Genetic diversity and biological characterization of watermelon mosaic virus isolates from Iran and Iraq.

No abstract Keywords: genetic diversity; Iran and Iraq; water melon; mosaic virus; cucurbits.

Identification of the experimental herbaceous host range of the Apscaviroids infecting citrus species.

Citrus viroid V (CVd-V), citrus dwarfing viroid (CDVd) and citrus bent leaf viroid (CBLVd) (the genus Apscaviroid, the family Pospiviroidae) have been reported to be restricted to citrus species naturally. The herbaceous host range of these viroids was identified using the viroids infectious clones. Several herbaceous plants from the Cucurbitaceae, Solanaceae, Fabaceae and Asteraceae families were found to be susceptible to CVd-V, CDVd and CBLVd. Also, the viroids could be transferred to these hosts through rubbing of monomeric DNA plasmids and through mechanical inoculation of infected sap. Keywords: citrus; viroid; host range; CVd-V; CBLVd; CDVd.

Molecular characterization of two sugarcane streak mosaic virus isolates from Iran with emphasis on its population structure.

Sugarcane streak mosaic virus (SCSMV; the genus Poacevirus, the family Potyviridae) is an economically important causal agent of sugarcane mosaic disease in Asia. In this study, for the first time, we determined the complete genomic sequences of two Iranian SCSMV isolates, IR-Khuz6 and IR-Khuz57 from sugarcane. The sequences of both isolates were 9,782 nucleotides (nt) long, excluding the 3' poly(A) tail. Both of them contained a 5'-untranslated region (UTR) of 199 nt, an open reading frame of 9,393 nt encoding a polyprotein of 3,130 amino acids (aa), and 3'-UTR of 190 nt. SCSMV-IR-Khuz6 and IR-Khuz57 genome nucleotide sequences were in 97.7% identical and shared identities of 81-92.4% with 10 other SCSMV isolates available in the GenBank. The highest identity was shared with the isolate PAK (NC_014037) from Pakistan. When separate genes were compared, most of the genes shared the highest identities with Pakistani isolate. Phylogenetic analysis of the complete genomic nucleotide and polyprotein amino acid sequences reveals that all SCSMV isolates clustered into two main groups. Both IR-Khuz6 and IR-Khuz57 clustered with isolates from Pakistan (PAK) and India (IND671) in group II but formed a separate subgroup. Population genetic analysis revealed greater between-group than within-group evolutionary divergence values, further supporting the results of the phylogenetic analysis. The results indicate that gene flow and selection pressure are important evolutionary factors shaping the genetic structure of SCSMV populations with implications for global exchange of sugarcane germplasm.

Dynamics of the population structure and genetic variability within Iranian isolates of grapevine fanleaf virus: evidence for polyphyletic origin.

To determine the genetic diversity and population structure of grapevine fanleaf virus (GFLV), the complete nucleotide sequence of the coat protein gene of 41 isolates from different regions in Iran was determined. Phylogenetic analyses of these isolates together with those available in the GenBank revealed two evolutionary divergent lineages, designated GFLV-G and GFLV-Ir that reflect origin of the isolates. Analysis of the genetic variability in the coat protein of these isolates revealed 37 genotype groups in GFLV population. Analyses indicate that GFLV-G and GFLV-Ir clades are significantly differentiated populations of GFLV. Also, geographical subpopulations of the virus in Iran were completely distinct from each other. Examination of nonsynonymous/synonymous nucleotide diversity showed that the CP gene has been under purifying selection. The neutrality tests indicate balancing selection operating within isolates of the northwest of Iran and purifying selection within the other populations.

Comparative genetic diversity of potato virus Y populations based on coat protein gene.

Potato virus Y (PVY) is an important plant pathogen with a wide host range including economically important crops of potato, tobacco, tomato, and pepper. The coat protein gene has been commonly used in studying molecular biology of plant viruses including PVY. In this study, we used a large dataset of CP sequences from isolates collected across the world to assess the detailed molecular evolution of PVY populations with a focus on the Iranian PVY population. Phylogenetic analysis showed that the world PVY population had two major lineages (O:C and N:NTN); each comprising several divergent sublineages. Results showed that the Iranian PVY isolates were distributed across the tree suggesting polyphyletic origin of the Iranian PVY population. Statistical analysis revealed great genetic differences between pairs of the PVY phylogenetic populations. Host populations and also geographical populations of PVY were genetically differentiated. The extent of the genetic diversification among PVY host and geographical populations were mild or moderate. Purifying selection was detected on the CP gene sequences of the PVY populations, suggesting that most of the mutations in the gene were harmful, thereby were eliminated by natural selection. We also detected a variety of recombination patterns to occur along the CP gene of the PVY strains. A significant number of the Iranian PVY isolates were found to be recombinant. Different analyses suggest that Iranian PVY population is highly diverse. In conclusion, results of this study demonstrated that different factors including mutation, host adaptation, geographical distinction and selection pressure shaped the genetic structure of the PVY populations.

Automated image analysis of Euglena gracilis Klebs (Euglenophyta) for measuring sublethal effects of three model contaminants.

The short-term impacts of atrazine (herbicide), tributyltin (organometal) and copper on the behaviour of Euglena gracilis Klebs (Euglenophyta) were assessed. First, the ECOTOX automated image analysis system was used, which measured swimming velocity, cell shape, percentage of cells swimming upwards, and randomness of swimming. Next, visual observation by microscopy was used to measure percentage of cell motility and cell shape. Behavioural changes can be used as an indicator of stress in less than 24 h, potentially making them suitable for inclusion in early-warning systems for water quality. Findings indicate that E. gracilis is a very sensitive organism to copper, showing inhibition of motility with visual observation at 0.8 µmol/L within 1 h. The image analysis system was in general less sensitive than visual observation for detecting behavioural changes after incubation in copper. In contrast, after exposure to organic contaminants atrazine and tributyltin, the ECOTOX system detected small changes in the number of cells swimming upwards (antigravitactic behaviour) at higher concentrations.

Iranian beet necrotic yellow vein virus (BNYVV): pronounced diversity of the p25 coding region in A-type BNYVV and identification of P-type BNYVV lacking a fifth RNA species.

Beet necrotic yellow vein virus (BNYVV) was detected in 288 of the 392 samples collected in Iran. A-type BNYVV was detected most frequently. The p25 coding region on BNYVV RNA-3 was amplified by RT-PCR and sequenced. Nine different variants of the highly variable amino acid tetrad at positions 67-70 of p25 were identified, i.e. ACHG, AHHG, AYHG, ALHG, AFHR, AFHG, AHYG, VLHG and VHHG. These are more different tetrad variants than have been reported from any other country. The first three variants were found most commonly. In 23 out of the 288 BNYVV-positive samples, we detected P-type BNYVV that had previously been identified only in France, Kazakhstan and recently in the UK. Surprisingly, none of these samples contained the fifth RNA species usually associated with P-type BNYVV in other countries. As in other BNYVV P-type sources, the p25 amino acid tetrad in positions 67-70 of the Iranian P-type consists of SYHG.