded mainly proteins related to phosphate, C-compound and carbohydrate metabolism and also protein modification. Overrepresentation analysis upon double infection with PLMVd and PNRSV revealed specific functional categories over- and underrepresented among the repressed genes indicating active counter-defense mechanisms of the pathogens during infection. Conclusions: Our results identify a novel synergistic effect of PLMVd and PNRSV on the transcriptome of peach fruits. We demonstrate that mixed infections, which occur frequently in field conditions, result in a more complex transcriptional response than that observed in single infections. Thus, our data demonstrate for the first time that the simultaneous infection of a viroid and a plant virus synergistically affect the host transcriptome in infected peach fruits. These field studies can help to fully understand plant-pathogen interactions and to develop appropriate crop protection strategies.We thank Drs M.A. Perez-Amador y J. Gadea for helping in the result analysis. This work was supported by grant BIO2011-25018 from the Spanish granting agency Direccion General de Investigacion Cientifica for the transcriptomic analyses and from the grant 2009CL0020 from the bilateral project INIA-Chile/CSIC-Spain for the phytosanitary evaluation. MC Herranz was the recipient of a contract from the Juan de la Cierva program of the Ministerio de Educacion y Ciencia of Spain.Herranz Gordo, MDC.; Niehl, A.; Rosales, M.; Fiore, N.; Zamorano, A.; Granell Richart, A.; Pallás Benet, V. (2013). 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Phytoplasmal diseases of peach and associated phytoplasma taxa

Phytoplasmal diseases occur wherever peach (Prunus persica) trees are grown. However, the causal agents differ considerably in taxonomy, insect vector relationships and geographic locations. X-disease of peach is widespread in North America, but does not occur elsewhere in the world. X-disease is induced by ‘Candidatus Phytoplasma pruni’, a member of the X-disease phytoplasma group (16SrIII group, subgroup 16SrIII-A). Peach rosette, peach red suture, and peach yellows, which occur in eastern United States and Canada are all caused by the X-disease phytoplasma. Another North America disease, peach yellow leaf roll (PYLR) is present in a limited area of northern California. Its causal agent is classified in the apple proliferation (AP) group, 16SrX group, as a subtype of the pear decline phytoplasma. In Europe, phytoplasmal diseases of peach are reported under the name European stone fruit yellows and incited by ‘Ca. P. prunorum’, a member of the AP group, subgroup 16SrX-B. ‘Ca. P. prunorum’ is closely related to the PYLR agent. In Lebanon and Iran, peach trees are affected by almond witches’ broom, a lethal disease incited by ‘Ca. P. phoenicium’, a member of the 16SrIX group, subgroup 16SrIX-B. Phytoplasmas of other phylogenetic groups, known to infect a wide range of plant hosts, have been identified in declining peach trees in several fruit-growing areas of the world. The pathological relevance of several ‘non-peach’ phytoplasmas requires further investigations as their presence was ascertained by nested PCR assays only