John E Thomas

University of Queensland, Brisbane, Queensland, Australia

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Publications (15)38.24 Total impact

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    ABSTRACT: In Sudan Chickpea chlorotic dwarf virus (CpCDV, genus Mastrevirus, family Geminiviridae) is an important pathogen of pulses that are grown both for local consumption, and for export. Although a few studies have characterised CpCDV genomes from countries in the Middle East, Africa and the Indian subcontinent, little is known about CpCDV diversity in any of the major chickpea production areas in these regions. Here we analyse the diversity of 147 CpCDV isolates characterised from pulses collected across the chickpea growing regions of Sudan. Although we find that seven of the twelve known CpCDV strains are present within the country, strain CpCDV-H alone accounted for ∼73% of the infections analysed. Additionally we identified four new strains (CpCDV-M, -N, -O and -P) and show that recombination has played a significant role in the diversification of CpCDV, at least in this region. Accounting for observed recombination events, we use the large amounts of data generated here to compare patterns of natural selection within protein coding regions of CpCDV and other dicot-infecting mastrevirus species. Copyright © 2014 Elsevier B.V. All rights reserved.
    Infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases 01/2015; 29:203-2015. DOI:10.1016/j.meegid.2014.11.024 · 3.22 Impact Factor
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    ABSTRACT: Phylodynamic evidence of the migration of turnip mosaic potyvirus from Europe to Australia and New Zealand Ryosuke Yasaka1, Kiho Ohba2, Mark W. Schwinghamer3, John Fletcher4, Francisco M. Ochoa-Corona5, John E. Thomas6, Simon Y. W. Ho7, Adrian J. Gibbs8 and Kazusato Ohshima, PhD (ohshimak@cc.saga-u.ac.jp)9 + Author Affiliations 1 Saga University, Kagoshima University 2 Saga University 3 Tamworth Agricultural Institute 4 The New Zealand Institute for Plant & Food Research Limited 5 Oklahoma State University 6 The University of Queensland 7 University of Sydney 8 Australian National University 9 Saga University Received 7 October 2014. Revised 5 November 2014. Accepted 6 November 2014. Abstract Turnip mosaic virus (TuMV) is a potyvirus that is transmitted by aphids and infects a wide range of plant species. We investigated the evolution of this pathogen by collecting 32 isolates of TuMV, mostly from Brassicaceae plants, in Australia and in New Zealand. We performed a variety of sequence-based phylogenetic and population genetic analyses of the complete genomic sequences and of three non-recombinogenic regions of those sequences. The substitution rates, divergence times, and phylogeographic patterns of the virus populations were estimated. Six inter- and five intralineage recombination type patterns were found in the genomes of the Australian and New Zealand isolates, and all were novel. Only one recombination type pattern has been found in both countries. Australian and New Zealand populations were genetically different, and were different from the European and Asian populations. Our Bayesian coalescent analyses, based on a combination of novel and published sequence data from three non-recombinogenic protein-encoding regions, showed that TuMV probably started to migrate from Europe to Australia and New Zealand more than 80 years ago, and that distinct populations arose as a result of evolutionary drivers such as recombination. The basal-B2 subpopulation in Australia and New Zealand seems to be older than those of the world-B2 and B3 populations. To our knowledge, our study presents the first population genetic analysis of TuMV in Australia and New Zealand. We have shown that the time of migration of TuMV correlates well with the establishment of agriculture and migration of Europeans to these countries.
    Journal of General Virology 12/2014; DOI:10.1099/jgv.0.000007 · 3.53 Impact Factor
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    ABSTRACT: Viruses of the genus Mastrevirus (family Geminiviridae) are transmitted by leafhoppers and infect either mono- or dicotyledonous plants. Here we have determined the full length sequences of 49 dicot-infecting mastrevirus isolates sampled in Australia, Eritrea, India, Iran, Pakistan, Syria, Turkey and Yemen. Comprehensive analysis of all available dicot-infecting mastrevirus sequences showed the diversity of these viruses in Australia to be greater than in the rest of their known range, consistent with earlier studies, and that, in contrast with the situation in monocot-infecting mastreviruses, detected inter-species recombination events outnumbered intra-species recombination events. Consistent with Australia having the greatest diversity of known dicot-infecting mastreviruses phylogeographic analyses indicating the most plausible scheme for the spread of these viruses to their present locations, suggest that most recent common ancestor of these viruses is likely nearer Australia than it is to the other regions investigated.
    Virology 07/2013; 444:282-291. DOI:10.1016/j.virol.2013.06.024 · 3.28 Impact Factor
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    ABSTRACT: Members of the Circoviridae family, specifically the Circovirus genus, were thought to infect only vertebrates; however, members of a sister group under the same family, the proposed Cyclovirus genus, have been detected recently in insects. In an effort to explore the diversity of cycloviruses and better understand the evolution of these novel single stranded DNA (ssDNA) viruses, here we present five cycloviruses isolated from three dragonfly species (Orthetrum sabina, Xanthocnemis zealandica and Aeshna multicolour) collected in Australia, New Zealand and the United States of America. The genomes of these five viruses share similar genome structure to other cycloviruses, with a circular ~1.7 kb genome and two major bidirectionally transcribed open reading frames (ORFs). The genomic sequence data gathered during this study were combined with all cyclovirus genomes available in public databases to identify conserved motifs and regulatory elements in the intergenic regions, as well as determine diversity and recombinant regions within their genomes. The genomes reported here represent four different cyclovirus species, three of which are novel. Our results confirm that cycloviruses circulate widely in winged insect populations; in eight different cyclovirus species identified in dragonflies to date, some of these exhibit a broad geographical distribution. Recombination analysis revealed both intra- and inter-species recombination events among cycloviruses, including genomes recovered from disparate sources (e.g., goat meat and human faeces). Similar to other well-characterised circular ssDNA viruses, recombination may play an important role in cyclovirus evolution.
    Journal of General Virology 04/2013; DOI:10.1099/vir.0.052654-0 · 3.53 Impact Factor
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    ABSTRACT: Monocotyledonous plant infecting mastreviruses (family Geminiviridae) have been found in the Old World. The greatest diversity of these viruses has been found in Africa but this may simply reflect the more extensive sampling that has been done there. To provide a better understanding of mastrevirus diversity in Australia, we have sequenced the genomes of 41 virus isolates found in naturalised and native grasses and identified four new species in addition to the four previously characterised species. Two of these species, which were recovered from a single Sporobolus plant, are highly divergent and are most closely related to the African streak viruses. This, coupled with the discovery of divergent dicotyledonous plant infecting mastreviruses in Australia brings into question the hypothesis that mastreviruses may have originated in Africa. We found that the patterns of inter- and intra-species recombination and the recombination hotspots mirror those found in both their African monocot-infecting counterparts and dicot-infecting mastrevirus.
    Virus Research 07/2012; 169(1):127-36. DOI:10.1016/j.virusres.2012.07.018 · 2.83 Impact Factor
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    ABSTRACT: Monocotyledonous and dicotyledonous plant infecting mastreviruses threaten various agricultural systems throughout Africa, Eurasia and Australasia. In Australia three distinct mastrevirus species are known to infect dicotyledonous hosts such as chickpea, bean and tobacco. Amongst 34 new "dicot-infecting" mastrevirus full genome sequences obtained from these hosts we discovered one new species, four new strains, and various variants of previously described mastrevirus species. Besides providing additional support for the hypothesis that evolutionary processes operating during dicot-infecting mastrevirus evolution (such as patterns of pervasive homologous and non-homologous recombination, and strong purifying selection acting on all genes) have mostly mirrored those found in their monocot-infecting counterparts, we find that the Australian dicot-infecting viruses display patterns of phylogeographic clustering reminiscent of those displayed by monocot infecting mastrevirus species such as Panicum streak virus and Maize streak virus.
    Virus Research 03/2012; 166(1-2):13-22. DOI:10.1016/j.virusres.2012.02.024 · 2.83 Impact Factor
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    ABSTRACT: Banana bunchy top virus (BBTV; family Nanoviridae, genus Babuvirus) is a multi-component, ssDNA virus, which causes widespread banana crop losses throughout tropical Africa and Australasia. We determined the full genome sequences of 12 BBTV isolates from the Kingdom of Tonga and analysed these together with previously determined BBTV sequences to show that reassortment and both inter- and intra-component recombination have all been relatively frequent occurrences during BBTV evolution. We found that whereas DNA-U3 components display evidence of complex inter- and intra-component recombination, all of the South Pacific DNA-R components have a common intra-component recombinant origin spanning the replication-associated protein gene. Altogether, the DNA-U3 and DNA-M components display a greater degree of inter-component recombination than the DNA-R, -S, -C and -M components. The breakpoint distribution of the inter-component recombination events reveals a primary recombination hotspot around the 5' side of the common region major and, in accordance with recombination hotspots detectable in related ssDNA viruses, a secondary recombination hotspot near the origin of virion-strand replication.
    Journal of General Virology 01/2012; 93(Pt 5):1103-19. DOI:10.1099/vir.0.040337-0 · 3.53 Impact Factor
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    ABSTRACT: Three monocot-infecting mastreviruses from Australia, all found primarily in pasture and naturalised grasses, have been characterised at the molecular level. Here, we present the full genome sequence of a fourth, Paspalum striate mosaic virus (PSMV), isolated from Paspalum dilatatum from south-east Queensland. The genome was 2816 nt long and had an organisation typical of other monocot-infecting mastreviruses. Its nearest relative is Bromus cartharticus striate mosaic virus (BCSMV), with which it shares an overall genome identity of 75%. Phylogenetic analysis of the complete genome and each of the putative viral proteins places PSMV in a group with the other three Australian striate mosaic viruses. PSMV, BCSMV and Digitaria didactyla striate mosaic virus all contain a similar, small recombinant sequence in the small intergenic region.
    Archives of Virology 01/2012; 157(1):193-7. DOI:10.1007/s00705-011-1129-2 · 2.28 Impact Factor
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    John E. Thomas, Visnja Steele
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    ABSTRACT: Panicum mosaic virus (PMV) was identified from Stenotaphrum secundatum (buffalo grass or St Augustine grass) showing leaf mosaic symptoms, from New South Wales. The isometric virions were decorated by antibodies to PMV by immunosorbent electron microscopy. The coat protein gene was 85% and 90% identical, at the nucleotide and amino acid levels, respectively, to the published sequence of PMV. This represents the first record for PMV for Australia, and the first outside North America.
    Australasian Plant Disease Notes 12/2011; DOI:10.1007/s13314-011-0005-y
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    ABSTRACT: The complete coat protein gene sequence is described for three isolates of Strawberry necrotic shock virus (SNSV) isolated from strawberry (Fragaria vesca) from Australia. Sequences for these isolates were found to have close identity to SNSV isolates from North America. This is the first report of SNSV from Australia.
    Australasian Plant Disease Notes 12/2011; DOI:10.1007/s13314-011-0018-6
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    ABSTRACT: In 1999, banana streak disease outbreaks occurred at two locations in Australia in new banana hybrids that were being screened for fusarium wilt resistance. Two different badnaviruses, banana streak GF virus and a newly discovered virus called banana streak IM virus (BSIMV), were detected in these plants. The complete nucleotide sequence of the BSIMV genome was determined and comprised 7768 nt. Three open reading frames were detected, the first beginning with a non-conventional start codon (CUG). A 55-nt repetition in the putative pregenomic RNA promoter was also identified. Phylogenetic analysis suggests that BSIMV is most closely related to banana streak VN virus.
    Archives of Virology 02/2011; 156(4):733-7. DOI:10.1007/s00705-011-0946-7 · 2.28 Impact Factor
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    ABSTRACT: Banana streak disease is caused by several distinct badnavirus species, one of which is Banana streak Obino l'Ewai virus. Banana streak Obino l'Ewai virus has severely hindered international banana (Musa spp.) breeding programmes, as new hybrids are frequently infected with this virus, curtailing any further exploitation. This infection is thought to arise from viral DNA integrated in the nuclear genome of Musa balbisiana (B genome), one of the wild species contributing to many of the banana cultivars currently grown. In order to determine whether the DNA of other badnavirus species is integrated in the Musa genome, PCR-amplified DNA fragments from Musa acuminata, M. balbisiana and Musa schizocarpa, as well as cultivars 'Obino l'Ewai' and 'Klue Tiparot', were cloned. In total, 103 clones were sequenced and all had similarity to open reading frame III in the badnavirus genome, although there was remarkable variation, with 36 distinct sequences being recognized with less than 85 % nucleotide identity to each other. There was no commonality in the sequences amplified from M. acuminata and M. balbisiana, suggesting that integration occurred following the separation of these species. Analysis of rates of non-synonymous and synonymous substitution suggested that the integrated sequences evolved under a high degree of selective constraint as might be expected for a living badnavirus, and that each distinct sequence resulted from an independent integration event.
    Journal of General Virology 03/2005; 86(Pt 2):511-20. DOI:10.1099/vir.0.80261-0 · 3.53 Impact Factor
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    ABSTRACT: Tomato spotted wilt virus (genus Tospovirus) is recorded on chickpea (Cicer arietinum) in Australia for the first time. It caused shoot tip symptoms of wilting, necrosis, bunching and chlorosis, followed by premature death of plants.
    Australasian Plant Pathology 01/2004; 33(4):597-599. DOI:10.1071/AP04065 · 1.04 Impact Factor
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    ABSTRACT: Banana streak virus strain OL (BSV-OL) commonly infects new Musa hybrids, and this infection is thought to arise de novo from integrated virus sequences present in the nuclear genome of the plant. Integrated DNA (Musa6+8 sequence) containing the whole genome of the virus has previously been cloned from cv. Obino l’Ewai (Musa AAB group), a parent of many of the hybrids. Using a Southern blot hybridization assay, we have examined the distribution and structure of integrated BSV-OL sequences in a range of Musa cultivars. For cv. Obino l’Ewai, almost every restriction fragment hybridizing to BSV-OL was predicted from the Musa6+8 sequence, suggesting that this is the predominant type of BSV-OL integrant in the genome. Furthermore, since only two junction fragments of Musa/BSV sequence were detected, and the Musa6+8 sequence is believed to be integrated as multiple copies in a tandem array, then the internal Musa spacer sequences must be highly conserved. Similarly sized restriction fragments were detected in four BB group cultivars, but not in six AA or AAA group cultivars, suggesting that the BSV-OL sequences are linked to the B-genome of Musa. We also provide evidence that cv. Williams (Musa AAA group) contains a distinct badnavirus integrant that is closely related to the ‘dead’ virus integrant previously characterized from Calcutta 4 (Musa acuminata ssp. burmannicoides). Our results suggest that the virus integrant from cv. Williams is linked to the A-genome, and the complexity of the hybridization patterns suggest multiple sites of integration and/or variation in sequence and structure of the integrants.
    Molecular Plant Pathology 06/2001; 2(4):207 - 213. DOI:10.1046/j.1464-6722.2001.00071.x · 4.49 Impact Factor
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    ABSTRACT: A multiplex, immunocapture PCR (M-IC-PCR) was developed for the simultaneous detection of three viruses from crude sap extracts of banana and plantain (Musa spp.). A reverse transcription step was required for Banana bract mosaic virus and Cucumber mosaic virus, which have ssRNA genomes. The detection of Banana bunchy top virus (ssDNA genome) was not adversely affected by inclusion in this step. All the three viruses could be detected simultaneously from a mixed infection. Identification and detection of individual viruses was achieved through the visualisation of discretely sized PCR amplicons by gel electrophoresis. Alternatively, a colourimetric microplate detection system utilising digoxigenin-labelled virus-specific probes was used. The latter assay was up to five times more sensitive than detection by gel electrophoresis and between 25 and 625 times more sensitive than ELISA for the various viruses. Careful selection of PCR primers was necessary to ensure the detection of a wide range of virus isolates and to avoid detrimental interactions between heterologous templates and primers.
    Journal of Virological Methods 10/2000; 89(1-2):75-88. DOI:10.1016/S0166-0934(00)00204-4 · 1.88 Impact Factor

Publication Stats

226 Citations
38.24 Total Impact Points

Institutions

  • 2011–2015
    • University of Queensland
      • • Centre for Plant Science
      • • Queensland Alliance for Agriculture and Food Innovation (QAAFI)
      Brisbane, Queensland, Australia
  • 2013
    • Girne American University Canterbury
      Cantorbery, England, United Kingdom
  • 2012
    • University of Canterbury
      • School of Biological Sciences
      Christchurch, Canterbury, New Zealand