Complete nucleotide sequence of sugarcane streak Monogeminivirus

Incidence, Geographical Distribution, and Genetic Diversity of Sugarcane Striate Virus in Saccharum Species in China

A novel virus of the genus Mastrevirus, family Geminivirdae, has been reported in sugarcane germplasm collections in Florida, Guadeloupe, and Réunion, and was named sugarcane striate virus (SStrV). Although the full-length sequence of an SStrV isolate from China was obtained in 2015, the incidence, geographical distribution, and genetic diversity of this virus remained unclear. A single leaf sample from 2,368 sugarcane plants from main sugarcane-producing regions of China and germplasm collections were tested for SStrV by PCR. Average virus incidence was 25.1% for field-collected samples, and SStrV was detected in most Saccharum species and two sugarcane-related species, with the highest incidence in Saccharum officinarum (44.1%) followed by Saccharum spp. local varieties (33.3%) grown for chewing cane for a long time. The virus incidence was much lower (6.8%) in modern commercial cultivars (Saccharum spp. hybrids). Phylogenetic trees based on full-length genomes of 157 SStrV isolates revealed that Chinese isolates comprised strains A and B, but not C and D, that were reported in Florida, U.S.A. SStrV strain A was the most prominent (98.7%) and widespread strain in China and was further divided into eight subgroups. Almost half (45.6%) of the SStrV-positive samples from S. officinarum and Saccharum spp. local varieties were coinfected with sugarcane mosaic disease viruses or sugarcane yellow leaf virus. Interestingly, most of the plants infected by strain A of SStrV were asymptomatic. SStrV appears to be widespread in China, and its influence on chewing cane deserves further investigation.

Occurrence of a novel mastrevirus in sugarcane germplasm collections in Florida, Guadeloupe and Réunion

BACKGROUND

In Africa and Asia, sugarcane is the host of at least seven different virus species in the genus Mastrevirus of the family Geminiviridae. However, with the exception of Sugarcane white streak virus in Barbados, no other sugarcane-infecting mastrevirus has been reported in the New World. Conservation and exchange of sugarcane germplasm using stalk cuttings facilitates the spread of sugarcane-infecting viruses.

METHODS

A virion-associated nucleic acids (VANA)-based metagenomics approach was used to detect mastrevirus sequences in 717 sugarcane samples from Florida (USA), Guadeloupe (French West Indies), and Réunion (Mascarene Islands). Contig assembly was performed using CAP3 and sequence searches using BLASTn and BLASTx. Mastrevirus full genomes were enriched from total DNA by rolling circle amplification, cloned and sequenced. Nucleotide and amino acid sequence identities were determined using SDT v1.2. Phylogenetic analyses were conducted using MEGA6 and PHYML3.

RESULTS

We identified a new sugarcane-infecting mastrevirus in six plants sampled from germplasm collections in Florida and Guadeloupe. Full genome sequences were determined and analyzed for three virus isolates from Florida, and three from Guadeloupe. These six genomes share >88% genome-wide pairwise identity with one another and between 89 and 97% identity with a recently identified mastrevirus (KR150789) from a sugarcane plant sampled in China. Sequences similar to these were also identified in sugarcane plants in Réunion.

CONCLUSIONS

As these virus isolates share <64% genome-wide identity with all other known mastreviruses, we propose classifying them within a new mastrevirus species named Sugarcane striate virus. This is the first report of sugarcane striate virus (SCStV) in the Western Hemisphere, a virus that most likely originated in Asia. The distribution, vector, and impact of SCStV on sugarcane production remains to be determined.

Molecular diversity, geographic distribution and host range of monocot-infecting mastreviruses in Africa and surrounding islands

Maize streak virus (MSV), an important pathogen of maize in Africa, is the most extensively studied member of the Mastrevirus genus in the family Geminiviridae. Comparatively little is known about other monocot-infecting African mastreviruses, most of which infect uncultivated grasses. Here we determine the complete sequences of 134 full African mastrevirus genomes from predominantly uncultivated Poaceae species. Based on established taxonomic guidelines for the genus Mastrevirus, these genomes could be classified as belonging to the species Maize streak virus, Eragrostis minor streak virus, Maize streak Reunion virus, Panicum streak virus, Sugarcane streak Reunion virus and Sugarcane streak virus. Together with all other publicly available African monocot-infecting mastreviruses, the 134 new isolates extend the known geographical distributions of many of these species, including MSV which we found infecting Digitaria sp. on the island of Grand Canaria: the first definitive discovery of any African monocot-infecting mastreviruses north-west of the Saharan desert. These new isolates also extend the known host ranges of both African mastrevirus species and the strains within these. Most notable was the discovery of MSV-C isolates infecting maize which suggests that this MSV strain, which had previously only ever been found infecting uncultivated species, may be in the process of becoming adapted to this important staple crop.

Geminivirus protein structure and function

Geminiviruses are a family of plant viruses that cause economically important plant diseases worldwide. These viruses have circular single-stranded DNA genomes and four to eight genes that are expressed from both strands of the double-stranded DNA replicative intermediate. The transcription of these genes occurs under the control of two bidirectional promoters and one monodirectional promoter. The viral proteins function to facilitate virus replication, virus movement, the assembly of virus-specific nucleoprotein particles, vector transmission and to counteract plant host defence responses. Recent research findings have provided new insights into the structure and function of these proteins and have identified numerous host interacting partners. Most of the viral proteins have been shown to be multifunctional, participating in multiple events during the infection cycle and have, indeed, evolved coordinated interactions with host proteins to ensure a successful infection. Here, an up-to-date review of viral protein structure and function is presented, and some areas requiring further research are identified.

Comparative analysis of Panicum streak virus and Maize streak virus diversity, recombination patterns and phylogeography

Background

Panicum streak virus (PanSV; Family Geminiviridae; Genus Mastrevirus) is a close relative of Maize streak virus (MSV), the most serious viral threat to maize production in Africa. PanSV and MSV have the same leafhopper vector species, largely overlapping natural host ranges and similar geographical distributions across Africa and its associated Indian Ocean Islands. Unlike MSV, however, PanSV has no known economic relevance.

Results

Here we report on 16 new PanSV full genome sequences sampled throughout Africa and use these together with others in public databases to reveal that PanSV and MSV populations in general share very similar patterns of genetic exchange and geographically structured diversity. A potentially important difference between the species, however, is that the movement of MSV strains throughout Africa is apparently less constrained than that of PanSV strains. Interestingly the MSV-A strain which causes maize streak disease is apparently the most mobile of all the PanSV and MSV strains investigated.

Conclusion

We therefore hypothesize that the generally increased mobility of MSV relative to other closely related species such as PanSV, may have been an important evolutionary step in the eventual emergence of MSV-A as a serious agricultural pathogen.

The GenBank accession numbers for the sequences reported in this paper are GQ415386-GQ415401

Recombination, decreased host specificity and increased mobility may have driven the emergence of maize streak virus as an agricultural pathogen

Maize streak virus (MSV; family Geminiviridae, genus Mastrevirus), the causal agent of maize streak disease, ranks amongst the most serious biological threats to food security in subSaharan Africa. Although five distinct MSV strains have been currently described, only one of these - MSV-A - causes severe disease in maize. Due primarily to their not being an obvious threat to agriculture, very little is known about the 'grass-adapted' MSV strains, MSV-B, -C, -D and -E. Since comparing the genetic diversities, geographical distributions and natural host ranges of MSV-A with the other MSV strains could provide valuable information on the epidemiology, evolution and emergence of MSV-A, we carried out a phylogeographical analysis of MSVs found in uncultivated indigenous African grasses. Amongst the 83 new MSV genomes presented here, we report the discovery of six new MSV strains (MSV-F to -K). The non-random recombination breakpoint distributions detectable with these and other available mastrevirus sequences partially mirror those seen in begomoviruses, implying that the forces shaping these breakpoint patterns have been largely conserved since the earliest geminivirus ancestors. We present evidence that the ancestor of all MSV-A variants was the recombinant progeny of ancestral MSV-B and MSV-G/-F variants. While it remains unknown whether recombination influenced the emergence of MSV-A in maize, our discovery that MSV-A variants may both move between and become established in different regions of Africa with greater ease, and infect more grass species than other MSV strains, goes some way towards explaining why MSV-A is such a successful maize pathogen.

The complete genome sequence for a Turkish isolate of Wheat dwarf virus (WDV) from barley confirms the presence of two distinct WDV strains

The complete genome for a barley isolate of Wheat dwarf virus (WDV) from Tekirdağ, Turkey, WDV-Bar[TR], was isolated and sequenced. The genome was found to be 2739 nucleotides long, which is shorter than wheat-infecting WDV isolates, and with a genome organization typical for mastreviruses. The complete genome of WDV-Bar[TR] showed 83-84% nucleotide identity to wheat isolates of WDV, with the non-coding regions SIR and LIR least conserved (72-74% identity). The deduced amino acid sequences for Rep and RepA were most conserved (92-93%), while CP and MP were less conserved (87% and 79-80%, respectively). The identity to other mastrevirus species was significantly lower. In phylogenetic analyses, the WDV isolates formed a distinct clade, well separated from the other mastreviruses with the wheat isolates grouping closely together. Phylogenetic analyses of WDV-Bar[TR], the partial sequence for another Turkish barley isolate (WDV-Bar[TR2]) and published WDV sequences further supported the division of WDV into two distinct strains. The barley strain could also be divided into three subtypes based on relationships and geographic origin. This study shows the first complete published sequence for a barley isolate of WDV.

Biological and Genomic Sequence Characterization of Maize streak virus Isolates from Wheat

ABSTRACT Maize streak virus (MSV) is best known as the causal agent of maize streak disease. However, only a genetically uniform subset of the viruses within this diverse species is actually capable of producing severe symptoms in maize. Whereas these "maize-type" viruses all share greater than 95% sequence identity, MSV strains isolated from grasses may share as little as 79% sequence identity with the maize-type viruses. Here, we present the complete genome sequences and biological characterization of two MSV isolates from wheat that share approximately 89% sequence identity with the maize-type viruses. Clonal populations of these two isolates, named MSV-Tas and MSV-VW, were leafhopper-transmitted to Digitaria sanguinalis and a range of maize, wheat, and barley genotypes. Whereas the two viruses showed some differences in their pathogenicity in maize, they were both equally pathogenic in D. sanguinalis and the various wheat and barley genotypes tested. Phylogenetic analyses involving the genome sequences of MSV-Tas and MSV-VW, a new maize-type virus also fully sequenced in this study (MSV-VM), and all other available African streak virus sequences, indicated that MSV-Tas and MSV-VW are close relatives that together represent a distinct MSV strain. Sequence analyses revealed that MSV-VM has a recombinant genome containing MSV-Tas/VW-like sequences within its movement protein gene.

Analysis of the diversity of African streak mastreviruses using PCR-generated RFLPs and partial sequence data

Maize streak virus (MSV) is the most economically significant member of a diverse group of African grass-infecting Mastrevirus species in the family Geminiviridae. We designed a single set of degenerate primers which enables the PCR amplification of an approximately 1300 bp DNA fragment spanning both conserved (the RepA gene) and variable (the long intergenic region and MP gene) portions of these viruses' genomes. Using restriction fragment length polymorphism (RFLP) analysis of PCR products obtained from 39 MSV, one SSV, and two PanSV isolates, it was possible to both identify the different virus species, which differ in nucleotide sequence by up to 40%, and to differentiate between MSV isolates sharing up to 99% sequence identity. The reliability of the RFLP data for typing the MSV isolates was verified by the phylogenetic analysis of the partial genomic nucleotide sequences of a representative subset of the MSV isolates. Based on both the RFLP and sequence data, the MSV isolates could be clearly differentiated into the four groups: these were a group of predominantly maize-infecting isolates, and three groups containing grass/wheat-infecting isolates. RFLP analysis also revealed a number of mixed virus infections in which, in certain instances, it was possible to identify individual population members.

Sensitive detection of the Egyptian species of sugarcane streak virus by PCR-probe capture hybridization (PCR-ELISA) and its complete nucleotide sequence

A rapid and sensitive assay for the specific detection of Sugarcane streak virus (SSV) using PCR-probe capture hybridization (PCR-ELISA) was developed. Nucleic acids suitable for PCR were extracted from SSV-infected tissue using organic solvents or Fast DNA kit. SSV cDNA was amplified using viral specific primers and the amplified SSV cDNA (amplicon) was DIG-labelled during the amplification process. The amplicon was then detected in a colorimetric hybridization system by a microtiter plate using a biotinylated cDNA (22 nt), cDNA (789 nt) or cRNA (789 nt) capture probe. This system combines the specificity of molecular hybridization, the ease of the colorimetric protocol, and is 10-100 fold more sensitive than agarose gel electrophoretic analysis in detecting the amplified product. Long cDNA or cRNA capture probe was 2-7 fold more sensitive than the oligo cDNA probe for the detection. Complete nucleotide sequence of SSV from Naga Hammady, Egypt, revealed that SSV-EG is a new species of SSV that shares 66% nucleotide identity with the virus species from Natal, South Africa.

Analysis of the genetic variability of maize streak virus

The nucleotide sequences of the small intergenic region (SIR) and the gene encoding the coat protein of 12 maize streak virus (MSV) isolates from different geographic locations have been determined. These have been used to assess the variability of the virus and to construct evolutionary dendrograms. For the viruses analyzed, the maximum levels of sequence divergence were found to be 10.9% and 2.0% at the nucleotide and amino acid levels, respectively. A genetically distinct strain of MSV was collected from islands in the Indian ocean. The significance of these findings for detection of the virus in epidemiological studies and breeding of resistant plant varieties is discussed.

A phylogenetic and evolutionary justification for three genera of Geminiviridae

Gene-by-gene phylogenetic analyses of all of the viruses for which sequences are known, as well as analysis of the coding capacities, clearly demonstrated that there are two major groups of viruses in the taxonomic family Geminiviridae. These are of the Subgroup I type, with one genomic component, which mainly infect monocots and are leafhopper-transmitted; and of the Subgroup III type, with one or two genomic components, which infect dicots and are whitefly-transmitted. The existence of "New World" and "Old World" clusters of Subgroup III viruses was confirmed, as well as the possession by the latter of an AV1 ORF not present in New World viruses. A third minor generic group is defined by viruses of the Subgroup II type, which have a single genomic component, infect dicots, and are leafhopper-transmitted. The latter group appear to be the result of an ancient recombination event between a Subgroup III-like and a Subgroup I-like virus. The question of whether one- and two-component Subgroup III viruses should be in the same taxon appears hard to resolve: the only distinguishing feature of the one-component Subgroup III viruses is that they apparently have no second component, as gene-for-gene comparisons of the "A" components of the viruses with other Subgroup III viruses place them within a larger Old World group of viruses, most of which are two component. The possibility exists that these viruses may either have independently lost their B components, or possess a B component that has simply not yet been found. Possible nomenclatural changes to accommodate viruses with the same name which are not closely related to one another, and possible evolutionary scenarios to account for the observed familial, generic and specific diversity of geminiviruses, are discussed.