Background"Candidatus Phytoplasma aurantifolia", is the causative agent of witches' broom disease in Mexican lime trees (Citrus aurantifolia L.), and is responsible for major losses of Mexican lime trees in Southern Iran and Oman. The pathogen is strictly biotrophic, and thus is completely dependent on living host cells for its survival. The molecular basis of compatibility and disease development in this system is poorly understood. Therefore, we have applied a cDNA- amplified fragment length polymorphism (AFLP) approach to analyze gene expression in Mexican lime trees infected by "Ca. Phytoplasma aurantifolia".ResultsWe carried out cDNA-AFLP analysis on grafted infected Mexican lime trees of the susceptible cultivar at the representative symptoms stage. Selective amplifications with 43 primer combinations allowed the visualisation of 55 transcript-derived fragments that were expressed differentially between infected and non-infected leaves. We sequenced 51 fragments, 36 of which were identified as lime tree transcripts after homology searching. Of the 36 genes, 70.5% were down-regulated during infection and could be classified into various functional groups. We showed that Mexican lime tree genes that were homologous to known resistance genes tended to be repressed in response to infection. These included the genes for modifier of snc1 and autophagy protein 5. Furthermore, down-regulation of genes involved in metabolism, transcription, transport and cytoskeleton was observed, which included the genes for formin, importin β 3, transducin, L-asparaginase, glycerophosphoryl diester phosphodiesterase, and RNA polymerase β. In contrast, genes that encoded a proline-rich protein, ubiquitin-protein ligase, phosphatidyl glycerol specific phospholipase C-like, and serine/threonine-protein kinase were up-regulated during the infection.ConclusionThe present study identifies a number of candidate genes that might be involved in the interaction of Mexican lime trees with "Candidatus Phytoplasma aurantifolia". These results should help to elucidate the molecular basis of the infection process and to identify genes that could be targeted to increase plant resistance and inhibit the growth and reproduction of the pathogen.

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The incidence and distribution of Tobacco mosaic virus (TMV) and related tobamoviruses was determined using an enzyme-linked immunosorbent assay on 1,926 symptomatic horticultural crops and 107 asymptomatic weed samples collected from 78 highly infected fields in the major horticultural crop-producing areas in 17 provinces throughout Iran. The results were confirmed by host range studies and reverse transcription-polymerase chain reaction. The overall incidence of infection by these viruses in symptomatic plants was 11.3%. The coat protein (CP) gene sequences of a number of isolates were determined and disclosed to be a high identity (up to 100%) among the Iranian isolates. Phylogenetic analysis of all known TMV CP genes showed three clades on the basis of nucleotide sequences with all Iranian isolates distinctly clustered in clade II. Analysis using the complete CP amino acid sequence showed one clade with two subgroups, IA and IB, with Iranian isolates in both subgroups. The nucleotide diversity within each sub-group was very low, but higher between the two clades. No correlation was found between genetic distance and geographical origin or host species of isolation. Statistical analyses suggested a negative selection and demonstrated the occurrence of gene flow from the isolates in other clades to the Iranian population.

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During 2009–2010, a survey was conducted in gardens and commercial fig orchards throughout Iran to determine the prevalence of Fig leaf mottle‐associated virus 1 (FLMaV‐1), Fig leaf mottle‐associated virus 2 (FLMaV‐2), Fig mild mottle‐associated virus (FMMaV), Fig latent virus 1 (FLV‐1) and Fig mosaic virus (FMV). Reverse transcription‐polymerase chain reaction and dot immunobinding assay (DIBA) were conducted on 104 fig samples collected from seven provinces. FLV‐1, FLMaV‐1 and FMV were found in 14.5, 11.5 and 8.6% of the samples, respectively, but FLMaV‐2 and FMMaV were absent. The overall average of infection reached 18.3%, with a peak of 42.9% in Semnan Province, followed by Golestan (40%), Tehran (32.3%), Lorestan (28.6%) and Mazandaran (25%) provinces. No infection was found in Fars and Gilan provinces. Fig samples from Varamin and Khorramabad districts showed high levels of mixed infections, 35.7 and 28.6%, respectively. The presence of FMV and FLV‐1 in the sap of symptomatic fig leaves was also ascertained by DIBA. Sequence analysis of amplified DNA from the partial RNA‐dependent RNA polymerase gene of two FMV isolates from Iran showed a low level of nucleotide variability (5%). The Iranian isolates shared a common phylogeny with other Mediterranean FMV isolates and in particular with those originating from Turkey already reported in GenBank. This is the first report on the presence of FLMaV‐1 and FLV‐1 in Iran and offers a preliminary insight into the unsatisfactory health status of fig in this country.