The informative gene sets identified and validated in this project has been developed into real-time quantitative PCR assays and integrated into genomics-based pathogen detection and monitoring tools.
A PCR assay is a reaction that amplifies a targeted DNA sequence by orders of magnitude to generate sufficient quantities for detection.Specific probes are designed to bind to the targeted sequences of pathogens. A positive signal is generated if the probe matches the sample DNA sequence in the reaction. A collection of assays will be put together strategically into an array. We are currently constructing 96 well and 384 well plates containing detection or diagnostic assays to form the array. These arrays can test a large number of targeted genes with a large number of samples and analysed simultaneously.
We currently have the following assays available for use. Please contact us if you are interested in these assays or should you wish to discuss on customizing an array.
|
Genera
|
Assay specific to – Species Name
|
Approach
|
|
Amylostereum
|
Amylostereum areolatum
|
SNP-based
|
|
Ceratocystis
|
Ceratocystis (C. coerulescens complex)
|
SNP-based
|
|
Ceratocystis polonica
|
SNP-based
|
|
Ceratocystis laricicola
|
SNP-based
|
|
Ceratocystis fujiensis
|
SNP-based
|
|
Ceratocystis fagacearum
|
SNP-based
|
|
Ceratocystis platani
|
SNP-based
|
|
Fusarium
|
Fusarium circinatum
|
SNP-based
|
|
Geosmithia
|
Geosmithia morbida
|
SNP-based
|
|
Gremmeniella
|
Gremmeniella abietina (EU race)
|
SNP-based
|
|
Heterobasidion
|
Heterobasidion annosum sensus lato
|
SNP-based
|
|
Heterobasidion irregulare
|
SNP-based
|
|
Heterobasidion occidentale
|
SNP-based
|
|
Hymenoscyphus
|
Chalara fraxinea
|
SNP-based
|
|
Lachnellula
|
Lachnellula willkommii
|
SNP-based
|
|
Marssonina
|
Marssonina brunnea
|
TAIGA – comparative genomics
|
|
Ophiostoma
|
Leptographium wageneri
|
SNP-based
|
|
Ophiostoma ulmi sensus lato
|
SNP-based
|
|
Ophiostoma ulmi sensus stricto
|
SNP-based
|
|
Ophiostoma novo-ulmi
|
SNP-based
|
|
Ophiostoma himal-ulmi
|
SNP-based
|
|
Phytophthora
|
Phytophthora quercina
|
SNP-based
|
|
Phytophthora cinnamomi
|
SNP-based
|
|
Phytophthora cinnamomi
|
TAIGA – comparative genomics
|
|
Phytophthora ramorum
|
TAIGA – comparative genomics
|
|
Phytophthora ramorum
|
SNP-based
|
|
P. ramorum NA1
|
TAIGA – comparative genomics
|
|
P. ramorum NA2
|
TAIGA – comparative genomics
|
|
P. ramorum EU1
|
TAIGA – comparative genomics
|
|
P. ramorum EU2
|
TAIGA – comparative genomics
|
|
Phytophthora lateralis
|
TAIGA – comparative genomics
|
|
P. lateralis + P. ramorum
|
TAIGA – comparative genomics
|
|
Phytophthora kernoviae
|
TAIGA – comparative genomics
|
|
Phytophthora pinifolia
|
TAIGA – comparative genomics
|
|
Pucciniales
|
Melampsora allii-populina (MAP)
|
TAIGA – comparative genomics
|
|
Melampsora pinitorqua (MP)
|
TAIGA – comparative genomics
|
|
Cronartium ribicola
|
TAIGA – comparative genomics
|
|
Cronartium comandrae
|
TAIGA – comparative genomics
|
|
Cronartium quercuum f. sp. fusiforme
|
TAIGA – comparative genomics
|
|
Endocronartium harknessii
|
TAIGA – comparative genomics
|
|
Rosellinia
|
Rosellinia necatrix
|
SNP-based
|
|
Sclerotinia
|
Sclerotinia pseudotuberosa
|
SNP-based
|
|
Xanthomonas
|
Xanthomonas populi
|
SNP-based
|
|
Venturia
|
Venturia nashicola
|
SNP-based
|