Cocksfoot Streak Virus Research Articles

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.

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.

Nucleotide bias of DCL and AGO in plant anti-virus gene silencing

Plant Dicer-like (DCL) and Argonaute (AGO) are the key enzymes involved in anti-virus post-transcriptional gene silencing (AV-PTGS). Here we show that AV-PTGS exhibited nucleotide preference by calculating a relative AV-PTGS efficiency on processing viral RNA substrates. In comparison with genome sequences of dicot-infecting Turnip mosaic virus (TuMV) and monocot-infecting Cocksfoot streak virus (CSV), viral-derived small interfering RNAs (vsiRNAs) displayed positive correlations between AV-PTGS efficiency and G+C content (GC%). Further investigations on nucleotide contents revealed that the vsiRNA populations had G-biases. This finding was further supported by our analyses of previously reported vsiRNA populations in diverse plant-virus associations, and AGO associated Arabidopsis endogenous siRNA populations, indicating that plant AGOs operated with G-preference. We further propose a hypothesis that AV-PTGS imposes selection pressure(s) on the evolution of plant viruses. This hypothesis was supported when potyvirus genomes were analysed for evidence of GC elimination, suggesting that plant virus evolution to have low GC% genomes would have a unique function, which is to reduce the host AV-PTGS attack during infections.

Detection of Cereal yellow dwarf virus using small interfering RNAs and enhanced infection rate with Cocksfoot streak virus in wild cocksfoot grass ( Dactylis glomerata)

Small RNA sequences were obtained from leaf extracts of wild Dactylis glomerata (cocksfoot grass) using deep sequencing (454 Life Sciences, Roche Diagnostics), and were screened against virus sequences in GenBank using a local BLASTn search program (BioEdit). Putative small interfering (si)RNAs complementary in sequence to Cereal yellow dwarf virus (CYDV, genus Luteovirus) genomes were identified. Primer sequences were made against the “high scoring” siRNA sequences and RT-PCR was used to amplify a 438 bp CYDV fragment in total RNA extracts from D. glomerata leaves. Sequencing of the RT-PCR product confirmed the occurrence of a previously undescribed CYDV population with phylogenetic affinity to CYDV-RPS. In D. glomerata the CYDV infection rates were 42.3% ( n = 78) in 2008 and 50.0% ( n = 48) in 2009. Specific RT-PCR tests also showed that this D. glomerata population harboured Cocksfoot streak virus (CSV, genus Potyvirus). Dual infections by these viruses were observed in 20.5–22.9% of all plants tested in 2008–2009. Interestingly, infections of either CYDV or CSV enhanced the occurrence of the other virus in individual grasses. Opportunities are discussed for using siRNA sequencing approaches in virus survey and other ecology studies under field conditions.

The complete sequence of the genome of Cocksfoot streak virus (CSV), a grass infecting Potyvirus.

The complete nucleotide sequence of Cocksfoot streak virus (CSV) has been determined. The viral genome comprises 9663 nucleotides, excluding a 3'-terminal poly(A) sequence. The genome of CSV has a 133 nt 5'-non coding and a 260 nt 3'-non coding region. The RNA of CSV encodes a single polyprotein of 3089 amino acid residues and has a deduced genome organization typical for a member of the family Potyviridae. CSV is transmissible by aphids and has a narrow host range in the Gramineae. It was compared to two potyviruses having monocotyledonous hosts (monocot potyviruses) and several potyviruses infecting dicotyledonous plants (dicot potyviruses). CSV is most closely related to other monocot potyviruses like Maize dwarf mosaic virus (MDMV) and Johnson grass mosaic virus (JGMV), but also closely related to the dicot potyviruses. On the other hand, CSV is less related to monocot viruses from the other genera (Rymovirus, Tritimovirus) within the Potyviridae. Specific motifs, described for potyviral polyproteins, are also present in the polyprotein of CSV. Only two motifs in the HC-Pro--motif involved in long distance movement and motif for HC-Pro self-interaction--were different in comparison to most of the dicot potyviruses.

Properties of cocksfoot streak and cocksfoot cryptic, two viruses infecting cocksfoot (Dactylis glomerate) in Scotland

SummaryA Scottish isolate of cocksfoot streak virus (CSV‐S) was found to have flexuous filamentous particles which, in sap of infected cocksfoot plants, had a modal length of 712 nm. It was transmitted from infected to healthy cocksfoot plants in a non‐persistent manner by Myzus persicae and by mechanical inoculation of infective sap extracts containing an anti‐oxidant. Apart from cocksfoot, mechanical inoculation of infective sap succeeded in infecting only four of 22 plant species tested. The infectivity of sap extracts containing 0.2% thioglycerol was lost after heating for 10 min at 55oC but not 50oC, storage at room temperature for 48 but not 24 hours, and after diluting 10‐2 to 10‐3. Highly purified preparations of CSV‐S particles sedimented as a single component with a sedimentation coefficient of 139S and had a buoyant density in rubidium bromide of 1.31 g/cm3. Virus particles were composed of one protein and one ssRNA species with estimated Mr of 31 000 and 3.2 times 106 respectively. In ELISA, an antiserum prepared to CSV‐S detected the virus in all aerial parts of infected cocksfoot plants and, when present in the ratio of 1 infected leaf: 1000 healthy leaves. Both CSV‐S‐infected and ‐uninfected cocksfoot also contained a previously undescribed virus with isometric particles c. 30 nm in diameter. This virus, named cocksfoot cryptic virus (CCV), was seed‐borne in two cvs of cocksfoot tested and its particles contained two dsRNA species of estimated Mt of 1.14 times 106 and 1.27 times 106. Despite the fact that particles of CSV‐S were largely free from CCV particles following exclusion chromatography on agarose beads prior to immunisation, immunoelectron microscopy (IEM) showed that the antiserum prepared to CSV‐S also contained some antibodies to CCV. Evidence from IEM suggested a possible distant serological relationship of CCV to ryegrass and beet (BCV 1 or BCV 2, or both) cryptoviruses, all members of sub‐group A of cryptoviruses.

Properties of cocksfoot streak and cocksfoot cryptic, two viruses infecting cocksfoot (Dactylis glomerata) in Scotland

SummaryA Scottish isolate of cocksfoot streak virus (CSV‐S) was found to have flexuous filamentous particles which, in sap of infected cocksfoot plants, had a modal length of 712 nm. It was transmitted from infected to healthy cocksfoot plants in a non‐persistent manner by Myzus persicae and by mechanical inoculation of infective sap extracts containing an anti‐oxidant. Apart from cocksfoot, mechanical inoculation of infective sap succeeded in infecting only four of 22 plant species tested. The infectivity of sap extracts containing 0.2% thioglycerol was lost after heating for 10 min at 55oC but not 50oC, storage at room temperature for 48 but not 24 hours, and after diluting 10‐2to 10‐3. Highly purified preparations of CSV‐S particles sedimented as a single component with a sedimentation coefficient of 139S and had a buoyant density in rubidium bromide of 1.31 g/cm3. Virus particles were composed of one protein and one ssRNA species with estimated Mr of 31 000 and 3.2 times 106respectively. In ELISA, an antiserum prepared to CSV‐S detected the virus in all aerial parts of infected cocksfoot plants and, when present in the ratio of 1 infected leaf: 1000 healthy leaves. Both CSV‐S‐infected and ‐uninfected cocksfoot also contained a previously undescribed virus with isometric particles c. 30 nm in diameter. This virus, named cocksfoot cryptic virus (CCV), was seed‐borne in two cvs of cocksfoot tested and its particles contained two dsRNA species of estimated Mr of 1.14 times 106and 1.27 times 106. Despite the fact that particles of CSV‐S were largely free from CCV particles following exclusion chromatography on agarose beads prior to immunisation, immunoelectron microscopy (IEM) showed that the antiserum prepared to CSV‐S also contained some antibodies to CCV. Evidence from IEM suggested a possible distant serological relationship of CCV to ryegrass and beet (BCV 1 or BCV 2, or both) cryptoviruses, all members of sub‐group A of crypto viruses.

The elimination of cocksfoot streak virus, cocksfoot mild mosaic virus and cocksfoot mottle virus from Dactylis glomerata by shoot tip and tiller bud culture

SUMMARYShoot tips from 0.2 to 4.8 mm long and tiller buds 0.2 to 5.1 mm long were cultured from cocksfoot (Dactylis glomerata) plants known to be infected with combinations of cocksfoot streak, cocksfoot mild mosaic and cocksfoot mottle viruses. Regenerated plants were tested for the presence of viruses by electron microscopy, serology and the expression of symptoms. All viruses were eliminated by culturing shoot tips and tiller buds less than 1.2 mm long but the maximum explant size capable of regenerating healthy plants depended upon the infecting virus. Viruses were not detected in shoot tip and tiller bud samples of similar size to the explants that gave healthy plants. The method is of value in eliminating viruses from desirable stocks of D. glomerata that must be vegetatively propagated.

Electron microscopy of cocksfoot streak virus and its differentiation from ryegrass mosaic virus in naturally infected Dactylis glomerata plants

SUMMARYThe length and rigidity of some cocksfoot streak virus (CSV) particles were greater (1) in ammonium molybdate negative stain at pH 5 than at pH 8 and (2) when magnesium was added either directly to extracted plant sap or indirectly via increased plant uptake. Most CSV particles were flexuous and 750–760 run long in low concentrations of magnesium but many were rigid and 800–810 nm long in higher concentrations. In sodium phosphotungstate and ammonium molybdate at pH 5, frequency distributions of particle lengths from cocksfoot plants infected with both CSV and ryegrass mosaic virus (RMV) produced two modal peaks, one at less than 700 nm (RMV) and the other at more than 750 nm (CSV); in ammonium molybdate at pH 8, however, only one peak (at 725 nm) was resolved.In ultrathin sections of CSV‐infected cocksfoot leaves, virus‐like particles were scattered or in bundles within the cytoplasm, or aligned in aggregates near the tonoplast. Some cells contained pinwheel inclusions, often with attached or associated laminar plates and occasionally with scroll‐like or circular tubes. These CSV‐induced inclusions were easily distinguished from those induced by RMV, even when both types occurred in the same cell.

THE SIGNIFICANCE OF VIRUS DISEASES FOR THE PRODUCTIVITY OF GRASSLAND

The effect of cocksfoot streak virus (CSV) on Dactylis glomerata L. and barley yellowdwarf virus (BYDV) on Lolium perenne L. was investigated under both single‐plant and simulated‐sward conditions. The effect of cocksfoot mottle (CFMV) was examined on single plants. CFMV was lethal, and in conditions of inter‐plant competition CSV was semi‐lethal and BYDV was non‐lethal. When the virus was lethal, a considerable lag‐phase was observed between mortality and complete compensation in yield. When the virus was non‐lethal, plant growth was restricted, either horizontally (CSV) or vertically (BYDV). In mixed, healthy and infected plant populations healthy individuals compensated only for reductions in lateral growth.CSV infection transformed plants of a pasture variety into ‘hay’ types and BYDV infection transformed plants of a hay variety into ‘pasture’ types. CSV increased the plant's aggressiveness in hay conditions, but reduced its ability to withstand frequent defoliation. Conversely, BYDV increased the plant's aggressiveness in pasture conditions, but reduced it in hay conditions. Compensation from healthy plants occurred only in CSV‐infected swards subjected to frequent defoliation. Some possible reasons for the absence of compensation in other treatments are discussed.

Effects of barley yellow dwarf virus on the growth and yield of single plants and simulated swards of perennial rye‐grass

SUMMARYIrish perennial rye‐grass plants infected with barley yellow dwarf virus (BYDV) showed inconspicuous leaf symptoms but were more stunted and yielded less total herbage, but more early spring herbage, than healthy plants. During a period of 2 years, infection did not decrease plant survival; infected plants produced more tillers and gave a higher ratio of vegetative to fertile tillers than healthy plants. BYDV caused a greater loss of yield in simulated rye‐grass swards cut twice a year than in those cut four times. Swards in which half the plants were infected gave yields intermediate between those of healthy and infected swards. Infected plants tended to dominate healthy ones in swards cut four times, but in those cut twice a year the initial status quo was maintained. In swards containing rye‐grass and white clover, the clover yielded more for most of the year when with BYDV‐infected than with healthy rye‐grass, but this trend was reversed in spring.The different effects of barley yellow dwarf virus on rye‐grass plants and of cocksfoot streak virus on cocksfoot seem reflected by the different effects of the viruses on the competition between infected grass, healthy grass and white clover plants, when these are grown in different combinations.

Influence of cocksfoot streak virus on the growth of single cocksfoot plants

SUMMARYHealthy and streak‐virus‐infected cocksfoot plants of a single genotype were examined over a 2‐year period. In the first year infection decreased tillering by about 40%, but in pot‐grown plants individual tiller weights were 30% higher so dry‐matter yield was decreased by only 10%. In the second year the larger tiller weights compensated completely for decreased tillering. No similar compensation was observed in field‐grown plants.The virus had the largest effects when soil fertility was highest, healthy plants producing significantly greater responses to nitrogen effects, but potassium, at certain times of the year, produced larger tiller weights in infected than in healthy plants. Infection decreased dry‐matter yield more in frequently than in infrequently cut plants.Infection greatly decreased the number of vegetative but not of fertile tillers. Infected plants tended to flower earlier and produced fewer, slightly smaller, viable seeds.

Influence of cocksfoot streak virus on the growth of cocksfoot swards

SUMMARYSmall experimental swards of three types‐healthy, 50% and 100% streak‐virus‐infected‐were established from single tillers of randomly selected cocksfoot genotypes. In these swards 44% of infected plants died within 2 years compared with 21% of healthy plants. Mortality of infected plants was not increased by the presence of healthy plants in the same sward. In swards containing both healthy and infected plants, increased growth of healthy plants compensated for the low yield of infected ones only when the swards were frequently defoliated. Infrequent cutting apparently allowed infected plants to check the growth of healthy ones, and 50% infected swards yielded little more than 100% infected swards. This difference in response was attributed to differences in the growth habits of healthy and infected plants. Few initially healthy plants became infected during 2 years of the experiment.