Sugarcane Mosaic Virus Isolates Research Articles

Genetic diversity and molecular evolution of sugarcane mosaic virus, comparing whole genome and coat protein sequence phylogenies

Sugarcane mosaic virus (SCMV) is a widely distributed potyvirus that causes mosaic disease in sugarcane, maize, sorghum, canna, and other monocot species worldwide. This study used 139 SCMV full-length genome sequences to analyze the phylogenetic relatedness of geographically distinct isolates. The phylogenetic analysis revealed four major groups of SCMV isolates that relate to their primary host. The geographic locations for some isolates appear to be mismatched within the tree, suggesting either that convergent molecular evolution has occurred or that the tree reconstruction produces statistically significant incongruences that create uncertainty in the true evolutionary relationships of these virus isolates. Recombination analysis showed hot spots across most of the genome except in the coat protein (CP) coding region. We examined 161 SCMV CP sequences from the GenBank database, including sequences from samples collected in Pakistan, a region that has not been included in prior phylogenetic studies. These data suggest that the SCMV isolates from sugarcane (Saccharum officinarum) predate isolates from all other hosts, regardless of their geographic origins.

Eight Species of Poaceae Are Hosting Different Genetic and Pathogenic Strains of Sugarcane Mosaic Virus in the Everglades Agricultural Area.

Sugarcane mosaic virus (SCMV) was detected by reverse transcription polymerase chain reaction in eight different species of the Poaceae family in the Everglades Agricultural Area (EAA) of south Florida: broadleaf signalgrass (Urochloa platyphylla), Columbus grass (Sorghum almum), goosegrass (Eleusine indica), maize (Zea mays), sorghum (Sorghum bicolor), St. Augustine grass (Stenotaphrum secundatum), southern crabgrass (Digitaria ciliaris), and sugarcane (Saccharum interspecific hybrids). Based on their coat protein (CP) gene sequence, 62 isolates of SCMV from Florida and 29 worldwide isolates representing the known genetic diversity of this virus were distributed into eight major phylogenetic groups. SCMV isolates infecting Columbus grass, maize, and sorghum in Florida formed a unique group, whereas virus isolates infecting sugarcane in the United States (Florida and Louisiana) clustered with isolates from other countries. Based on the entire genome coding region, SCMV isolates infecting sugarcane in Florida were closest to virus isolates infecting sorghum species or St. Augustine grass. Virus isolates from Columbus grass, St. Augustine grass, and sugarcane showed different virulence patterns after mechanical inoculation of Columbus grass, St. Augustine grass, and sugarcane plants, thus proving that these isolates were different pathogenic strains. Sugarcane was symptomless and tested negative for SCMV by tissue blot immunoassay after inoculation with crude sap from SCMV-infected Columbus grass, indicating that Columbus grass was not a reservoir for SCMV infecting sugarcane in the EAA. Close CP sequence identity between isolates of SCMV from Columbus grass, maize, and sorghum suggested that the same virus strain was naturally spreading between these three plants in south Florida.

Presence of Potyvirus in the Norte de Santander department and molecular characterization of NIb protein in Colombian SCMV isolates

Potyviruses are the largest genus of plant viruses that cause significant losses over a wide range of crops. In this paper, the presence of potyvirus in different plant crops in the provinces of Ocaña and Pamplona located in the north and south of the Department of Norte de Santander (Colombia) was evaluated with RT-PCR analysis using universal oligonucleotides specific to the region that encodes the NIB protein. The results indicate the presence of several potyvirus in Pamplona in economically important crops such as corn (Zea mays), tomato (Solanum lycopersicum), potato (Solanum tuberosum) and zucchini (Cucurbita pepo). In Ocaña, potyvirus was found in bean (Phaseolus vulgaris), corn and pumpkin (Cucurbita maxima). In corn, one of the most important crops, the presence of the Sugarcane mosaic virus (SCMV) was confirmed with nucleotide sequencing. This is the first report of this virus in the department. The presence of several potyviruses in different crops in Norte de Santander indicate an alarming phytosanitary condition that must be addressed with priority to establish detection and control systems that maximize production, ensure agricultural sustainability, and propose certification schemes and improvement programs to reduce economic losses.

Sugarcane mosaic virus infects Stenotaphrum secundatum in Australia

This study presents the first report of sugarcane mosaic virus (SCMV) infecting Stenotaphrum secundatum (buffalo grass) in Australia, from a turf farm in the Hunter Valley, New South Wales. The plant displayed mosaic symptoms and contained flexuous, filamentous virions of 700–750 × 10–11 nm typical of members of the genus Potyvirus. Infection of the sample by SCMV was confirmed by double antibody sandwich ELISA and RT-PCR amplification of the coat protein coding region of the viral genome. In a phylogenetic analysis, the buffalo grass isolate was sister to a clade of maize-infecting isolates of SCMV from eastern Africa and was 75.8% and 79.4% identical to the exemplar isolate of SCMV at nucleotide and amino acid levels, respectively.

Screening for sugarcane yellow leaf virus in sorghum in Florida revealed its occurrence in mixed infections with sugarcane mosaic virus and a new marafivirus

Sugarcane yellow leaf virus (SCYLV) is an aphid-transmitted virus for which Melanaphis sacchari is the main vector. Almost all sugarcane varieties grown in Florida are susceptible to SCYLV infection. In this study, we investigated the prevalence of SCYLV in accessions of Sorghum bicolor which is another natural host of this virus. Two field experiments, one in 2016 with 19 sorghum lines and the other in 2017 with 15 lines, were established at Belle Glade, FL. Stalks collected randomly in planted and ratoon crops were tested by tissue-blot immunoassay (TBIA) and reverse transcription-polymerase chain reaction (RT-PCR). Over the two-year period, 366 of 423 S. bicolor samples tested positive by TBIA but SCYLV was detected by RT-PCR in only 12 of 161 randomly selected subsamples. Full genome sequences of SCYLV, sugarcane mosaic virus (SCMV) and a new marafivirus were obtained by high-throughput sequencing (HTS) from three TBIA positive sorghum samples. HTS data for all three viruses were confirmed by RT-PCR. The SCMV isolates from S. bicolor appeared to be a new strain of this virus species. Positive reaction of S. bicolor by TBIA using SCYLV antibodies could not be systematically associated with plant infection by SCYLV or another virus. This suggested the occurrence of a non-specific serological reaction with an unknown S. bicolor antigen. SCMV and the new marafivirus were also detected in Sorghum almum, suggesting that this weed is a reservoir for S. bicolor-infecting viruses in Florida.

Molecular characterization of viruses causing maize lethal necrosis disease in South-Rift region, Kenya

The first report of Maize lethal necrosis (MLN) disease in Africa was in Bomet, Kenya, nine years ago. It has since spread in East and Central African (ECA) countries, causing massive yield losses. Currently, 90% of the preferred commercial maize germplasm grown by farmers in Kenya is susceptible to MLN disease. As such, the disease has continued to pose a serious challenge to food security in the ECA region. This study sought to characterize the MLN, causing viruses present in the maize leaf samples collected from the South-Rift region. Using total RNA extracted from 60 leaf samples collected from Bomet, Kericho, and Kisumu Counties, reverse transcription-polymerase chain reaction (RT-PCR) was carried out. The PCR products with the strongest bands were purified and sequenced using the Sanger sequencing technique. The results showed that samples from the three counties were positive for maize chlorotic mottle virus (MCMV) (MH645622 and MH645621) and sugarcane mosaic virus (SCMV) (MH645623, MH645624 and MH645625) and negative to wheat streak mosaic virus (WSMV). The coat protein (CP) sequences of MCMV isolates were closely related to the sequences of MCMV isolates, which had been previously reported from Eastern and Sub-Saharan Africa. For the CP sequences of SCMV isolates, only one sequence of the isolate KCO59 was similar to the sequence of a Kenyan isolate (JX286708). Sequences of isolates KCO5 and KCO24 were not identical to those of the Kenyan isolate (JX286708). Based on these results, in the surveyed counties, isolates of SCMV are genetically diverse, while those of MCMV are not. There exists a new variant of SCMV, which appears to be the main potyvirus in synergism with MCMV in causing MLN disease in Kenya. Key words: Maize lethal necrosis (MLN), maize chlorotic mottle virus (MCMV), sugarcane mosaic virus (SCMV), wheat streak mosaic virus (WSMV).

Status and Epidemiology of Maize Lethal Necrotic Disease in Northern Tanzania.

Sustainable control of plant diseases requires a good understanding of the epidemiological aspects such as the biology of the causal pathogens. In the current study, we used RT-PCR and Next Generation Sequencing (NGS) to contribute to the characterization of maize lethal necrotic (MLN) viruses and to identify other possible viruses that could represent a future threat in maize production in Tanzania. RT-PCR screening for Maize Chlorotic Mottle Virus (MCMV) detected the virus in the majority (97%) of the samples (n = 223). Analysis of a subset (n = 48) of the samples using NGS-Illumina Miseq detected MCMV and Sugarcane Mosaic Virus (SCMV) at a co-infection of 62%. The analysis further detected Maize streak virus with an 8% incidence in samples where MCMV and SCMV were also detected. In addition, signatures of Maize dwarf mosaic virus, Sorghum mosaic virus, Maize yellow dwarf virus-RMV and Barley yellow dwarf virus were detected with low coverage. Phylogenetic analysis of the viral coat protein showed that isolates of MCMV and SCMV were similar to those previously reported in East Africa and Hebei, China. Besides characterization, we used farmers’ interviews and direct field observations to give insights into MLN status in different agro-ecological zones (AEZs) in Kilimanjaro, Mayara, and Arusha. Through the survey, we showed that the prevalence of MLN differed across regions (P = 0.0012) and villages (P < 0.0001) but not across AEZs (P > 0.05). The study shows changing MLN dynamics in Tanzania and emphasizes the need for regional scientists to utilize farmers’ awareness in managing the disease.

Extensive recombination challenges the utility of Sugarcane mosaic virus phylogeny and strain typing

Sugarcane mosaic virus (SCMV) is distributed worldwide and infects three major crops: sugarcane, maize, and sorghum. The impact of SCMV is increased by its interaction with Maize chlorotic mottle virus which causes the synergistic maize disease maize lethal necrosis. Here, we characterised maize lethal necrosis-infected maize from multiple sites in East Africa, and found that SCMV was present in all thirty samples. This distribution pattern indicates that SCMV is a major partner virus in the East African maize lethal necrosis outbreak. Consistent with previous studies, our SCMV isolates were highly variable with several statistically supported recombination hot- and cold-spots across the SCMV genome. The recombination events generate conflicting phylogenetic signals from different fragments of the SCMV genome, so it is not appropriate to group SCMV genomes by simple similarity.

Characterization of a highly divergent Sugarcane mosaic virus from Canna indica L. by deep sequencing

BackgroundCannas are popular ornamental plants and widely planted for the beautiful foliage and flower. Viral disease is a major threaten to canna horticulture industry. In the city of Beijing, mosaic disease in canna was frequently observed, but the associated causal agent and its biological characterization is still unknown.ResultsAfter small RNA deep sequencing, 36,776 contigs were assembled and 16 of them shared high sequence identities with the different proteins of Sugarcane mosaic virus (SCMV) of the size ranging from 86 to 1911 nt. The complete genome of SCMV isolate (canna) was reconstructed by sequencing all cDNA clones obtained from RT-PCR and 5′\\3′ RACE amplifications. SCMV-canna isolate showed to have a full RNA genome of 9579 nt in length and to share 78% nt and 85% aa sequence identities with SCMV isolates from other hosts. The phylogenetic tree constructed based on the full genome sequence of SCMV isolates allocated separately the canna-isolate in a distinct clade, indicating a new strain. Recombination analyses demonstrated that SCMV-canna isolate was a recombinant originating from a sugarcane-infecting isolate (major parent, acc. no. AJ310103) and a maize-infecting isolate (minor parent, acc. no. AJ297628). Pathogenicity test showed SCMV-canna could cause typical symptoms of mosaic and necrosis in some tested plants with varying levels of severity but was less virulent than the isolate SCMV-BJ. Field survey showed that the virus was widely distributed.ConclusionsThis study identified SCMV as the major agent causing the prevalent mosaic symptom in canna plants in Beijing and its genomic and biological characterizations were further explored. All these data enriched the knowledge of the viruses infecting canna and would be helpful in effective disease management in canna.

A sugarcane mosaic virusvector for gene expression in maize.

Zea mays L. ssp. mays (maize) is an important crop plant as well as model system for genetics and plant biology. The ability to select among different virus‐based platforms for transient gene silencing or protein expression experiments is expected to facilitate studies of gene function in maize and complement experiments with stable transgenes. Here, we describe the development of a sugarcane mosaic virus (SCMV) vector for the purpose of protein expression in maize. An infectious SCMV cDNA clone was constructed, and heterologous genetic elements were placed between the protein 1 (P1) and helper component‐proteinase (HC‐Pro) cistrons in the SCMV genome. Recombinant SCMV clones engineered to express green fluorescent protein (GFP), β‐glucuronidase (GUS), or bialaphos resistance (BAR) protein were introduced into sweet corn (Golden × Bantam) plants. Documentation of developmental time courses spanning maize growth from seedling to tasseling showed that the SCMV genome tolerates insertion of foreign sequences of at least 1,809 nucleotides at the P1/HC‐Pro junction. Analysis of insert stability showed that the integrity of GFP and BAR coding sequences was maintained longer than that of the much larger GUS coding sequence. The SCMV isolate from which the expression vector is derived is able to infect several important maize inbred lines, suggesting that this SCMV vector has potential to be a valuable tool for gene functional analysis in a broad range of experimentally important maize genotypes.

First Report of Sugarcane Mosaic Virus on Pumpkin Plants Exhibiting Mosaic and Mottling Symptoms in China

Sugarcane mosaic virus (SCMV) is responsible for economic losses in sorghum, maize, and sugarcane worldwide. Only some monocot plants are natural hosts of SCMV. In July 2017, mosaic symptoms such as irregular chlorosis and mottling were observed in the leaves of pumpkin (Cucurbita moschata) plants at Fujian Agriculture and Forestry University, Fuzhou, Fujian Province. Seven pumpkin plants with typical mosaic symptoms were tested by double antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) using antibodies for cucumber mosaic virus (Agdia, Elkhart, IN) and squash mosaic virus (Agdia), respectively. However, neither of these two pathogens was detected. Because the sugarcane plants growing near pumpkin plants had been confirmed to be infected by SCMV isolate FZC1 (Deng et al. 2016), we presumed that the mosaic symptoms on pumpkin plants were owing to SCMV infection. Using the SCMV-specific antibodies (Agdia), the ELISA assays showed that six of the seven pumpkin plants were infected by SCMV. To identify the strains of SCMV infecting the pumpkin plants, total RNA was extracted from leaves of all six pumpkin plants and two sugarcane plants infected by SCMV from the neighboring field using a TransZol Up Plus RNA Kit (Transgen, Beijing, China). The cDNA synthesis was performed using M4T primer (5′-GTTTTCCCAGTCACGAC[T]₁₅-3′) (Chen et al. 2001) by reverse transcription. Subsequently, polymerase chain reaction was performed using an SCMV-specific primer (SCMV7-F, 5′-ATTTATGGAGGAGTGGGAGC-3′) and M4 primer (5′-GTTTTCCCAGTCACGAC-3′) (Deng et al. 2016) with the amplification program as follows: 94°C for 4 min, followed by 35 cycles of 94°C for 30 s, 55°C for 30 s, and 72°C 2 min, with a final extra 7 min at 72°C. The expected 1,925-bp amplicons were produced from all eight samples. The amplicons were cloned into a pMD19-T Vector System (Takara, Dalian, China) and sequenced. The sequences of the two amplicons from sugarcane plants were identical to the corresponding fragment of SCMV isolate FZC1. The sequences of the six amplicons from pumpkin plants were identical and were subjected to BLASTn search in GenBank. The results showed that the query sequence (GenBank: MK680822) had the highest nucleotide similarity, 95.97%, and the highest amino acid identity of 99.04% with SCMV isolate FZC1 (GenBank: KR108212) Phylogenetic analysis based on the SCMV coat protein showed that the pumpkin SCMV isolate was clustered into the same subgroup with FZC1. We prepared inoculum by homogenizing approximately 1 g of symptomatic leaves of SCMV-infected sugarcane plants grown in the vicinity of pumpkins in 3 ml of 0.01 M phosphate buffer (pH 7.0). Then healthy pumpkin plants (cv. BeiBei) were mechanically inoculated with the inoculum and cultured in the greenhouse under the following conditions: photoperiod 14-h light/10-h dark, light intensity 600 μmol/m²/s, temperature regime 30°C day/25°C night. Three weeks later, 7 out of 10 inoculated pumpkin plants developed mosaic symptoms, and the DAS-ELISA assays confirmed presence of SCMV in symptomatic pumpkin leaves. To our knowledge, this is the first report of SCMV infection of pumpkins and disease symptoms of this virus on a dicotyledonous plant. These findings will benefit the epidemiology and management of SCMV in China.

Phylogenetic analysis and signature of recombination hotspots in sugarcane mosaic virus infecting sugarcane in India

Sugarcane mosaic virus (SCMV) one of the causative viruses of mosaic disease in sugarcane occurs in sugarcane growing countries worldwide. India is the second largest sugarcane producing country and genome of SCMV from India has not been characterized so far. Hence detailed studies were carried out to characterize the virus isolates based on its complete genome. Comparative genome analyses of five new isolates were performed with previously reported SCMV full genome sequences of isolates infecting sugarcane, maize, sorghum and Canna. Sequence identity matrix and phylogenetic analyses clearly represented that Indian isolates are closely related to sugarcane infecting isolates reported from Australia, Argentina, China and Iran and they diverged as a separate subgroup from other reported maize infecting isolates from Mexico, China, Ohio, Spain, Germany, Iran, Ethiopia, Kenya and Eucador. Selection pressure analysis clearly depicted the predomination of strong purifying selection throughout the viral genome, and strongest in CI and HC-Pro gene. Evidence for few positively selected sites was identified in all the cistrons except in 6 K1 and Nib rep. Among the genomic region, CI gene has exhibited comparatively more recombination hotspots followed by HC-Pro unlike other reported isolates. As the cultivation of sugarcane first originated in India, our results from the recombination events strongly suggest that Indian SCMV populations contribute for the emergence of upcoming new recombinant SCMV isolates not only within the sugarcane isolates but also with maize infecting isolates of SCMV in other countries irrespective of geographic origin and host type.

Prevalence and Genome Characterization of Field Isolates of Sugarcane Mosaic Virus (SCMV) in Nigeria.

Maize and sugarcane are two economically important crops often grown in adjacent fields or co-cultivated in the northern guinea savannah agroecological zone, a major cereal production region of Nigeria. This study was conducted to determine the prevalence of mosaic disease in sugarcane and maize fields in the northern guinea savannah agroecological zone and to molecularly characterize the associated sugarcane mosaic virus (SCMV, genus Potyvirus) isolates. Surveys were conducted from June to July 2015, and sugarcane mosaic disease (SCMD) incidence was assessed across 21 farmer's fields. Mean SCMD incidence varied across states with ∼82% (308/376), ∼66% (143/218), and ∼67% (36/54) recorded in Kaduna, Kano, and Katsina states, respectively. RT-PCR analysis of 415 field-collected samples using genus-specific primers confirmed potyvirus infection in 63.7% (156/245) of sugarcane, 29.7% (42/141) of maize crops, and 45% (13/29) of itch grass samples. Cloning and sequencing of gene-specific DNA amplicons from a subset of 45 samples (sugarcane = 33, maize = 9, itch grass = 3) confirmed their specificities to SCMV. Phylogenetic analysis of the partial gene sequences showed that they all belong to a single monophyletic clade of SCMV. These results were supported by analysis of complete polyprotein sequences of representative maize and sugarcane isolates from Nigeria. Both isolates shared 94.9%/97.3% complete polyprotein nucleotide (nt)/amino acid (aa) identities with each other and 75.2%/97.6% nt/aa identities with corresponding sequences of global SCMV isolates. The detection of identical populations of SCMV isolates in both crop species and a weed host suggests possible vector mediated interspecies spread within cereal landscapes in the study area with implications for the integrated and sustainable management of SCMD in cereal cropping systems in Nigeria.

Hubei poty-like virus 1 is likely an interspecies recombinant of sugarcane mosaic virus and putative bean yellow mosaic virus.

In 2016, Shi et al. (Nature 540:539-543. https://doi.org/10.1038/nature20167 2016) reported Hubei poty-like virus 1 (HuPLV1) to be a new member of the family Potyviridae. At that time, its polyprotein shared the highest sequence identity (80%) with sugarcane mosaic virus (SCMV). A year later, two isolates of SCMV from Canna sp. whose sequences were submitted to the GenBank database showed 91% identity to the HuPLV1 polyprotein sequence. Based on the species demarcation criteria forthe family Potyviridae, HuPLV1 should possibly be considered an isolate of SCMV. To resolve this taxonomical inconsistency, we carried out a phylogenetic and recombination analysis and found that HuPLV1 is an interspecies recombinant of SCMV and bean yellow mosaic virus (BYMV).

English

Experiments were conducted in season 2014B at Naivasha maize lethal necrosis screening facility to evaluate Tanzanian maize germplasms for resistance to maize lethal necrosis (MLN). One hundred and fifty-two maize landraces and 33 inbreed lines were artificially inoculated with maize chlorotic mottle virus and sugarcane mosaic virus isolates in two trials arranged in a completely randomized design (CRD) and two replications. Inocula for both virus isolates were prepared, combined and applied to the trials by a 12 L backpack mist blower 4 and 5 weeks after planting. Disease incidence was assessed based on a 1 to 5 MLN rating scale 14, 28, 42 and 72 days post inoculation (dpi) for landraces and 7, 14, 21 and 52 dpi for inbred lines. Significant phenotypic variations (P 0.05) were detected on inbreed lines as all materials were susceptible to MLN with scores ranging from 4.5 to 5 except for resistant check CML494 (mean score of 3.75). In this study, five maize landraces were identified as tolerant candidates against MLN. The identified landraces should be subjected to further MLN testing to explore their potential in breeding for MLN resistance. Key words: Zea mays, maize chlorotic mottle virus, sugarcane mosaic virus, maize lethal necrosis, maize landraces.

Detección del Virus del mosaico de la caña de azúcar (SCMV) en Saccharum spp. en México y origen filogenético de un aislado de Jalisco

&lt;p&gt;El &lt;em&gt;Virus de mosaico de la caña de azúcar&lt;/em&gt; (SCMV) es uno de los principales agentes virales que infectan a caña de azúcar (&lt;em&gt;Saccharum &lt;/em&gt;spp.). En México la detección del SCMV se ha basado en sintomatología típica de la enfermedad, por lo que la información no es concluyente, además hay poca información sobre su origen filogenético. El objetivo del trabajo fue detectar mediante RTPCR La presencia y distribución del SCMV en las zonas cañeras de los estados de Colima, Jalisco y Nayarit, México y determinar el origen filogenético de un aislado de Jalisco. Los resultados obtenidos demuestran la amplia distribución del SCMV en la región cañera del Pacífico de México. De las 242 muestras analizadas se detectó al virus en 33 de ellas, lo que corresponde a un 13.63%. Las variedades Mex 69-290 y CP 72-2086 fueron las que presentaron los síntomas de mosaico más severos. El análisis filogenético con la secuencia parcial HC-Pro del SCMV aislado de Jalisco (JalMex-126) sugiere una estrecha relación con aislados de la India, Australia, China y Argentina, por lo que probablemente compartan un origen genético común y se hayan dispersado a través de germoplasma de caña de azúcar infectado.&lt;/p&gt;

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.

Molecular Variability and Distribution of Sugarcane Mosaic Virus in Shanxi, China.

BackgroundSugarcane mosaic virus (SCMV) is responsible for large-scale economic losses in the global production of sugarcane, maize, sorghum, and some other graminaceous species. To understand the evolutionary mechanism of SCMV populations, this virus was studied in Shanxi, China. A total of 86 maize leaf samples (41 samples in 2012 and 45 samples in 2013) were collected from 4 regions of Shanxi.ResultsDouble-antibody sandwich (DAS)-ELISA and RT-PCR showed 59 samples (30 samples in 2012 and 29 samples in 2013) to be positive for SCMV, from which 10 new isolates of SCMV were isolated and sequenced. The complete genomes of these isolates are 9610 nt long, including the 5′ and 3′ non-coding regions, and encode a 3063-amino acid polyprotein. Phylogenetic analyses revealed that 24 SCMV isolates could be divided on the basis of the whole genome into 2 divergent evolutionary groups, which were associated with the host species. Among the populations, 15 potential recombination events were identified. The selection pressure on the genes of these SCMV isolates was also calculated. The results confirmed that all the genes were under negative selection.ConclusionsNegative selection and recombination appear to be important evolutionary factors shaping the genetic structure of these SCMV isolates. SCMV is distributed widely in China and exists as numerous strains with distinct genetic diversity. Our findings will provide a foundation for evaluating the epidemiological characteristics of SCMV in China and will be useful in designing long-term, sustainable management strategies for SCMV.

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.

First Report of a Potyvirus Infecting Albuca rautanenii in the Namib Desert.

Chlorotic, streak-like symptoms were observed in April 2013 on a single specimen of Albuca rautanenii (Schinz) J.C.Manning & Goldblatt (Family: Hyacinthaceae) found among other plants near Homeb in the Namib Desert, Namibia. No potential insect vectors (e.g., aphids) were observed on or around the infected plant. An extract from symptomatic leaves was assessed by transmission electron microscopy (leaf dip method) to ascertain if the symptoms were viral in origin. Long, flexuous threadlike particles 687 to 825 nm in length and 12.5 nm in diameter were observed. The morphology and size of the particles were indicative of a putative member of the taxonomic family Potyviridae. To confirm this, RT-PCR using universal potyvirus primers which amplify part of the nuclear inclusion b gene (NIb) was conducted (1) on total RNA extracted from leaf tissue (Qiagen RNeasy Plant Mini Kit). The triplicated reaction yielded amplicons of the expected size (~350 bp), which were cloned into the pJET 1.2 vector (Thermo Scientific, Waltham, MA) according to manufacturer's instructions. The sequences of 10 clones were trimmed to remove vector and primer ends and were deposited in the EBI database under the accession numbers LK995422 to LK995431. Curated sequences were used to search the GenBank database using BLASTn and tBLASTx, as well as for phylogenetic analysis. Intra-clonal nucleotide sequence similarity ranged from 97.99 to 99.72%. BLASTn searches showed all clones were 72% identical to Papaya ringspot virus isolate 1 accession JQ314105.1 (87% coverage), followed by Bean yellow mosaic virus clone Brn167 accession JF707769.1 (72% identity with 86% sequence coverage). The translated peptide fragment was most similar to Sugarcane mosaic virus isolate Beijing (AY042184.1), with a query cover of 98% and a similarity of 81%. Phylogenetic analysis was performed with a set of 57 reference potyvirus genomes, with their NIb regions aligned with the cloned nucleotide sequences according to the parameters used previously (1). The clones formed a distinct cluster, at a node with Cocksfoot streak virus (CSV) (NC_003742.1). An identity matrix of the aligned NIb clones and CSV showed a nucleotide identity range of 68.79 to 70.23%. These results suggest that the virus isolate belongs to the family Potyviridae, genus Potyvirus, supported by the characteristic morphological features of the virion and its relatedness to CSV. Moreover, the clustering of all sequences at a single node suggests a homogeneous viral population, without significant strain variation. Genetic distance inferred by phylogenetic analysis further suggests that the isolate is a novel species within the genus, which we tentatively name Albuca mosaic virus, AlbMV. To our knowledge, this is the first report of any plant virus infection in the native Namib Desert ecosystem. This is particularly relevant due to the scarcity and uniqueness of plant life in this hyperarid desert environment, and additional monitoring of this virus infection and other desert plant species is encouraged. Reference: (1) L. Zheng et al. Plant Pathol. 59:211, 2010.