Complete genome sequence of ornithogalum virus 3.

Ornithogalum thyrsoides, a widely cultivated bulbous ornamental plant endemic to South Africa, has significant commercial value as a pot plant and for the production of cut flowers. However, infection by viruses threatens the success of commercial cultivation, as symptoms negatively affect the appearance of the plant and flowers. To date, four Ornithogalum-infecting viruses have been reported. Complete genome sequence data are available for three of these viruses, but the genome of the potyvirus ornithogalum virus 3 (OV3) has not been fully sequenced. In this study, the complete sequence of OV3 was determined by high-throughput sequencing (HTS) and validated by Sanger sequencing. Based on recognition of protease cleavage patterns and multiple sequence alignments with closely related viruses, the polyprotein of OV3 was predicted to be proteolytically cleaved to produce 10 mature peptides containing domains conserved in members of the genus Potyvirus. Phylogenetic analysis and species demarcation criteria confirm the previous classification of OV3 as a member of a separate species in this genus. This is the first report of a complete genome sequence of OV3.

Complete genome sequence of a novel polerovirus in Ornithogalum thyrsoides from South Africa.

Ornithogalum thyrsoides, commonly known as chincherinchee, is an indigenous ornamental plant widely cultivated in South Africa. It is commercially valued as a flowering pot plant and for the production of cut flowers. Virus infections resulting in the development of severe necrotic mosaic symptoms threaten the success of commercial cultivation. The virome of an O. thyrsoides plant displaying necrotic mosaic symptoms was determined using high-throughput sequencing (HTS). In this plant, ornithogalum mosaic virus and ornithogalum virus 3 were identified, as well as a previously unknown virus. The full genome sequence of this virus was confirmed by Sanger sequencing using overlapping amplicons combined with rapid amplification of cDNA ends (RACE). Based on genome organisation and phylogenetic analysis, this novel virus can be classified as a polerovirus.

In Silico Probe-Based Detection of Citrus Viruses in NGS Data.

The conservation of plant biosecurity relies on the rapid identification of pathogenic organisms, including viruses. With next-generation sequencing (NGS), it is possible to identify multiple viruses within a metagenomic sample. In this study, we explored the use of electronic probes (e-probes) for the simultaneous detection of 11 recognized citrus viruses. E-probes were designed and screened against raw sequencing data to minimize the bioinformatic processing time required. The e-probes were able to accurately detect their cognate viruses in simulated datasets, without any false negatives or positives. The efficiency of the e-probe-based approach was validated with NGS datasets generated from different RNA preparations: double-stranded RNA (dsRNA) from 'Mexican' lime infected with different Citrus tristeza virus (CTV) genotypes, dsRNA from field samples, and small RNA and total RNA from grapefruit infected with the CTV T3 genotype. A set of probes was made available that is able to accurately detect CTV in sequence data regardless of the input dataset or the genotype that plants are infected with.

Relative quantitation goes viral: An RT-qPCR assay for a grapevine virus.

Accurate detection and quantitation of viruses can be beneficial to plant-virus interaction studies. In this study, three SYBR green real-time RT-PCR assays were developed to quantitate grapevine leafroll-associated virus 3 (GLRaV-3) in infected vines. Three genomic regions (ORF1a, coat protein and 3'UTR) were targeted to quantitate GLRaV-3 relative to three stably expressed reference genes (actin, GAPDH and α-tubulin). These assays were able to detect all known variant groups of GLRaV-3, including the divergent group VI, with equal efficiency. No link could be established between the concentration ratios of the different genomic regions and subgenomic RNA (sgRNA) expression. However, a significant lower virus concentration ratio for plants infected with variant group VI compared to variant group II was observed for the ORF1a, coat protein and the 3'UTR. Significant higher accumulation of the virus in the growth tip was also detected for both variant groups. The quantitation of viral genomic regions under different conditions can contribute to elucidating disease aetiology and enhance knowledge about virus ecology.

MicroRNAs in fruit trees: discovery, diversity and future research directions.

Since the first description of microRNAs (miRNAs) 20 years ago, the number of miRNAs identified in different eukaryotic organisms has exploded, largely due to the recent advances in DNA sequencing technologies. Functional studies, mostly from model species, have revealed that miRNAs are major post-transcriptional regulators of gene expression in eukaryotes. In plants, they are implicated in fundamental biological processes, from plant development and morphogenesis, to regulation of plant pathogen and abiotic stress responses. Although a substantial number of miRNAs have been identified in fruit trees to date, their functions remain largely uncharacterised. The present review aims to summarise the progress made in miRNA research in fruit trees, focusing specifically on the economically important species Prunus persica, Malus domestica, Citrus spp, and Vitis vinifera. We also discuss future miRNA research prospects in these plants and highlight potential applications of miRNAs in the on-going improvement of fruit trees.

Complete nucleotide sequence of a new strain of grapevine leafroll-associated virus 3 in South Africa.

The complete genome sequences of two newly identified genetic variants of grapevine leafroll-associated virus 3 (GLRaV-3) are described. Two isolates, GH11 (18671 nt) and GH30 (18576 nt) were sequenced and found to be less than 70 % similar to other South African GLRaV-3 variants. The genome organization of GH11 and GH30 is similar to that of previously described GLRaV-3 isolates. However, no corresponding open reading frame 2 (ORF2) could be identified. Phylogenetic analysis indicates that GH11 and GH30 cluster in a subgroup (group VI) that is separate from the previously described GLRaV-3 isolates and should be regarded as a different strain of GLRaV-3.

A transient expression assay for the in planta efficacy screening of an antimicrobial peptide against grapevine bacterial pathogens.

AIMS: Natural and synthetic antimicrobial peptides (AMPs) are of increasing interest as potential resistance conferring elements in plants against pathogen infection. The efficacy of AMPs against pathogens is prescreened by in vitro assays, and promising AMP candidates are introduced as transgenes into plants. As in vitro and in planta environments differ, a prescreening procedure of the AMP efficacy in the plant environment is desired. Here, we report the efficacy of the purified synthetic peptide D4E1 against the grapevine-infecting bacterial pathogens Agrobacterium vitis and Xylophilus ampelinus in vitro and describe for the first time an in planta prescreening procedure based on transiently expressed D4E1. METHODS AND RESULTS: The antimicrobial effect of D4E1 against Ag. vitis and X. ampelinus was shown by a reduction in colony-forming units in vitro in a traditional plate-based assay and by a reduction in bacterial titres in planta as measured by quantitative real-time PCR (qPCR) in grapevine leaves transiently expressing D4E1. A statistically significant reduction in titre was shown for X. ampelinus, but for Ag. vitis, a significant reduction in titre was only observed in a subset of plants. CONCLUSIONS: The titres of both grapevine-infecting bacterial pathogens were reduced in an in vitro assay and for X. ampelinus in an in planta assay by D4E1 application. This widens the applicability of D4E1 as a potential resistance-enhancing element to additional pathogens and in a novel plant species. SIGNIFICANCE AND IMPACT OF THE STUDY: D4E1 is a promising candidate to confer enhanced resistance against the two tested grapevine bacterial pathogens, and the applied transient expression system proved to be a valuable tool for prescreening of D4E1 efficacy in an in planta environment. The described prescreening procedure can be used for other AMPs and might be adapted to other plant species and pathogens before the expensive and tedious development of stably transgenic lines is started.

Three genetic grapevine leafroll-associated virus 3 variants identified from South African vineyards show high variability in their 5'UTR.

Three genetic variants of grapevine leafroll-associated virus 3 (GLRaV-3) were identified in vineyards of the Western Cape, South Africa. The GLRaV-3 variants were identified by single-strand conformation polymorphism (SSCP) profiles generated from a region amplified in ORF5. ORF5 sequence data confirmed the three genetic variant groups, and a specific SSCP profile was assigned to each variant group. The results of SSCP analysis of this region in ORF5 showed that this method gives a fast and reliable indication of the GLRaV-3 variant status of a plant, which in many instances showed mixed infections. The full genome sequence of one representative of each variant group i.e. isolates 621 (group I), 623 (group II) and PL-20 (group III), was determined by sequencing overlapping cloned fragments of these isolates. The sequences of genomic 5' ends of these isolates were determined by RLM-RACE. Sequence alignment of the 5'UTRs indicated significant sequence and length variation in this region between the three South African variant groups. Alignment of the Hsp70h and CP gene regions of these isolates with those of isolates from elsewhere in the world, followed by phylogenetic analysis, further supported the presence of three variants of GLRaV-3 in South Africa and the presence of two or three additional variant groups elsewhere in the world.

First Report of Aster Yellows Phytoplasma in Grapevines in South Africa.

For many years phytoplasma diseases have caused serious losses in most of the major grape-growing regions of the world, except South Africa, where a mixed phytoplasma infection was first reported in 2006 (1). During the early growing season of 2006, symptoms consistent with phytoplasma disease were observed in vineyards in the Olifants River Valley. Symptoms included yellowing of leaves, incomplete lignification of shoots, shortening of internodes, and the abortion of growth tips and immature bunches. Symptomatic shoots and leaves from grapevine cultivars (Merlot, Shiraz, Cabernet Sauvignon, Ruby Cabernet, Pinotage, Corinth, Chardonnay, Columbar, Chenin blanc, Sauvignon blanc, Sultana, and Regal) were collected during the early growing season (November) of 2006, 2007, and 2008. Total DNA was extracted from 32 of these samples (from single plants in the same vineyards over the 3 years) with the Invisorb Spin Plant Mini Kit (Invitek, Berlin, Germany) and tested by nested PCR using two universal primer pairs, P1/P7 and R16F2n/R16R2 (3). The first round of PCR of the 2006 samples yielded 1.8-kb fragments for 17 of the samples, while the nested PCR yielded an additional seven positive samples, confirming the necessity of nested PCR for reliable diagnosis. A similar trend was observed in the 2007 and 2008 PCR test results. All asymptomatic plants, which were included as negative controls, and water controls were negative by nested PCR. Twenty-four 1,245-bp amplicons, generated by nested PCR, were excised from gels, purified with a NucleoSpin Extract II Kit (Macherey-Nagel, Düren, Germany) and directly sequenced. Sequence data was compiled with the BioEdit Version 7.0.4.1 sequence alignment editor software (2), aligned using ClustalW Version 1.4 (4), and a consensus sequence was generated (GenBank Accession No. GQ365729). A BLAST search of the NCBI GenBank database using the individual sequences revealed high sequence identities (≥99%) with the aster yellows phytoplasma group (16SrI) and specifically with the subgroup 16SrI-B. In a comparison of the sequences of the 1.2-kb PCR fragments of 24 local samples with each other, sequence identities of ~99% were observed. These results clearly illustrate that all vines screened were infected with the same phytoplasma. Single nucleotide differences observed between different isolates may indicate the presence of closely related sequence variants of this phytoplasma. Aster yellows occurs worldwide and has been reported to infect grapevine-South Africa can now be added to this list. During the three seasons of our study, the area in which symptomatic vineyards were observed increased significantly, indicating spread by a biological vector. Moreover, infected vineyards were noticed in two other South African grape-growing regions. In contrast to the previous report, which reported a mixed infection of phytoplasmas of groups 16SrXII-A and 16SrII-B (1), PCR screening and sequencing of more than 40 individual samples from these areas confirmed these all to be infected with aster yellows phytoplasma only. To our knowledge, this is the first report of the detection and identification of an aster yellows phytoplasma causing grapevine yellows disease in South Africa. References: (1) S. Botti and A. Bertaccini. Plant Dis. 90:1360, 2006. (2) T. A. Hall. Nucleic Acids. Symp. Ser. 41:95, 1999. (3) I.-M. Lee et al. Phytopathology 83:834, 1993. (4) J. D. Thompson et al. Nucleic Acids Res. 22:4673, 1994.

Molecular divergence of Grapevine virus A (GVA) variants associated with Shiraz disease in South Africa.

Shiraz disease (SD) is a highly destructive, insect-transmitted disease of noble grapevine cultivars, such as Shiraz and Merlot, in South Africa. Earlier studies revealed that, of the three molecular groups of GVA that were detected in local vineyards, variants of group II are closely associated with expression of this disease, and variants of group III are commonly present in GVA-infected SD-negative plants [Goszczynski, D.E., 2007. Single-strand conformation polymorphism (SSCP), cloning and sequencing of Grapevine virus A (GVA) reveal a close association between related molecular variants of the virus and Shiraz disease in South Africa. Plant Pathol. 56, 755-762]. Among many GVA variants transmitted to Nicotiana benthamiana from various grapevines with different SD status, a variant of group II, referred to here as GTR1-2, was also isolated from a consistently SD-negative Shiraz plant. The genome of this variant, along with 7 other GVA variants of the 3 molecular groups, including 4 variants of molecular group II associated with strong symptoms of SD, were sequenced. Results of comparative analysis of these genomes, with emphasis on differences between GTR1-2 and other variants of molecular group II, are presented. Among the many differences that were found, a 119 nt ORF2-related fragment was discovered within the native ORF2 of a GVA variant, P163-M5. This variant was isolated from a grapevine used by local industry as a reliable positive control for SD in woody indexing. The variant induced symptoms in N. benthamina that were significantly more severe than those of other variants of molecular group II.

Iris yellow spot virus in Onion Seed Crops in South Africa.

In December 2006, symptoms typical of iris yellow spot caused by Iris yellow spot virus (IYSV; genus Tospovirus, family Bunyaviridae) were observed on scapes (seed stalks) in an onion (Allium cepa L.) seed crop in the Klein Karoo of the Western Cape Province, South Africa. Symptoms included diamond-shaped chlorotic or necrotic lesions on the scapes, some of which had 'green-islands' with nested diamond-shaped lesions, as well as indistinct, circular to irregular, chlorotic or necrotic lesions of various sizes. At the time symptoms were observed, approximately 5% of the scapes had lodged as a result of extensive lesions resembling those caused by IYSV. The crop was 2 to 3 weeks from harvest. Symptomatic tissue from two plants (two samples from one plant and four samples from the other plant) was tested for IYSV by reverse-transcriptase (RT)-PCR. Total RNA was extracted from symptomatic scape tissue with the SV Total RNA Isolation System (Promega, Madison, WI) according to the manufacturer's instructions. First strand cDNA was synthesized with the RevertAid H Minus First Strand cDNA Synthesis kit (Fermentas Inc., Hanover, MD), followed by PCR amplification with primers IYSV-For (TGG YGG AGA TGY RGA TGT GGT) and IYSV-Rev (ATT YTT GGG TTT AGA AGA CTC ACC), which amplify the nucleocapsid (NP) gene of IYSV. An amplicon of expected size (approximately 750 bp) was observed for each of the symptomatic plants assayed and was sequenced. Comparison of the sequence (GenBank Accession No. EF579801) with GenBank sequences revealed 95% sequence identity with the NP gene of IYSV GenBank Accession No. EF419888, with eight amino acid differences. The known geographic distribution of IYSV in onion bulb or seed crops has increased rapidly in recent years in many areas of the world (1). To our knowledge, this is the first confirmation of IYSV in South Africa. Approximately 6,100 ha of onion bulb crops are grown annually in South Africa in the Western Cape, Kwazulu Natal, Limpopo, and Northern Cape provinces, and 600 ha of onion seed crops are grown primarily in the semi-arid regions of the Western Cape. Examination of an additional 10 onion seed crops in the Klein Karoo during January 2007 revealed the presence of iris yellow spot in three more crops at approximately 5% incidence in each crop. The four symptomatic crops had all been planted as bulb-to-seed crops, using vernalized bulbs produced on the same farm. This suggests that IYSV may have been disseminated into the seed crops on the vernalized bulbs, either as infected bulb tissue or in viruliferous thrips on the bulbs. Reference: (1) D. H. Gent et al. Plant Dis. 90:1468, 2006.

Pearl millet transformation system using the positive selectable marker gene phosphomannose isomerase.

Fertile transgenic pearl millet plants expressing a phosphomannose isomerase (PMI) transgene under control of the maize ubiquitin constitutive promoter were obtained using the transformation system described here. Proliferating immature zygotic embryos were used as target tissue for bombardment using a particle inflow gun. Different culture and selection strategies were assessed in order to obtain an optimised mannose selection protocol. Stable integration of the manA gene into the genome of pearl millet was confirmed by PCR and Southern blot analysis. Stable integration of the manA transgene into the genome of pearl millet was demonstrated in T1 and T2 progeny of two independent transformation events with no more than four to ten copies of the transgene. Similar to results obtained from previous studies with maize and wheat, the manA gene was shown to be a superior selectable marker gene for improving transformation efficiencies when compared to antibiotic or herbicide selectable marker genes.

Cloning, sequencing, and expression in Escherichia coli of the coat protein gene of a new potyvirus infection South African Passiflora.

Complementary DNA representing 1418 nucleotides (nt) of the 3'-poly(A)-proximal tract of the genomic RNA of a potyvirus causing woodiness disease in South African passion fruit, was cloned and sequenced. The sequence contained a single long open reading frame (ORF) of 1188 nt with no initiation codon, and a 3'-non-coding region (3'-NCR) of 230 nt followed by a poly-adenylate tract. Comparison of the ORF with other potyviral coat protein (CP) sequences led to the prediction that a 279 residue CP of MW 31722 is encoded by 836 nt at the 3'-terminus of the ORF. This virus is not merely a South African strain of passion fruit woodiness virus (PWV): the deduced CP sequence is only distantly related to CPs of other sequenced strains of PWV, although it is part of a distinct subgroup of potyviruses related to PWV. The virus was therefore designated as South African passiflora virus (SAPV). The DNA containing the putative CP was cloned into the pUEX2 bacterial expression vector and expressed in Escherichia coli as a beta-gal-CP fusion protein. The fusion protein reacted with polyclonal antisera raised against the native virus, and antisera raised against partially purified fusion protein reacted with viral CP in Western blots.

The molecular cloning and nucleotide sequencing of the 3'-terminal region of Ornithogalum mosaic virus.

DNA complementary to the 3'-terminal 3684 nucleotides of the Ornithogalum mosaic potyvirus (OMV) genome was cloned and sequenced. The sequence consisted of a single large open reading frame which probably starts upstream of the cloned region. By comparison to other sequenced potyviruses, it was estimated that the clone contained the 3' non-coding (3'-NC) region, the coat protein (CP) gene and the large nuclear inclusion protein (NIb) gene, as well as approximately 85% of the small nuclear inclusion protein (NIa) gene. The 3'-NC region of 274 nucleotides showed 38% to 45% similarity to the corresponding regions of other potyviruses. The putative CP gene could encode a 253 amino acid coat protein with a calculated Mr of 28,807. Analysis of the amino acid sequences of OMV and other potyvirus proteins showed similarities of 66% to 77% for CP, 72% to 73% for NIb and 63% to 71% for NIa proteins. These data, as well as phylogenetic analysis of the CP sequences, suggested that OMV is a typical but taxonomically distinct potyvirus.