A comprehensive study on the whole spectrum of viruses and viroids in five Iranian grapevine cultivars was carried out using sRNA libraries prepared from phloem tissue. A comparison of two approaches to virus detection from sRNAome data indicated a significant difference in the results and performance of the aligners in viral genome reconstruction. The results showed a complex virome in terms of viral composition, abundance, and richness. Thirteen viruses and viroids were identified in five Iranian grapevine cultivars, among which the grapevine red blotch virus and grapevine satellite virus were detected for the first time in Iranian vineyards. Grapevine leafroll-associated virus 1 (GLRaV1) and grapevine fanleaf virus (GFLV) were highly dominant in the virome. However, their frequency and abundance were somewhat different among grapevine cultivars. The results revealed a mixed infection of GLRaV1/grapevine yellow speckle viroid 1 (GYSVd1) and GFLV/GYSVd1 in grapevines that exhibited yellows and vein banding. We also propose a threshold of 14% of complete reconstruction as an appropriate threshold for detection of grapevine viruses that can be used as indicators for reliable grapevine virome profiling or in quarantine stations and certification programs.

Iran is the main world producer of saffron (Crocus sativus L.), but a bacterial disease continues to threaten saffron production, causing severe flower failure, rot on flowering tubes, delayed vegetative growth, premature yellowing of leaves, bare patches in saffron farms, reddish-brown lesions in the germination zones of roots, and rot of saffron corms. Field surveys in Razavi-Khorasan and Southern-Khorasan provinces revealed high incidence of Burkholderia gladioli dry rot symptoms in saffron farms, with symptoms observed during flowering on leaves and corms. Twenty-four bacterial isolates from symptomatic saffron corms from different parts of Iran were characterized. These bacteria were identified as Burkholderia gladioli, based using phenotypic characteristics, species-specific PCR, and sequencing analyses of the 16S rRNA and 16S-23S intergenic transcribed spacer regions. All 24 isolates triggered hypersensitive reactions in tobacco and pelargonium leaves, although pathogenicity tests showed that only 21 isolates were capable of causing rots on saffron corms.

Knowledge of the molecular changes in resistant and susceptible cultivars during nematode attack is essential for developing plant resistance. Increased expression of genes related to the synthesis and signaling of salicylic acid, jasmonic acid, and ethylene is known to induce expression of genes related to defense against plant parasitic nematodes. Here, we inoculated approximately 3000 s-stage juveniles (J2s) of Meloidogyne javanica to moderately resistant and highly susceptible tomato cultivars (ALYSTE F-1 and Dutch Mobil, respectively) to compare the developmental disease stages. The roots of each cultivar were collected daily until 30 days after inoculation (DAI). The roots were stained with acid-fuchsin and dissected under a microscope. The results showed that a few parasitic J2s were converted to J3s in the moderately resistant cultivar at 14 DAI, at which time, the highly susceptible cultivar had the highest number of J3s. Comparison of hormonal pathways in the two cultivars revealed that the expression of genes related to the ethylene pathway in ALYSTE F-1 was more strongly upregulated than in Dutch Mobil at 14 DAI. Moreover, the jasmonic acid pathway in the roots of both cultivars decreased at 14 DAI. The expression of genes related to salicylic acid synthesis and signaling was not significantly different between the two cultivars with regard to their non-inoculated controls, respectively, but ALYSTE F-1 in general showed constitutively higher levels of these genes compared to Dutch Mobil at 14 DAI. These results suggest that constitutive and induced expression of genes related to the salicylic acid pathway and ethylene pathway, respectively, delay the development of M. javanica J2s in ALYSTE F-1.

We report the characterization and genetic variations of a novel betanucleorhabdovirus infecting sugar beet in Iran. Pairwise comparison of the obtained betanucleorhabdovirus sequence with betanucleorhabdoviruses from GenBank showed that it shares the highest nucleotide identity with tomato betanucleorhabdovirus 2 (TBRV2) and Sambucus betanucleorhabdovirus 4. The obtained sequence contained six open reading frames (ORFs) in antigenomic sense flanked by complementary 3? leader and 5? trailer sequences (3?-N-P-P3-M-G-L-5?). In the phylogenetic tree, the detected isolate was clustered with the betanucleorhabdoviruses and was most closely related to TBRV2, tomato betanucleorhabdovirus 1, and Sambucus betanucleorhabdovirus 1 to 5. The genome organization, phylogenetic relationships, and sequence similarities to other betanucleorhabdoviruses suggest that the virus is a new member of the genus Betanucleorhabdovirus, which we propose to name beet betanucleorhabdovirus 1 (BNRV1). The virus?s partial spread and host-range investigations revealed that sugar beet fields in northeast Iran were infected by BNRV1, which also infects Chenopodium album, Malva neglecta, and Carthamus oxyacanthus weeds. Low values of Ks*, Kst*, Z*, and Snn indicate no substantial genetic differentiation between populations of this virus. Selection pressures on a portion of the BNRV1 N gene analyzed were negative, showing purifying selection was occurring. The magnitude of negative selection in the BNRV1 N gene was consistent with what has been reported for other betanucleorhabdoviruses.