Molecular characterization of Cucumber mosaic virus (CMV) was done by using samples from tomato and cucurbitaceous plants collected from different locations in the northwest region of Iran. After screening by enzyme-linked immunosorbent assay, 91 CMV-infected samples were identified. Biological properties of eight representative isolates were compared with each other revealing two distinct phenotypes on squash and tomato plants. Phylogenetic analyses based on nucleotide sequences of the coat protein (CP), movement protein (MP) and 2b of the new isolates, together with that of previously reported isolates, led to the placement of the Iranian isolates in subgroups IA and IB according to CP and MP genes, but in subgroup IA according to the 2b gene. These data suggest that reassortment may have been a major event in the evolution of CMV in Iran, and that the Iranian isolates are derived from a common recent ancestor that had passed through a bottleneck event.
In this study, Russian olive trees exhibiting witches’-broom symptoms were collected from urban green areas in Tabriz, in the northwest of Iran. PCR analysis confirmed that phytoplasma caused the disease and, according to the resulting Sanger sequencing electropherogram, a mixed infection with two or more phytoplasma species within the Russian olive trees was revealed. Next-generation sequencing analyses, using the Illumina method, were performed on total DNA from the infected Russian olive plants to recognize the microbial genomic content and assemble the whole genome of the causative pathogen(s). The use of MetaphlAn2 and Kraken2 to analyze species composition revealed the very diverse and unique compositions of different Prokaryotic and Eukaryotic species within the infected plants. Several bacteria and fungi were discovered inside the samples, among which Mycoplasmatota was significantly dominating. Interestingly, the results also revealed a high level of endosymbiotic bacteria and Archaea (Methanobacteria) genome contents within the samples. Bowtie2, metaSPAdes, and CD-HIT pipelines were used to perform the initial genome assembly, and the whole genome of the notable phytoplasma species was assembled and submitted to Genbank.
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