Mark Whattam
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View article: Protecting Australia’s plant health: plant quarantine in an evolving biosecurity system†
Protecting Australia’s plant health: plant quarantine in an evolving biosecurity system† Open
As a geographically isolated and island continent, Australia has historically been protected from the impact of many damaging plant pests found overseas. However, the advent of modern transport systems and greater global trade in live plan…
View article: Development of a rapid, accurate, and field deployable LAMP-CRISPR-Cas12a integrated assay for Xylella fastidiosa detection and surveillance
Development of a rapid, accurate, and field deployable LAMP-CRISPR-Cas12a integrated assay for Xylella fastidiosa detection and surveillance Open
Xylella fastidiosa is an aggressive plant pathogenic bacterium of significant quarantine concern. Accurate and reliable detection tools are essential to minimise the risk of the pathogen’s spread and for outbreak control, as limited post-i…
View article: Implementation of GA-VirReport, a Web-Based Bioinformatics Toolkit for Post-Entry Quarantine Screening of Virus and Viroids in Plants
Implementation of GA-VirReport, a Web-Based Bioinformatics Toolkit for Post-Entry Quarantine Screening of Virus and Viroids in Plants Open
High-throughput sequencing (HTS) of host plant small RNA (sRNA) is a popular approach for plant virus and viroid detection. The major bottlenecks for implementing this approach in routine virus screening of plants in quarantine include lac…
View article: Side-by-Side Comparison of Post-Entry Quarantine and High Throughput Sequencing Methods for Virus and Viroid Diagnosis
Side-by-Side Comparison of Post-Entry Quarantine and High Throughput Sequencing Methods for Virus and Viroid Diagnosis Open
Rapid and safe access to new plant genetic stocks is crucial for primary plant industries to remain profitable, sustainable, and internationally competitive. Imported plant species may spend several years in Post Entry Quarantine (PEQ) fac…
View article: Complete Genome Sequence of a Novel Potyvirus Infecting Miscanthus Sinensis (Silver Grass)
Complete Genome Sequence of a Novel Potyvirus Infecting Miscanthus Sinensis (Silver Grass) Open
Here, we describe the full-length genome sequence of a novel potyvirus, tentatively named “miscanthus sinensis mosaic virus” (MsiMV), isolated from Miscanthus sinensis (silver grass) held in a post entry quarantine facility following its i…
View article: A Rapid and Cost-Effective Identification of Invertebrate Pests at the Borders Using MinION Sequencing of DNA Barcodes
A Rapid and Cost-Effective Identification of Invertebrate Pests at the Borders Using MinION Sequencing of DNA Barcodes Open
The rapid and accurate identification of invertebrate pests detected at the border is a challenging task. Current diagnostic methods used at the borders are mainly based on time consuming visual and microscopic examinations. Here, we demon…
View article: Evolution of Plant Virus Diagnostics Used in Australian Post Entry Quarantine
Evolution of Plant Virus Diagnostics Used in Australian Post Entry Quarantine Open
As part of a special edition for MDPI on plant virology in Australia, this review provides a brief high-level overview on the evolution of diagnostic techniques used in Australian government Post-Entry Quarantine (PEQ) facilities for testi…
View article: Start Clean, Stay Clean
Start Clean, Stay Clean Open
Starting clean and staying clean is one of the simplest ways to maximise. [...]
View article: Additional file 11: of An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids
Additional file 11: of An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids Open
Summary of VirFind screening of small RNA-Seq datasets collected from quarantined plants. A) VirFind blastn results. Identified viruses/viroids were also identified using our VSD toolkit. B) VirFind blastx results. Identified viruses/viroi…
View article: Additional file 12: of An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids
Additional file 12: of An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids Open
VirFind BLASTX results for contigs with sequence simalrity to viruses or viroids. (XLSX 50Â kb)
View article: Additional file 4: of An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids
Additional file 4: of An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids Open
Paired sample t-test of contigs produced by SPAdes, Velvet, ABySS and SOAPdenovo assemblers. Our optimised ‘SPAdes K15-17-19_cap3’ (SPAdes assembly; dataset = 21–22 nt; kmer set =15,17 and 19; and scaffolded with CAP3) (SP22_K15-17-19_cap3…
View article: Additional file 1: of An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids
Additional file 1: of An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids Open
Adaptor clipped and quality trimmed read statistics of small RNA-Seq datasets. Clean reads = Adaptor clipped small RNA reads provided by BGI service provider; QC = Quality Control consisting of adaptor clipping and poor base call trimming;…
View article: Additional file 6: of An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids
Additional file 6: of An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids Open
Statistics of the viral sequences assembled using 21–25 nt, 21–22 nt and 24 nt small RNA subsets. *Virus name: GRSPaV = Grapevine rupestris stem pitting-associated virus; GVB = Grapevine virus B; GFkV = Grapevine fleck virus; GLRaV-3 = Gra…
View article: Additional file 14: of An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids
Additional file 14: of An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids Open
VirFind contigs annotated with hits to viruses were run through the Yabi VSD toolkit pipeline. Top BLASTX hits (Evalueâ =â < 1e-5) to a combined plant and virus protein database are reported. VirFind assembled contigs with a top hit to a p…