A Survey on the Methods of Primer Design Among Plant Pathologists in Australia and New Zealand

Designing primers for PCR-based diagnostics was achieved by executing sight searches on DNA sequences. Visual searching for specific DNA targets is time consuming, subjective and requires optimisation among numerous candidate primer sets. Several primer design software have been linked to useful bioinformatic packages to speed the development of PCR assays. Despite the software options available, primer design has remained a challenging aspect of incursion responses, biosecurity emergencies and microbial forensic applications. Two surveys were conducted among 45 plant virologists and 21 other plant pathologists during the 7th Australasian Plant Virology Workshop and the 16th Biennial Australasian Plant Pathology Conference in 2006 and 2007, respectively. Results show that most primer design learning occurs scientist to scientist rather than during academic teaching. This tendency matches with 16% of scientists users of PCR, who do not engage in primer design and 25% designing primers only by visual means, combining a pool of 41% who if trained, would likely enhance their performance in primer design. Only 13 out of 58 scientists ranked themselves as experts. Implementing primer design in study programs and regional training will benefit plant pathology and entomology, and the responsiveness and performance of biosecurity and microbial forensics in the South Pacific.

One stop shop IV: taxonomic update with molecular phylogeny for important phytopathogenic genera: 76-100 (2020)

This is a continuation of a series focused on providing a stable platform for the taxonomy of phytopathogenic fungi and fungus-like organisms.This paper focuses on one family:Erysiphaceae and 24 phytopathogenic genera:Armillaria,Barrio-psis,Cercospora,Cladosporium,Clinoconidium,Colletotrichum,Cylindrocladiella,Dothidotthia,,Fomitopsis,Ganoderma,Golovinomyces,Heterobasidium,Meliola,Mucor,Neoerysiphe,Nothophoma,Phellinus,Phytophthora,Pseudoseptoria,Pythium,Rhizopus,Stemphylium,Thyrostroma and Wojnowiciella.Each genus is provided with a taxonomic background,distribution,hosts,disease symptoms,and updated backbone trees.Species confirmed with pathogenicity studies are denoted when data are available.Six of the genera are updated from previous entries as many new species have been described.

One stop shopⅢ:taxonomic update with molecular phylogeny for important phytopathogenic genera:51–75(2019)

This is a continuation of a series focused on providing a stable platform for the taxonomy of phytopathogenic fungi and organisms.This paper focuses on 25 phytopathogenic genera:Alternaria,Capnodium,Chaetothyrina,Cytospora,Cyphellophora,Cyttaria,Dactylonectria,Diplodia,Dothiorella,Entoleuca,Eutiarosporella,Fusarium,Ilyonectria,Lasiodiplodia,Macrophomina,Medeolaria,Neonectria,Neopestalotiopsis,Pestalotiopsis,Plasmopara,Pseudopestalotiopsis,Rosellinia,Sphaeropsis,Stagonosporopsis and Verticillium.Each genus is provided with a taxonomic background,distribution,hosts,disease symptoms,and updated backbone trees.A new database(Onestopshopfungi)is established to enhance the current understanding of plant pathogenic genera among plant pathologists.

One stop shop Ⅱ:taxonomic update with molecular phylogeny for important phytopathogenic genera:26–50(2019)

This paper is the second in a series focused on providing a stable platform for the taxonomy of phytopathogenic fungi.It focuses on 25 phytopathogenic genera:Alternaria,Bipolaris,Boeremia,Botryosphaeria,Calonectria,Coniella,Corticiaceae,Curvularia,Elsinoe,Entyloma,Erythricium,Fomitiporia,Fulviformes,Laetisaria,Limonomyces,Neofabraea,Neofusicoccum,Phaeoacremonium,Phellinotus,Phyllosticta,Plenodomus,Pseudopyricularia,Tilletia,Venturia and Waitea,using recent molecular data,up to date names and the latest taxonomic insights.For each genus a taxonomic background,diversity aspects,species identification and classification based on molecular phylogeny and recommended genetic markers are provided.In this study,varieties of the genus Boeremia have been elevated to species level.Botryosphaeria,Bipolaris,Curvularia,Neofusicoccum and Phyllosticta that were included in the One Stop Shop 1 paper are provided with updated entries,as many new species have been introduced to these genera.

First determination of the highly genotoxic fungal contaminant altertoxin II in a naturally infested apple sample

Altertoxin II is an epoxide-holding perylene quinone and secondary metabolite produced by Alternaria molds.Its genotoxic potential and the high concentrations determined in laboratory fungal cultures resulted in an increased scientific interest in this emerging contaminant.However,no natural occurrence in food has been reported to date to the best of our knowledge.Here,we unambiguously identified altertoxin II in a naturally infected,unprocessed apple.Applying a validated LC-MS/MS method,fruit peel spots(approx.1 mm in diameter),typically associated with Alternaria infestation,were tested for 17 mycotoxins produced by this genus.Negligible concentrations of tentoxin were determined 24 h after harvest,and the dibenzopyrones alternariol,alternariol monomethyl ether(AME)and AME-3-sulfate after six months of storage.Overall,these contamination patterns can be considered unlikely to be of toxicological concern for consumers.However,an inconspicuous peel lesion(0.5×1 cm)separately sampled from a stored apple,exhibited considerably high concentrations of 14 Alternaria toxins,including dibenzopyrones,their barely studied modified forms(glucosides and sulfates),as well as genotoxic perylene quinones including altertoxin II.Considering the toxicological potential of this compound,contaminations in such infected fruit parts should not be underestimated,e.g.in the case of exposure through the consumption of fresh smoothies or fruit juices.