Assessment of the phenotypic and genotypic diversity of endophytic strains of Bacillus and closely related genera from Carpinus betulus in the Hyrcanian forests of Iran.

BACKGROUND: Identification and characterization of the endophytic microorganism, is gaining their underestimated significance in influencing health, performance, and other biological attributions of plants in general and forest tree species in particular. Because of the scarcity of information on the endophytic microbiome of the Hyrcanian forests species, including hornbeam (Carpinus betulus L.) trees, as a major constituent thereof, the present study aimed at the identification and partial characterization of the endophytic Bacillus species of Carpinus betulus as the first step in this context. METHODS AND RESULTS: Shoot samples were collected from the Hyrcanian forest locations of Mazandaran and Golestan provinces in Iran. Bacterial strains were isolated from the surface-disinfected shoot segments and subjected to phenotypic characterization. Following assessment of the genetic diversity of the isolates by BOX-PCR fingerprinting, the representative isolates of each of the 15 groups were used for further characterization. Analysis of the nucleotide sequences of the 16S rDNA and HSP60 gene of the isolates led to the identification of 10 species. The predominant species was B. cereus followed by B. subtilis. The other species encountered were B. thuringiensis, Priestia filamentosa, B. velezensis, B. mojavensis, B. amyloliquefaciens, B. safensis, P. aryabhattai, and Gottfriedia acidiceleris. Most isolates possessed characteristics which could contribute to the biocontrol potential of the isolates, including formation of biofilm, production of hydrogen cyanide, tolerant to relatively high concentration of sodium chloride, and antibacterial activity. CONCLUSIONS: Ten Bacillus species were identified as the prevailing endophytic species of C. betulus in the Hyrcanian forest of northern Iran, most turned up to possess biological activities involved in biocontrol capability of the isolates against some plant pathogens. These potentially capable bacteria could be implemented in the promotion of plant growth as well as in the biological control of pathogens. This is the first report on the characterization and elucidation of the diversity of the potentially beneficial endophytic species of Bacillus and the closely related genera living in the internal tissues of hornbeam trees.

Iranian johnsongrass mosaic virus: the complete genome sequence, molecular and biological characterization, and comparison of coat protein gene sequences.

Iranian johnsongrass mosaic virus (IJMV) is one of the most prevalent viruses causing maize mosaic disease in Iran. An IJMV isolate, Maz-Bah, was obtained from the maize showing mosaic symptoms in Mazandaran, north of Iran. The complete genomic sequence of Maz-Bah is 9544 nucleotides, excluding the poly(A) tail. It contains one single open reading frame of 9165 nucleotides and encodes a large polyprotein of 3054 amino acids, flanked by a 5'-untranslated region (UTR) of 143 nucleotides and a 3'-UTR of 236 nucleotides. The entire genomic sequence of Maz-Bah isolate shares identities of 84.9 and 94.2 % with the IJMV (Shz) isolate, the lone complete genome sequence available in the GenBank at the nucleotide (nt) and deduced amino acid (aa) levels, respectively. The whole genome sequences share identities of 51.5-69.8 and 44.9-74.3 % with those of other Sugarcane mosaic virus (SCMV) subgroup potyviruses at nt and aa levels, respectively. In phylogenetic trees based on the multiple alignments of the entire nt and aa sequences, IJMV isolates formed a separate sublineage of the tree with potyviruses infecting monocotyledons of cereals, indicating that IJMV is a member of SCMV subgroup of potyviruses. IJMV is most closely related to Sorghum mosaic virus and Maize dwarf mosaic virus and less closely related to the Johnsongrass mosaic virus and Cocksfoot streak virus. To further investigate the genetic relationship of IJMV, 9 other isolates from different hosts were cloned and sequenced. The identity of IJMV CP nt and aa sequences of 11 Iranian isolates ranged from 86.4 to 99.8 % and 90.5 to 99.7 %, respectively, indicating a high nt variability in CP gene. Furthermore, in the CP-based phylogenetic tree, IJMV isolates were clustered together with a maize potyvirus described as Zea mosaic virus from Israel (with 86-89 % nt identity), indicating that both isolates probably are the strains of the same virus.

The complete genome sequences of two naturally occurring recombinant isolates of Sugarcane mosaic virus from Iran.

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.

Genetic structure and molecular variability of potato virus M 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.

Application of High-Throughput Sequencing for Comprehensive Virome Profiling in Grapevines Shows Yellows in Iran.

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.

Diversity of beet curly top Iran virus isolated from different hosts in Iran.

Beet curly top Iran virus (BCTIV) is a major pathogen of sugar beet in Iran. In order to study diversity of BCTIV, we sampled 68 plants in Iran during the summer of 2010 with curly top disease symptoms on beans (Phaseolus vulgaris), cowpeas (Vigna unguiculata), tomatoes (Solanum lycopersicum L.), sea beets (Beta vulgaris subsp. maritima), and sugar beets (Beta vulgaris). Plant samples showing leaf curling, yellowing, and/or swelling of veins on the lower leaf surfaces were collected from various fields in Khorasan Razavi, Northern Khorasan (north-eastern Iran), East Azarbayejan, West Azarbayejan (north-western Iran), and Fars (southern Iran) provinces. Using rolling circle amplification coupled with restriction digests, cloning, and Sanger sequencing, we determined the genomes of nine new BCTIV isolates from bean, cowpea, tomato, sea beet, and sugar beet in Iran. Our analysis reveals ~11 % diversity amongst BCTIV isolates and we detect evidence of recombination within these genomes.

First report of Turnip mosaic virus infecting saffron in Iran.

Saffron (Crocus sativus) is widely used as an important herbal medicine crop worldwide. Iran is the largest producer and exporter of saffron in the world. Turnip mosaic virus (TuMV) is a species of the genus Potyvirus, which infects a wide range of plants species. During the autumn of 2019, saffron plants with symptoms including colour breaking of the flowers, chlorosis and mild mosaic of leaves were collected from the major saffron cultivation areas of Iran. After the isolation of total RNA from diseased samples, RT-PCR was done using TuMV-specific primers. Amplicons of two selected isolates were purified, cloned, and sequenced. BLASTn of obtained sequences indicated high similarity with TuMV sequences. To the best of our knowledge, this is the first finding of TuMV infection in the saffron plant of Iran.

Whole-Genome Characterization of Alfalfa Mosaic Virus Obtained from Metagenomic Analysis of Vinca minor and Wisteria sinensis in Iran: with Implications for the Genetic Structure of the Virus.

Alfalfa mosaic virus (AMV), an economically important pathogen, is present worldwide with a very wide host range. This work reports for the first time the infection of Vinca minor and Wisteria sinensis with AMV using RNA sequencing and reverse transcription polymerase chain reaction confirmation. De novo assembly and annotating of contigs revealed that RNA1, RNA2, and RNA3 genomic fragments consist of 3,690, 2,636, and 2,057 nucleotides (nt) for IR-VM and 3,690, 2,594, and 2,057 nt for IR-WS. RNA1 and RNA3 segments of IR-VM and IR-WS closely resembled those of the Chinese isolate HZ, with 99.23-99.26% and 98.04-98.09% nt identity, respectively. Their RNA2 resembled that of Canadian isolate CaM and American isolate OH-2-2017, with 97.96-98.07% nt identity. The P2 gene revealed more nucleotide diversity compared with other genes. Genes in the AMV genome were under dominant negative selection during evolution, and the P1 and coat protein (CP) proteins were subject to the strongest and weakest purifying selection, respectively. In the population genetic analysis based on the CP gene sequences, all 107 AMV isolates fell into two main clades (A, B) and isolates of clade A were further divided into three groups with significant subpopulation differentiation. The results indicated moderate genetic variation within and no clear geographic or genetic structure between the studied populations, implying moderate gene flow can play an important role in differentiation and distribution of genetic diversity among populations. Several factors have shaped the genetic structure and diversity of AMV: selection, recombination/reassortment, gene flow, and random processes such as founder effects.

Molecular characterization of two highly divergent Iranian johnsongrass mosaic virus isolates from Zea mays.

Iranian johnsongrass mosaic virus (IJMV, genus Potyvirus, family Potyviridae) is one of the most prevalent viruses causing maize mosaic disease in Iran. In this study, the complete genomes (9,618 and 9,543 nucleotides) of two highly divergent IJMV isolates (Maz2 and Maz3) were obtained from the metagenomic analysis of Zea mays RNAs using Illumina sequencing. The genome contained a single open reading frame (9,165 nucleotides) encoding a polyprotein of 3,054 amino acids, flanked by a 5'-untranslated region (UTR) of 216 and 143 nucleotides and a 3'-UTR of 237 and 235 nucleotides. A comparative analysis of the complete genome showed that IJMV-Maz2 and Maz3 had 85.99% nucleotide and 94.56% amino acid sequence identity with each other and shared 84.87-88.74% nt and 94.24-96.17% aa identity with those of two other IJMV isolates available in the GenBank. The coat protein of Maz2 and Maz3 showed 86.40-95.72% nt sequence identity (90.79-97.70% aa identity) to 12 other IJMV isolates available in GenBank. Our results indicated a relatively stable and conserved genomic composition with a low codon usage bias in all of the assayed IJMV coding sequences. Analysis of various population genetics parameters and distribution of synonymous and nonsynonymous mutations revealed that purifying selection pressure was the major force acting upon the IJMV genome. The outcome of the study provides valuable insights on the evolution of IJMV genome, for which there are few genome sequences available, and informs the current breeding efforts towards resistance for IJMV.

Complete Genomic Characterization of Two Beet Soil-Borne Virus Isolates from Turkey: Implications of Comparative Analysis of Genome Sequences.

Sugar beet (Beta vulgaris L.) is known as a key product for agriculture in several countries across the world. Beet soil-borne virus (BSBV) triggers substantial economic damages to sugar beet by reducing the quantity of the yield and quality of the beet sugars. We conducted the present study to report the complete genome sequences of two BSBV isolates in Turkey for the first time. The genome organization was identical to those previously established BSBV isolates. The tripartite genome of BSBV-TR1 and -TR3 comprised a 5,835-nucleotide (nt) RNA1, a 3,454-nt RNA2, and a 3,005-nt RNA3 segment. According to sequence identity analyses, Turkish isolates were most closely related to the BSBV isolate reported from Iran (97.83-98.77% nt identity). The BSBV isolates worldwide (n = 9) were phylogenetically classified into five (RNA-coat protein read through gene [CPRT], TGB1, and TGB2 segments), four (RNA-rep), or three (TGB3) lineages. In genetic analysis, the TGB3 revealed more genetic variability (Pi = 0.034) compared with other regions. Population selection analysis revealed that most of the codons were generally under negative selection or neutral evolution in the BSBV isolates studied. However, positive selection was detected at codon 135 in the TGB1, which could be an adaptation in order to facilitate the movement and overcome the host plant resistance genes. We expect that the information on genome properties and genetic variability of BSBV, particularly in TGB3, TGB1, and CPRT genes, assist in developing effective control measures in order to prevent severe losses and make amendments in management strategies.

Analysis of the molecular and biological variability of Zucchini yellow mosaic virus isolates from Iran and Iraq.

During the growing season of 2018, several field-grown cucurbit plants in different parts of Iraq and Iran were surveyed for the presence of zucchini yellow mosaic virus (ZYMV), using two degenerate primer pairs (CIF/Rev and NIb2F/3R) targeting the two separated partial regions of the potyvirus genome (CI and NIb respectively). 7 out of 20 samples were confirmed to be infected with ZYMV. Phylogenetic analyses based on the CI gene grouped all Iranian and two Iraqi (ZYMV1 and ZYMV2) isolates together with isolates from the Middle East in the subgroup (AI), whereas the other Iraqi (ZYMV3 and ZYMV4) isolates were clustered in the subgroup (DI), which was only consisted of American isolates. The highest and lowest identity between the studied isolates and the GenBank isolates showed that the two genes (CI, NIb) of each isolate particularly the Iraqi isolates were more similar to a specific and geographically scattered mosaic of worldwide isolates, suggestive of mixed infection might have occurred between different worldwide isolates in Iraq. Furthermore, the first complete nucleotide sequence of an Iraqi ZYMV (ZYMV-Iq) isolate was done, using the Illumina sequencing technique. The complete nucleotide sequence of ZYMV-Iq isolate was 9650 nt, excluding the 3'poly (A) tail. ZYMV-Iq isolate shared the highest nt identity of 98.8% with an American (KC665630) isolate. Phylogenetic analysis based on the full genome sequence placed ZYMV-Iq in subgroup A of group I alongside 18 isolates from the US and two isolates from Australia. In addition, recombination analysis detected lone significant recombination between ZYMV-Iq and South Korean (AY279000) isolate. Moreover, the results showed that symptom intensity was varied across experimental host plants.

Identification of garlic-infecting leek yellow stripe virus through deep-sequencing analyses from Iran.

In the study presented here, the first complete genome sequence of Leek yellow stripe virus (LYSV) designated as isolate LYSV-AE65 from Southwest of Iran, was reported. The small RNA deep sequencing analysis showed that, the Iranian isolate has a full RNA genome of 10,142 nucleotide in length (Except for poly (A) tail) and it was shared 77.91-92.16% nucleotide (nt) and 83.62-96.35% amino acid (aa) sequences identities with other known LYSV isolates. The coat protein (CP) region showed 80.21-95.24% nucleotide identity to those of other isolates, while high degrees of nucleotide sequence identity with G77-LYSV isolate (MN059504) from China. Phylogenetic analysis based on full genome sequence of LYSV-AE65, showed the closest relationship with LYSV isolates from China, Australia, Spain and Mexico. Also, phylogenetic analysis of the 5´-untranslated region (UTR)-P1 gene sequences of 44 isolates, confirmed the formation of two main groups, N-type and S-type, in agreement with the previous studies. Isolate LYSV-AE65 was similar to the members of clade S and has two large deletions in P1 gene. Recombination analysis demonstrated that LYSV-AE65 was a recombinant with most part of its genome was derived from already reported LYSV isolates infecting allium species. To the best of our knowledge, this is the first report of complete genome sequencing of LYSV isolate infecting garlic through small RNA deep sequencing method in Iran. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at (10.1007/s13337-021-00733-z).

Whole genome characterization of wisteria vein mosaic virus from Iran and its relationship to other members of bean common mosaic virus group.

To date, the complete genome of two wisteria vein mosaic virus (WVMV) has been sequenced worldwide. Here, the genomic sequence of WVMV isolated from Wisteria sinensis in Iran was determined for the first time, using deep RNA sequencing and RT-PCR followed by Sanger sequencing. The sequence was 9694 nucleotides in length; excluding the 3'-poly(A) tail and contained a single open reading frame of 9279 nucleotides encoding a large polyprotein of 3092 amino acids and predicted molecular weight of 35,368 KDa. The genome contained nine putative proteolytic cleavage sites and motifs conserved in homologous proteins of other potyviruses. Sequence analysis suggested that WVMV-Ir sequence shared 76.37-86.01% nucleotide (nt) identity and 82.45-91.91% amino acid (aa) identity with two other isolates (Beijing and JEBU-p) available in the GenBank, the highest with the Chinese isolate Beijing (86.01% nt identity, 91.91% aa identity). Sequence identities over most of the genome were within the range 80-86% and 85-95% at the nt and aa levels, respectively; however, high variability was observed in the 5'-UTR (51.62%), P1 (62.03% nt identity, 50.78% aa identity) and P3 (79.82%nt identity, 78.67% aa identity) regions, suggesting that Ir, Beijing, and JEBU-p are three different strains. These variabilities may be due to different mutation phenomena of a common ancestor virus or mutations caused by different selection pressures in different agro-ecological regions. The results of the phylogenetic analysis indicated that WVMV was most closely related to soybean mosaic virus and watermelon mosaic virus and less closely related to the zantedeschia mild mosaic virus and dasheen mosaic virus. In the greenhouse, WVMV-Ir caused severe symptoms in Phaseolus vulgaris, Vicia faba, W. sinensis, Chenopodium quinoa, C. amaranticolor, and Nicotiana benthamiana. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-021-02957-8.

A full-length infectious clone of beet soil-borne virus indicates the dispensability of the RNA-2 for virus survival in planta and symptom expression on Chenopodium quinoa leaves.

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.

Genetic diversity and biological characterization of sugarcane streak mosaic virus isolates from Iran.

Sugarcane streak mosaic virus (SCSMV; genus Poacevirus, family Potyviridae) is a major causal agent of sugarcane mosaic disease in Asia. A survey of SCSMV was conducted in cultivated fields in Khuzestan province, southwestern Iran. Sixty-five sugarcane leaf samples showing mosaic symptoms were collected and investigated by RT-PCR. Almost one-fourth of the samples were found to be infected by SCSMV. To verify molecular variability, 12 SCSMV isolates were sequenced and analyzed by comparing partial NIb-CP gene sequences. The nucleotide identity among Iranian isolates was 83.1-99.8%, indicating high nucleotide variability, while amino acid identity was 95.2-100%, which suggesting selection for amino acid conservation. They shared nucleotide identities of 76.2-99.1% with those of other SCSMV isolates available in GenBank, the highest with isolates from Pakistan (PAK), India (IND671) and China (M117, KT257289). Further analysis was conducted based on complete CI coding region to gain more insight into the phylogenetic relationships of Iranian SCSMV compared to those from other Asian countries. Iranian isolates shared identities of 79.8-89.0% (nucleotide) and 94.8-98.6% (amino acid) with those from other geographical regions in the CI gene. The highest nucleotide identity of Iranian isolates was with isolates PAK (Pakistan), M121 (JQ975096, China) and IND671 (India), respectively. The phylogenetic trees (based on CI and NIb-CP) revealed the segregation of SCSMV isolates into two major divergent evolutionary lineages that reflect geographical origin of the isolates (with minor exception). Phylogenetic analyses grouped Iranian SCSMV isolates together with isolates from Pakistan, India and just one Chinese isolate in group II. Biological results showed that Iranian SCSMV isolates infect sugarcane, sorghum, maize and some wild grasses, causing mosaic symptoms on the leaves.

Occurrence and Evolutionary Analysis of Coat Protein Gene Sequences of Iranian Isolates of Sugarcane mosaic virus.

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.

Nucleotide sequence analyses of coat protein gene of peanut stunt virus isolates from alfalfa and different hosts show a new tentative subgroup from Iran.

Alfalfa cultivars grown in 14 provinces in Iran were surveyed for the relative incidence of peanut stunt virus (PSV) during 2013-2016. PSV were detected in 41.89% of symptomatic alfalfa samples and a few alternate hosts by plate-trapped antigen ELISA. Among other hosts tested only Chenopodium album, Robinia pseudoacacia and Arachis hypogaea were found naturally infected with PSV. Twenty five isolates of PSV were chosen for biological and molecular characterizations based on their geographical distributions. There was not any differences in experimental host range of these isolates; however, variation in systemic symptoms observed on Nicotiana glutinosa. Total RNA from 25 of viral isolates were subjected to reverse transcription polymerase chain reaction analysis using primers directed against coat protein (CP) gene. The CP genes of 25 Iranian PSV isolates were either 651 or 666 nucleotides long. The nucleotide and amino acid identities for CP gene among Iranian PSV isolates were 79.3-99.7 and 72-100%, respectively. They also shared between 67.4 and 82.4% pairwise nucleotide identity with other PSV isolates reported elsewhere in the world. Phylogenetic analyses of CP gene sequences showed formation of a new subgroup comprising only the Iranian isolates. Natural infection of a few alternate hosts with PSV is reported for the first time from Iran.

Molecular variability in the cysteine rich protein of potato virus M.

The potato virus M (PVM), belonging to the genus Carlavirus, is a worldwide endemic pathogen in potato fields. p11 is an 11-16 kDa protein encoded by the last open reading frame of PVM which contains cysteine rich proteins (CRPs) motif. CRPs have been identified as suppressors of gene silencing. In this study the p11 gene from 28 PVM isolates, including 16 new isolates from Iran, were used to determine the global genetic structure of PVM populations. Pairwise nucleotide sequence identity scores showed that global PVM CRP sequence similarity was between 69.3 and 100 %. This genetic diversity divided the 28 isolates into two main divergent phylogenetic clades. The rate of genetic diversity and non-synonymous to synonymous mutations (dN/dS) were significantly different between these two clades. Analysis showed that PVM CP is under significant negative selection pressure with the global ω value of 0.260.