Sugarcane mosaic virus (SCMV) is one of the most damaging viruses infecting sugarcane, maize and some other graminaceous species around the world. To investigate the genetic diversity of SCMV in Iran, the coat protein (CP) gene sequences of 23 SCMV isolates from different hosts were determined. The nucleotide sequence identity among Iranian isolates was more than 96%. They shared nucleotide identities of 75.5–99.9% with those of other SCMV isolates available in GenBank, the highest with the Egyptian isolate EGY7-1 (97.5–99.9%). The results of phylogenetic analysis suggested five divergent evolutionary lineages that did not completely reflect the geographical origin or host plant of the isolates. Population genetic analysis revealed greater between-group than within-group evolutionary divergence values, further supporting the results of the phylogenetic analysis. Our results indicated that natural selection might have contributed to the evolution of isolates belonging to the five identified SCMV groups, with infrequent genetic exchanges occurring between them. Phylogenetic analyses and the estimation of genetic distance indicated that Iranian isolates have low genetic diversity. No recombination was found in the CP cistron of Iranian isolates and the CP gene was under negative selection. These findings provide a comprehensive analysis of the population structure and driving forces for the evolution of SCMV with implications for global exchange of sugarcane germplasm. Gene flow, selection and somehow homologous recombination were found to be the important evolutionary factors shaping the genetic structure of SCMV populations.

To investigate the genetic diversity of potato virus M (PVM; genus Carlavirus, family Betaflexiviridae), the complete nucleotide sequence of the coat protein gene of 30 PVM isolates from a major potato-growing region in Iran were determined. Phylogenetic analysis of these Iranian PVM isolates together with those available in the GenBank database suggested two divergent evolutionary lineages that did not reflect the origin of the isolates, and these were designated as PVM-o and PVM-d. Examination of the genetic variability of the coat protein of Iranian isolates and their counterparts whose sequences are available in the Genbank database revealed 16 genotype groups in the PVM population. Analysis of the synonymous-tononsynonymous ratio showed strong purifying selection in the CP gene in the genotype groups of divergent clades.

For a better understanding of the functionality and pathogenicity of beet soil-borne virus (BSBV), full-length cDNA clones have been constructed for the three genomic RNAs. With the aim of assessing their effectiveness and relative contribution to the virus housekeeping functions, transcripts were inoculated on Chenopodium quinoa and Beta macrocarpa leaves using five genome combinations. Both RNAs-1 (putative replicase) and -3 (putative movement proteins) proved to be essential for virus replication in planta and symptom production on C. quinoa, whereas RNA-2 (putative coat protein, CP, and a read-through domain, RT) was not. No symptoms were recorded on B. macrocarpa, but viral RNAs were detected. In both host plants, the 19 kDa CP was detected by Western blotting as well as a 115 kDa protein corresponding to the CP-RT.Beet soil-borne virus (BSBV) is a pomovirus transmitted to Chenopodiaceae by the protist Polymyxa betae (Ivanović et al., 1983), which is also the vector of the aetiological agent of the rhizomania syndrome of sugar beet, beet necrotic yellow vein virus (BNYVV) (Tamada & Baba, 1973). Originally reported in Italy (Canova, 1959), rhizomania disease is now widespread in most countries where sugar beet is grown (McGrann et al., 2009) and BSBV is often found in beet infected with BNYVV (Meunier et al., 2003). However, the pathogenicity of BSBV and its contribution to the rhizomania syndrome remain unclear, with opinions still divided on this (Prillwitz & Schlösser, 1992;Kaufmann et al., 1993;Lindsten, 1993;Rush & Heidel, 1995).The BSBV genome consists of three single-stranded RNAs of positive polarity, packaged into rod-shaped particles (Koenig et al., 1996(Koenig et al., , 1997Koenig & Loss, 1997). RNA-1 (5.8 kb) encodes the putative viral replicase. The 19 kDa coat protein (CP) and a putative 85 kDa read-through (RT) domain are encoded by RNA-2 (3.5 kb). RNA-3 (3.0 kb) comprises three open reading frames (ORFs) encoding three putative proteins (48, 13 and 22 kDa) thought to be responsible for the viral cell-to-cell movement, resembling the well-known triple gene block proteins (TGBs) (Fig. 1).In this study, the contribution of each RNA component to virus survival and symptom expression was investigated through the use of full-length cDNA clones on two host plants, Chenopodium quinoa and Beta macrocarpa. This last plant species was preferred to the natural host Beta vulgaris with a view of developing the basis for further molecular analysis of viral systemicity, following the example of previous studies on BNYVV (Lauber et al., 1998).Full-length cDNA sequences were generated from an Iranian BSBV isolate (Nyshabour, Khorasan Razavi Province), which was trapped from infested soil in roots of B. vulgaris. After total RNA extraction from sugar beet roots using the SV total RNA isolation kit (Promega), the three genomic RNAs were reverse transcribed and amplified by PCR (RT-PCR) using expand reverse transcriptase and the expand long template PCR System (Roche). Primers matching the extremities of the t...

Sugarcane mosaic virus (SCMV) is the most prevalent virus causing sugarcane mosaic and maize dwarf mosaic diseases. Here, we presented the first two complete genomic sequences of Iranian SCMV isolates, NRA and ZRA from sugarcane and maize. The complete genome sequences of NRA and ZRA were, respectively, 9571 and 9572 nucleotides (nt) in length, excluding the 3'-terminal poly(A) tail. Both isolates contained a 5'-untranslated region (UTR) of 149 nt, an open reading frame of 9192 nt encoding a polyprotein of 3063 amino acids (aa), and 3'-UTR of 230 nt for NRA and 231 nt for ZRA. SCMV-NRA and -ZRA genome nucleotide sequences were 97.3 % identical and shared nt identities of 79.1-92 % with those of other 21 SCMV isolates available in the GenBank, highest with the isolate Bris-A (AJ278405) (92 and 91.7 %) from Australia. When compared for separate genes, most of their genes shared the highest identities with Australian and Argentinean isolates. Phylogenetic analysis of the complete genomic sequences reveals that SCMV can be clustered to three groups. Both NRA and ZRA were clustered with sugarcane isolates from Australia and Argentina in group III but formed a separate sublineage. Recombination analysis showed that both isolates were intraspecific recombinants, and represented two novel recombination patterns of SCMV (in the P1 coding region). NRA had six recombination sites within the P1, HC-Pro, CI, NIa-Vpg, and NIa-pro coding regions, while ZRA had four within the P1, HC-Pro, NIa-Pro, and NIb coding regions.