High-resolution mapping of the barley Ryd3 locus controlling tolerance to BYDV

Barley yellow dwarf disease (BYD) is transmitted by aphids and is caused by different strains of Barley yellow dwarf virus (BYDV) and Cereal yellow dwarf virus (CYDV). Economically it is one of the most important diseases of cereals worldwide. Besides chemical control of the vector, growing of tolerant/resistant cultivars is an effective way of protecting crops against BYD. The Ryd3 gene in barley (Hordeum vulgare L.) confers tolerance to BYDV-PAV and BYDV-MAV and the locus was previously mapped on the short arm of barley chromosome 6H near the centromere. We applied a strategy for high-resolution mapping and marker saturation at the Ryd3 locus by exploiting recent genomic tools available in barley. In a population of 3,210 F2 plants, 14 tightly linked markers were identified, including 10 that co-segregated with Ryd3. The centromeric region where Ryd3 is located suffers suppressed recombination or reduced recombination rate, suggesting potential problems in achieving (1) map-based cloning of Ryd3 and (2) marker selection of the resistance in breeding programmes without the introduction of undesirable traits via linkage drag.     

Cloning and Phylogenetic Analysis of Coat Protein of Barley yellow dwarf virus Isolates from Different Regions of Pakistan

Barley yellow dwarf virus (BYDVs) is an emerging threat for wheat and may seriously threaten its production, especially as climate change may result in increased infestation by aphids, the insect vectors of the virus. To assess the possibility of using pathogen‐derived resistance against the virus, the genetic diversity of BYDVs originating from different wheat‐growing areas of Pakistan where its incidence has been higher was investigated. Wheat samples with suspected symptoms of BYDVs were screened for the presence of Barley yellow dwarf and Cereal yellow dwarf viruses (B/CYDVs) subgroup 1 (Barley yellow dwarf virus‐PAV, BYDV‐MAV, BYDV‐SGV) and subgroup II (BYDV‐RPV, CYDV‐RPV, BYDV‐GPV) by PCR using basic multiplex oligonucleotides designed on coat protein (CP) of the virus. Of 37 samples tested, 13 were positive for BYDV subgroup I and only one sample was positive for BYDV subgroup II. Samples positive for subgroup I were further tested by PCR, and results showed that 10 samples were positive for BYDV‐PAV and three for BYDV‐MAV. DNA sequences of CP region of nine isolates (BYDV‐PAV) were determined and compared with available sequences in databases. Sequence analysis showed that three isolates (from Fatehjang, Nowshera and Attock districts) had maximum identity (92.8–94.6%) to BYDV‐PAS, and six isolates (from Peshawar, Islamabad Swabi and Faisalabad districts) had maximum identity (99.3–99.7%) to BYDV‐PAV. Thus BYDV‐PAV species may be dominant in northern wheat‐growing areas of Pakistan. The conserved nature of the BYDVs suggests that pathogen‐derived resistance strategies targeting the coat protein of the virus are likely to provide protection under field conditions.     

Virus Resistance in Cereals: Sources of Resistance, Genetics and Breeding

In cereals, soil-borne viruses transmitted by the plasmodiophorid Polymyxa graminis (e.g., Barley mild mosaic virus , Barley yellow mosaic virus or Soil-borne cereal mosaic virus ), have increased in importance due to the increase of the acreage infested and because yield losses cannot be prevented by chemical measures. Due to global warming, it is also expected that insect transmitted viruses vectored by aphids (e.g., Barley yellow dwarf virus , Cereal yellow dwarf virus ), leafhoppers ( Wheat dwarf virus ) or mites (e.g., Wheat streak mosaic virus ), will become much more important even in cooler regions. The environmentally most sound and also most cost effective approach to prevent high yield losses caused by these viruses is breeding for resistance. Therefore, in contrast to other reviews on cereal viruses, this study briefly reviews present knowledge on cereal-infecting viruses and emphasizes especially the sources of resistance or tolerance to these viruses and their use in molecular breeding schemes.     

Distribution of Cereal Luteoviruses and Molecular Diversity of BYDV‐PAV Isolates in Central and Southern Iran: Proposal of a New Species in the Genus Luteovirus

During a survey , 148 wheat, 70 barley and 24 wild grass samples of plants showing symptoms of yellowing or reddening of leaves and general stunting were collected in central and southern provinces of Iran and tested for Barley yellow dwarf virus (BYDV) and Cereal yellow dwarf virus (CYDV) infection by enzyme‐linked immunosorbent assay (ELISA) and tissue print immunoassay (TPIA). The results showed the presence of the viruses in most regions. Positive reactions to BYDV‐PAV, BYDV‐MAV, CYDV‐RPV and BYDV‐SGV antisera were recorded. BYDV‐PAV was the most prevalent virus. The genetic diversity of BYDV‐PAV isolates in central and southern provinces was studied by analysing ORF1 (903 nt) and read through domain (RTD) (575 nt) of 13 and nine isolates respectively. Sequence analysis of RTD at nucleotide and amino acid levels revealed a high identity (91.8–97.2% and 91.4–100% respectively) between Iranian and other available isolates in the GenBank. However, in regards to ORF1, a high genetic diversity among Iranian and other known PAV isolates at both amino acid (2–16.9%) and nucleotide (4.1–16.5%) levels were detected. Based on phylogenetic analysis of ORF1, two major groups of BYDV‐PAV isolates were distinguished. The Iranian isolates were divided between the two clusters. Our results suggest that the occurrence of two genetically distinct groups of PAV isolates in central and southern Iran, from which according to the ICTV criteria for species demarcation in the family Luteoviridae, four isolates from central parts of the country, qualify for designation as new species.     

Selective pressure, putative recombination events and evolutionary relationships among members of the family Closteroviridae: A proposal for a new classification

Molecular evolution of viruses is driven by both positive selection and recombination. In an effort to determine putative recombination events in the entire genome of members of the family Closteroviridae comprising 54 accessions retrieved from the international databases, a detail study was carried out by using RDP algorithm version 3.31β. Only isolates of Citrus tristeza virus and Grapevine leafroll-associated virus 3 were potential recombinants. None of members of Crinivirus genus was possible recombinant, but in turn, they were under positive selection that might be correlated with vector and/or host interactions. In contrast, Citrus tristeza virus isolates were under purifying selection as well as one-third of isolates of Grapevine leafroll-associated virus 3. The evolutionary history of all members of the Closteroviridae showed that they split into three distinct clusters corresponding to the three genera constituting this family. Moreover, the inferred phylogeny reshuffled the existing classification actually adopted by the International Committee on Taxonomy of Viruses. In this regard, each genus should be constituted by two distinct subgroups.     

Response of maize (Zea mays L.) lines carrying Wsm1, Wsm2, and Wsm3 to the potyviruses Johnsongrass mosaic virus and Sorghum mosaic virus

Maize dwarf mosaic disease is one of the most important viral diseases of maize (Zea mays L.) throughout the world. It is caused by several virus species in the family Potyviridae, genus Potyvirus, including Maize dwarf mosaic virus (MDMV), Sugarcane mosaic virus (SCMV), Johnsongrass mosaic virus (JGMV) and Sorghum mosaic virus (SrMV). Resistance to another member of the family Potyviridae, Wheat streak mosaic virus (WSMV), is conferred by three alleles (Wsm1, Wsm2, Wsm3) in the maize inbred line Pa405, and these or closely linked genes were previously shown to confer resistance to the potyviruses MDMV and SCMV. In this study, we assessed whether Wsm alleles are linked to resistance to JGMV and SrMV. Near isogenic lines (NILs) carrying one or two of the Wsm alleles introgressed into the susceptible line Oh28 and F1 progeny from NIL × Oh28 were tested for their response to JGMV and SrMV. Our results indicate that Wsm1 provides resistance to both JGMV and SrMV in a dose-dependent manner. Wsm2 and Wsm3 each provide limited resistance, and combining Wsm alleles enhances that resistance.     

Species composition of aphid vectors (Hemiptera: Aphididae) of barley yellow dwarf virus and cereal yellow dwarf virus in Alabama and western Florida

Yellow dwarf is a major disease problem of wheat, Triticum aestivum L., in Alabama and is estimated to cause yield loss of 21-42 bu/acre. The disease is caused by a complex of viruses comprising several virus species, including Barley yellow dwarf virus-PAV and Cereal yellow dwarf virus-RPV. Several other strains have not yet been classified into a specific species. The viruses are transmitted exclusively by aphids (Hemiptera:Aphididae). Between the 2005 and 2008 winter wheat seasons, aphids were surveyed in the beginning of each planting season in several wheat plots in Alabama and western Florida Collected aphids were identified and bioassayed for their yellow dwarf virus infectivity. This survey program was designed to identify the aphid species that serve as fall vectors of yellow dwarf virus into winter wheat plantings. From 2005 to 2008, bird cherry-oat aphid, Rhopalosiphum padi (L.); rice root aphid, Rhopalosiphum rufiabdominale (Sasaki); and greenbug, Schizaphis graminum (Rondani), were found consistently between October and December. The species of aphids and their timing of appearance in wheat plots were consistent with flight data collected in North Alabama between 1996 and 1999. Both R. padi and R. rufiabdominale were found to carry and transmit Barley yellow dwarf virus-PAV and Cereal yellow dwarf virus-RPV. The number of collected aphids and proportion of viruliferous aphids were low. Although this study has shown that both aphids are involved with introduction of yellow dwarf virus to winter wheat in Alabama and western Florida, no conclusions can be made as to which species may be the most important vector of yellow dwarf virus in the region.     

Molecular phylogeny of Phoma and allied anamorph genera: Towards a reclassification of the Phoma complex

The present generic concept of Phoma is broadly defined, with nine sections being recognised based on morphological characters. Teleomorph states of Phoma have been described in the genera Didymella, Leptosphaeria, Pleospora and Mycosphaerella, indicating that Phoma anamorphs represent a polyphyletic group. In an attempt to delineate generic boundaries, representative strains of the various Phoma sections and allied coelomycetous genera were included for study. Sequence data of the 18S nrDNA (SSU) and the 28S nrDNA (LSU) regions of 18 Phoma strains included were compared with those of representative strains of 39 allied anamorph genera, including Ascochyta, Coniothyrium, Deuterophoma, Microsphaeropsis, Pleurophoma, Pyrenochaeta, and 11 teleomorph genera. The type species of the Phoma sections Phoma, Phyllostictoides, Sclerophomella, Macrospora and Peyronellaea grouped in a subclade in the Pleosporales with the type species of Ascochyta and Microsphaeropsis. The new family Didymellaceae is proposed to accommodate these Phoma sections and related anamorph genera. The present study demonstrated that Phoma radicina, the type species of Phoma sect. Paraphoma and Phoma heteromorphospora, the type species of Phoma sect. Heterospora can be assigned to the Phaeosphaeriaceae and Leptosphaeriaceae respectively.     

Structure and development of the style base in Abildgaardia, Bulbostylis, and Fimbristylis (Cyperaceae,Cyperoideae, Abildgaardieae)

The Abildgaardieae tribe within the family Cyperaceae comprises six or seven genera, among which Abildgaardia, Bulbostylis and Fimbristylis pose a challenge regarding their morphological delimitation. Molecular phylogenetic analyses including species of Abildgaardieae are rare, but in most of those studies, Abildgaardia and Fimbristylis appear as more closely related to each other than to the Bulbostylis genus. Duration of the style base has been one of the most widely used characters for delimiting these three genera. The style base is a persistent structure in most species of Bulbostylis and deciduous in Abildgaardia and Fimbristylis. The reasons why the style base may persist or fall off have been scarcely discussed. The assumption that abscission layers are present in the style base of all three genera and the fact that tracheids have been observed in the style base of Bulbostylis suggest that this structure might have histological complexity. In view of this, a complete ontogenetic and anatomical study of the gynoecium has been carried out for all these three genera. It turned out that the style base is histologically simple in Abildgaardia, Bulbostylis and Fimbristylis and shows similar structure and development in all three genera. The fact that the style base has a shorter duration in Abildgaardia and Fimbristylis than in Bulbostylis might be related to the lower number of sclerotised cells that make up such structures in the mature fruit of the former two genera. Abscission of the style and style base may be the result of much simpler reasons than the differentiation of an abscission layer, resulting merely from mechanical shear force effects. Differences among genera have been observed in the shape of the style base and the development of the style. The histological simplicity of the style base is consistent with the homoplastic appearance of this structure in genera that are not closely related (e.g. Rhynchospora). Because of this, while the presence of the thickened style base seems to be a synapomorphy in species of Abildgaardieae, its persistence on or detachment from the fruit might have emerged repeatedly during this clade evolution and might not be a suitable character for genera delimitation.     

Evolutionary history of frogfishes (Teleostei: Lophiiformes: Antennariidae): a molecular approach

Fishes of the family Antennariidae (order Lophiiformes) are primarily shallow-water benthic forms found in nearly all tropical and subtropical oceans and seas of the world, with some taxa extending into temperate waters. Despite an earlier attempt based on morphology, no previous hypothesis of intergeneric relationships of the Antennariidae exists. To resolve phylogenetic relationships within the Antennariidae, and to test the validity of species groups within Antennarius, DNA sequences from the mitochondrial 16S and cytochrome oxidase c subunit 1 (COI) genes, and nuclear recombination activating gene 2 (RAG2), for 25 described and four undescribed antennariid species, representing 10 of 12 known genera and one undescribed genus, were unambiguously aligned and analyzed using Bayesian and maximum likelihood methods. The markers were partitioned and analyzed for substitution saturation and only the third codon position of COI (COI-3) was found to have reached saturation. However, analysis of both datasets, one with the saturated data and one without, differed only slightly. All molecular analyses recovered two major clades, one comprised of Fowlerichthys, Antennarius, Histrio, and Antennatus; and another containing Rhycherus, Antennariidae gen. et sp. nov., Kuiterichthys, Phyllophryne, Echinophryne, Tathicarpus, Lophiocharon, and Histiophryne. Evidence is presented to illustrate a correlation between phylogeny, geographic distribution, and reproductive life history. The results of these analyses provide the first hypothesis of evolutionary relationships within the Antennariidae.     

Pleomorphic configuration of the trimeric capsid proteins of Rice dwarf virus that allows formation of both the outer capsid and tubular crystals

In the double-shelled capsid of Phytoreovirus, the outer capsid attaches firmly to the 3-fold axes of the T = 1 core. It then forms a T = 13 lattice via lateral interactions among the P8 trimers (Wu et al., 2000, Virology 271, 18-25). Purified P8 molecules also assemble into hexagonal monolayers as well as tubular crystals. To explore the mechanisms of formation of these structures, the configurations of P8 trimers were compared and verified in particles of Rice dwarf virus and in tubular crystals (tubes) whose structure was determined by cryoelectron microscopy using helical reconstruction technique. Remarkable variations in intertrimer contacts were observed in the tubes and in the surface lattice of Rice dwarf virus capsid. Superposition of the atomic structure of P8 trimers in the structures analyzed by cryoelectron microscopy allowed us to identify groups of specific and stable interactions, some of which were preserved in the tubes and the quasi-equivalent T = 13 icosahedral lattice of the virion's shell. The flexible nature of the binding between P8 trimers, created via electrostatic interactions that hold radially inward, appears to allow the outer-capsid P8 trimers to envelop the ragged surface of the core, forming the double shell of an intact viral particle.     

Genomic characterization of a novel virus of the family tymoviridae isolated from mosquitoes

Background

The family Tymoviridae comprises three plant virus genera, including Tymovirus, Marafivirus, and Maculavirus, which are found in most parts of the world and cause severe agricultural losses. We describe a putatively novel member of the family Tymoviridae, which is isolated from mosquitoes (Culex spp.), referred to as CuTLV.

Methods and Results

The CuTLV was isolated by cell culture, which replicates and causes cytopathic effects in Aedes albopictus C6/36 cells, but not in mammalian BHK-21 or Vero cells. The complete 6471 nucleotide sequence of CuTLV was determined. The genome of CuTLV is predicted to contain three open reading frames (ORFs). The largest ORF1 is 5307 nucleotides (nt) in length and encodes a putative polypeptide of 1769 amino acids (aa), which contains the conserved motifs for the methyltransferase (MTR), Tymovirus endopeptidase (PRO), helicase (HEL), and RNA-dependent RNA polymerase (RdRp) of the replication-associated proteins (RPs) of positive-stranded RNA viruses. In contrast, the ORF1 sequence does not contain the so-called “tymobox” or “marafibox”, the conserved subgenomic RNA promoter present in all tymoviruses or marafiviruses, respectively. ORF2 and ORF3 putatively encode a 248-aa coat protein (CP) and a proline-rich 149-aa polypeptide. The whole genomic nucleotide identity of CuTLV with other members of family Tymoviridae ranged from 46.2% (ChiYMV) to 52.4% (GFkV). Phylogenetic analysis based on the putative RP and CP genes of CuTLV demonstrated that the virus is most closely related to viruses in the genus Maculavirus.

Conclusions

The CuTLV is a novel virus related to members of the family Tymoviridae, with molecular characters that are distinct from those of tymoviruses, marafiviruses, and other maculaviruses or macula-like viruses. This is the first report of the isolation of a Tymoviridae-like virus from mosquitoes. Further investigations are required to clarify the origin, replication strategy, and the public health or agricultural importance of the CuTLV.     

Genetic diversity and genetic relationships in Hyacinthaceae in India using RAPD and SRAP markers

Genetic diversity and relationship among three genera namely Drimia, Dipcadi and Ledebouria of Hyacinthaceae in India was studied using RAPD and SRAP markers. Twenty one RAPD primers and nine SRAP were used for analyzing 41 accessions. RAPD gave an average 12.6 markers per primer, while SRAP generated 10.1 markers per primer pair. The family emerged very diverged with high polymorphism. The study resolved the three genera into monophyletic groups corresponding to three subfamilies; Urginoideae, Hyacinthoideae and Ornithogaloideae. Drimia wightii emerged a very distinct species and species specific markers were obtained with both marker systems. AMOVA analysis also revealed the genera to be quite well diverged. The two markers showed high correlation (r = 0.932) in Mantel matrix crresspondance test. The combined data also showed a very good correlation with the respective markers individually.     

Phylogeny of Celastraceae tribe Euonymeae inferred from morphological characters and nuclear and plastid genes

The phylogeny of Celastraceae tribe Euonymeae (∼230 species in eight genera in both the Old and New Worlds) was inferred using morphological characters together with plastid (matK, trnL-F) and nuclear (ITS and 26S rDNA) genes. Tribe Euonymeae has been defined as those genera of Celastraceae with generally opposite leaves, isomerous carpels, loculicidally dehiscent capsules, and arillate seeds (except Microtropis). Euonymus is the most diverse (129 species) and widely cultivated genus in the tribe. We infer that tribe Euonymeae consists of at least six separate lineages within Celastraceae and that a revised natural classification of the family is needed. Microtropis and Quetzalia are inferred to be distinct sister groups that together are sister to Zinowiewia. The endangered Monimopetalum chinense is an isolated and early derived lineage of Celastraceae that represents an important component of phylogenetic diversity within the family. Hedraianthera is sister to Brassiantha, and we describe a second species (Brassiantha hedraiantheroides A.J. Ford) that represents the first reported occurrence of this genus in Australia. Euonymus globularis, from eastern Australia, is sister to Menepetalum, which is endemic to New Caledonia, and we erect a new genus (Dinghoua R.H. Archer) for it. The Madagascan species of Euonymus are sister to Pleurostylia and recognized as a distinct genus (Astrocassine ined.). Glyptopetalum, Torralbasia, and Xylonymus are all closely related to Euonymus sensu stricto and are questionably distinct from it. Current intrageneric classifications of Euonymus are not completely natural and require revision.     

Phylogenetic relationships among Southeast Asian climbing bamboos (Poaceae: Bambusoideae) and the Bambusa complex

A phylogenetic analysis of Bambusa and allies based on the plastid DNA non-coding regions rps16-trnQ, trnC-rpoB, trnH-psbA and trnD-T, and a partial nuclear GBSSI gene, was carried out. This included representatives from all four Bambusa subgenera (including type species), a group of segregate Southeast Asian genera distinctive by their climbing–scrambling culms (Dinochloa, Holttumochloa, Kinabaluchloa, Maclurochloa, Soejatmia, Sphaerobambos), and two other Bambusinae genera (Dendrocalamus, Gigantochloa). The results do not support the present subgeneric classification of Bambusa. The climbing Southeast Asian genera, all of which include species previously placed in Bambusa, are distinct from the “core Bambusa group” (type species and alliance) and the Bambusa complex generally.     

Phylogeny of the Rhizobium–Allorhizobium–Agrobacterium clade supports the delineation of Neorhizobium gen. nov.

The genera Agrobacterium, Allorhizobium, and Rhizobium belong to the family Rhizobiaceae. However, the placement of a phytopathogenic group of bacteria, the genus Agrobacterium, among the nitrogen-fixing bacteria and the unclear position of Rhizobium galegae have caused controversy in previous taxonomic studies. To resolve uncertainties in the taxonomy and nomenclature within this family, the phylogenetic relationships of generic members of Rhizobiaceae were studied, but with particular emphasis on the taxa included in Agrobacterium and the “R. galegae complex” (R. galegae and related taxa), using multilocus sequence analysis (MLSA) of six protein-coding housekeeping genes among 114 rhizobial and agrobacterial taxa. The results showed that R. galegae, R. vignae, R. huautlense, and R. alkalisoli formed a separate clade that clearly represented a new genus, for which the name Neorhizobium is proposed. Agrobacterium was shown to represent a separate cluster of mainly pathogenic taxa of the family Rhizobiaceae. A. vitis grouped with Allorhizobium, distinct from Agrobacterium, and should be reclassified as Allorhizobium vitis, whereas Rhizobium rhizogenes was considered to be the proper name for former Agrobacterium rhizogenes. This phylogenetic study further indicated that the taxonomic status of several taxa could be resolved by the creation of more novel genera.