Cooperative Research Center for Plant Biosecurity

Bruce, Australia

Cooperative Research Center for Plant Biosecurity

Bruce, Australia
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Maina S.,University of New South Wales | Maina S.,Cooperative Research Center for Plant Biosecurity | Edwards O.R.,Cooperative Research Center for Plant Biosecurity | Edwards O.R.,CSIRO | And 7 more authors.
Genome Announcements | Year: 2016

We present the first complete Sweet potato virus G (SPVG) genome from sweet potato in East Timor and compare it with seven complete SPVG genomes from South Korea (three), Taiwan (two), Argentina (one), and the United States (one). It most resembles the genomes from the United States and South Korea. © 2016 Maina et al.


Maina S.,University of Western Australia | Maina S.,Cooperative Research Center for Plant Biosecurity | Edwards O.R.,Cooperative Research Center for Plant Biosecurity | Edwards O.R.,CSIRO | And 5 more authors.
Genome Announcements | Year: 2016

We present here the first complete Bean common mosaic necrosis virus (BCMNV) genomic sequence isolated from virusinfected common bean (Phaseolus vulgaris) in East Timor, and compare it with six complete BMCNV genomes from the Netherlands, and one each from the United States, Tanzania, and an unspecified country. It most resembled the Netherlands strain NL-8 genome. © 2016 Maina et al.


Maina S.,University of Western Australia | Maina S.,Cooperative Research Center for Plant Biosecurity | Coutts B.A.,Baron Hay Court | Edwards O.R.,CSIRO | And 6 more authors.
Plant Disease | Year: 2017

Zucchini yellow mosaic virus (ZYMV) isolates from cucurbit crops growing in northern Australia and East Timor were investigated to establish possible genetic connectivity between crop viruses in Australia and Southeast Asia. Leaves from symptomatic plants of pumpkin (Cucurbita moschata and C. maxima), melon (Cucumis melo), and zucchini (C. pepo) were sampled near Broome, Darwin, and Kununurra in northern Australia. Leaves from symptomatic plants of cucumber (C. sativus) and pumpkin sampled in East Timor were sent to Australia on FTA cards. These samples were subjected to high-throughput sequencing and 15 complete new ZYMV genomic sequences obtained. When their nucleotide sequences were compared with those of 48 others from GenBank, the East Timorese and Kununurra sequences (three per location) and single earlier sequences from Singapore and Reunion Island were all in major phylogroup B. The seven Broome and two Darwin sequences were in minor phylogroups I and II, respectively, within larger major phylogroup A. When coat protein (CP) nucleotide sequences from the 15 new genomes and 47 Australian isolates sequenced previously were compared with 331 other CP sequences, the closest genetic match for a sequence from Kununurra was with an East Timorese sequence (95.5% nucleotide identity). Analysis of the 63 complete genomes found firm recombination events in 12 (75%) and 2 (4%) sequences from northern Australia or Southeast Asia versus the rest of the world, respectively; therefore, the formers’ high recombination frequency might reflect adaptation to tropical conditions. Both parents of the recombinant Kununurra sequence were East Timorese. Phylogenetic analysis, nucleotide sequence identities, and recombination analysis provided clear evidence of genetic connectivity between sequences from Kununurra and East Timor. Inoculation of a Broome isolate to zucchini and watermelon plants reproduced field symptoms observed in northern Australia. This research has important biosecurity implications over entry of damaging viral crop pathogens not only into northern Australia but also moving between Australia’s different agricultural regions. © 2017 The American Phytopathological Society.


Maina S.,University of Western Australia | Maina S.,Cooperative Research Center for Plant Biosecurity | Coutts B.A.,Western Australian Department of Agriculture and Food | Edwards O.R.,CSIRO | And 6 more authors.
Plant Disease | Year: 2017

To examine possible genetic connectivity between crop viruses found in Southeast Asia and Australia, Papaya ringspot virus biotype W (PRSV-W) isolates from cucurbits growing in East Timor and northern Australia were studied. East Timorese samples from cucumber (Cucumis sativus) or pumpkin (Cucurbita moschata and C. maxima) were sent to Australia on FTA cards. These samples and others of pumpkin, rockmelon, honeydew melon (Cucumis melo), or watermelon (Citrullus lanatus) growing in one location each in northwest, north, or northeast Australia were subjected to high throughput sequencing (HTS). When the 17 complete PRSV genomic sequences obtained by HTS were compared with 32 others from GenBank, the five from East Timor were in a different major phylogroup from the 12 Australian sequences. Moreover, the East Timorese and Australian sequences each formed their own minor phylogroups named VI and I, respectively. A Taiwanese sequence was closest to the East Timorese (89.6% nt dentity), and Mexican and Brazilian sequences were the closest to the Australian (92.3% nt identity). When coat protein gene (CP) sequences from the 17 new genomic sequences were compared with 126 others from GenBank, three Australian isolates sequenced more than 20 years ago grouped with the new Australian sequences, while the closest sequence to the East Timorese was from Thailand (93.1% nt identity). Recombination analysis revealed 13 recombination events among the 49 complete genomes. Two isolates from East Timor (TM50, TM32) and eight from GenBank were recombinants, but all 12 Australian isolates were non-recombinants. No evidence of genome connectivity between Australian and Southeast Asian PRSV populations was obtained. The strand-specific RNA library approach used optimized data collection for virus genome assembly. When an Australian PRSV isolate was inoculated to plants of zucchini (Cucurbita pepo), watermelon, rockmelon, and honeydew melon, they all developed systemic foliage symptoms characteristic of PRSV-W, but symptom severity varied among melon cultivars. © 2017 The American Phytopathological Society.


Singh S.K.,CSIRO | Singh S.K.,Charles Sturt University | Singh S.K.,Cooperative Research Center for Plant Biosecurity | Ash G.J.,Charles Sturt University | Hodda M.,CSIRO
Biological Invasions | Year: 2014

Predicting which species will become invasive in each country or region before they arrive is necessary to devise and implement measures for minimising the costs of biological invasions. Metaphorically, this is keeping one step ahead of invasive species. A structured and systematic approach for screening large numbers of species and identifying those likely to become invasive is proposed in this paper. The Pest Screening and Targeting (PeST) framework integrates heterogeneous information and data on species biogeography, biotic and abiotic factors to first determine a preliminary risk index, then uses this index to identify species for a second, more detailed, risk evaluation process to provide a final ranking. Using the PeST framework, 97 species of plant-parasitic nematodes were evaluated for their biosecurity risks to Australia. The species identified as greatest risks included both previously unrecognised and currently-recognised species. The former included Heterodera zeae, Meloidogyne graminicola, M. enterolobii, M. chitwoodi and Scutellonema bradys, while the latter included Bursaphelenchus xylophilus, Ditylenchus destructor, Globodera pallida, Heterodera glycines and H. filipjevi. Of the ten criteria used in the PeST framework, emerging pest status, pathogenicity, host range and species biogeography most strongly influenced overall risk. The PeST framework also identified species where research to fill in critical knowledge gaps will be most beneficial (e.g. Globodera tabacum, Heterodera cajani, H. filipjevi, Meloidogyne ethiopica, Pratylenchus fallax and P. sudanensis). Where data were available, the information and associated metadata gathered for the PeST framework can be used to guide biosecurity decision making; determine species which require pre border certification and target sampling at the borders. © 2014 Springer International Publishing Switzerland.


Singh S.K.,CSIRO | Singh S.K.,Charles Sturt University | Singh S.K.,Cooperative Research Center for Plant Biosecurity | Ash G.J.,Charles Sturt University | Hodda M.,CSIRO
Biological Invasions | Year: 2015

Predicting which species will become invasive in each country or region before they arrive is necessary to devise and implement measures for minimising the costs of biological invasions. Metaphorically, this is keeping one step ahead of invasive species. A structured and systematic approach for screening large numbers of species and identifying those likely to become invasive is proposed in this paper. The Pest Screening and Targeting (PeST) framework integrates heterogeneous information and data on species biogeography, biotic and abiotic factors to first determine a preliminary risk index, then uses this index to identify species for a second, more detailed, risk evaluation process to provide a final ranking. Using the PeST framework, 97 species of plant-parasitic nematodes were evaluated for their biosecurity risks to Australia. The species identified as greatest risks included both previously unrecognised and currently-recognised species. The former included Heterodera zeae, Meloidogyne graminicola, M. enterolobii, M. chitwoodi and Scutellonema bradys, while the latter included Bursaphelenchus xylophilus, Ditylenchus destructor, Globodera pallida, Heterodera glycines and H. filipjevi. Of the ten criteria used in the PeST framework, emerging pest status, pathogenicity, host range and species biogeography most strongly influenced overall risk. The PeST framework also identified species where research to fill in critical knowledge gaps will be most beneficial (e.g. Globodera tabacum, Heterodera cajani, H. filipjevi, Meloidogyne ethiopica, Pratylenchus fallax and P. sudanensis). Where data were available, the information and associated metadata gathered for the PeST framework can be used to guide biosecurity decision making; determine species which require pre border certification and target sampling at the borders. © 2014, Springer International Publishing Switzerland.


Singh S.K.,CSIRO | Singh S.K.,Charles Sturt University | Singh S.K.,Cooperative Research Center for Plant Biosecurity | Paini D.R.,CSIRO | And 3 more authors.
Biological Invasions | Year: 2014

The biosecurity risks from many plant-parasitic nematode (PPN) species are poorly known and remain a major challenge for identifying potentially invasive species. A self organising map (SOM) was used to prioritise biosecurity risks from PPN to the whole of continental Australia as well as each of the states and the Northern Territory separately. The SOM used the recorded worldwide distributions of 250 systematically selected species from 43 genera, and identified 18 different countries spanning Asia, Africa, North and Central America, Europe and the Pacific with very similar PPN assemblages to Australia as a whole. Many of the species in these countries are not recorded in Australia, and therefore pose a biosecurity risk. Analysed separately, the states and territories were identified as forming five separate clusters, each with a different region of the world, and with different characteristic PPN. Many of the PPN found in the regions clustered with an Australian state have not been recorded from anywhere in Australia, and others have very restricted distributions within Australia, thus posing different biosecurity risks. The SOM analysis ranked the risks of the different PPN based on likelihoods of establishment. The rankings confirmed the risks from frequently quarantined PPN, but more importantly identified species, which upon further investigation could be new threats. This method can be used to identify previously overlooked species for more detailed risk assessments. © 2013 Springer Science+Business Media Dordrecht.


Kriticos D.J.,CSIRO | Kriticos D.J.,Charles Sturt University | Kriticos D.J.,Cooperative Research Center for Plant Biosecurity | Le Maitre D.C.,South African Council for Scientific and Industrial Research | And 2 more authors.
Journal of Biogeography | Year: 2013

A recent review by Dormann et al. (2012, Journal of Biogeography, 39, 2119-2131) has proposed that methods for the modelling of species distributions be considered as a continuum. We disagree with this thesis, and contend that attempting to present the diverse range of methods as a continuum is unhelpful and ultimately not convincing. It adds to the confusion about the strengths and weaknesses of the diversity of available modelling methods, what exactly it is that they model, and the most appropriate applications. We highlight variation within and between modelling methods that is obscured by the continuum framework and propose that context of application and clarity of method are critical elements for future discourse on the topic. © 2013 Blackwell Publishing Ltd.


Singh S.K.,CSIRO | Singh S.K.,Graham Center for Agricultural Innovation | Singh S.K.,Cooperative Research Center for Plant Biosecurity | Hodda M.,CSIRO | And 2 more authors.
Annals of Applied Biology | Year: 2013

Few species of plant-parasitic nematodes (PPN) are currently recognised as invasive but this is largely because of insufficient investigation and recognition. We compared the characteristics of PPN with those of invasive species generally, using the propagule pressure, abiotic and biotic factors (PAB) framework. Most PPN had many of the characteristics of invasive species and hence have the potential to become invasive. The most common characteristics included: adaptations for human mediated dispersal; multiple entry pathways; microscopic size; large number of propagules; high fecundity; many or cosmopolitan hosts; short lifecycle; ability to survive harsh or unfavourable conditions; ability to vary sex ratios; and ability to overcome host plant resistance. Information is lacking for many characteristics of many species and their impacts remain unquantified, which leaves some important unanswered questions and challenges for assessing PPN as invasive species. However many economically important PPN species have not been recognised as invasive, even when most of the known characteristics and data suggests they should be. © 2013 Association of Applied Biologists.


Cui F.,Kansas State University | Cui F.,CAS Institute of Zoology | Cui F.,Cooperative Research Center for Plant Biosecurity | Michael Smith C.,Kansas State University | And 4 more authors.
Insect Science | Year: 2012

The Russian wheat aphid (RWA), Diuraphis noxia (Mordvilko) (Homoptera: Aphididae), is a major pest of small grains. As with plant-feeding aphids in general, the interaction between RWA and host plants is governed, on the insect side, by proteins and enzymes in saliva. In this work, we examined sequence variations in transcripts encoding proteins and enzymes of RWA salivary glands. We conducted reverse transcription - polymerase chain reaction in RWA biotypes 1 and 2 using primers derived from pea aphid orthologs, and cloned regions of 17 putative salivary gland transcripts. For four of the transcripts, we observed no difference in sequences between the two biotypes. For the other 13 transcripts, for example, the transcripts encoding sucrase, trehalase and protein C002, large amount of variations, both within each biotype and between the two biotypes, were observed. Usually the two biotypes shared only one variant, which was typically the most common variant in both biotypes. Most of the transcripts had more non-synonymous than synonymous codon changes among their variants. Our results offer possible molecular markers for distinguishing the two biotypes and insights into their evolution. © 2012 The Authors Insect Science © 2012 Institute of Zoology, Chinese Academy of Sciences.

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