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ARS Home » Pacific West Area » Corvallis, Oregon » Forage Seed and Cereal Research Unit » Research » Publications at this Location » Publication #357196
Title: Genome sequencing and transcriptome analysis of the hop downy mildew pathogen Pseudoperonospora humuli reveal species-specific genes for molecular detection

Author
item RAHMAN, A - North Carolina State University
item GONGORA-CASTILLO, E - North Carolina State University
item BOWMAN, M - Michigan State University
item CHILDS, K - Michigan State University
item Gent, David - Dave
item Martin, Frank
item QUESADA-OCAMPO, L - North Carolina State University

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/26/2019
Publication Date: 6/26/2019
Citation: Rahman, A., Gongora-Castillo, E., Bowman, M., Childs, K., Gent, D.H., Martin, F.N., Quesada-Ocampo, L.M. 2019. Genome sequencing and transcriptome analysis of the hop downy mildew pathogen Pseudoperonospora humuli reveal species-specific genes for molecular detection. Phytopathology. 109(8):1354-1366. https://doi.org/10.1094/PHYTO-11-18-0431-R.
DOI: https://doi.org/10.1094/PHYTO-11-18-0431-R

Interpretive Summary: Downy mildew is an important disease of hop in many production regions. In this research, we developed improved molecular markers that can be used to conclusively identify the pathogen and differentiate the pathogen on hop from closely related downy mildew on other host plants. To do, an isolate of the hop downy mildew pathogen was obtained and the genome partially sequenced. Genes uniquely expressed in the pathogen were identified from multiple isolates. Ultimately, four molecular markers were identified that were robust across all samples and did not give false positive reactions with a broad collection of other organisms tested. These candidate markers can be used for pathogen diagnostics in infected tissue and planting material, or may be adapted for biosurveillance of airborne spores.

Technical Abstract: Pseudoperonospora humuli is an obligate oomycete pathogen of hop (Humulus lupulus) that causes downy mildew, an important disease in most production regions in the northern hemisphere. The pathogen can cause a systemic infection in hop, overwinter in the root system, and infect propagation material. Substantial yield loss may occur due to P. humuli infection of strobiles (seed cones), shoots, and cone-bearing branches. Fungicide application and cultural practices are the primary methods to manage hop downy mildew . However, effective, sustainable, and cost effective management of downy mildew can be improved by developing early detection systems to inform disease risk and better time fungicide usage. However, no species-specific diagnostic assays or genomic resources are available for P. humuli. The genome of isolate P. humuli OR502AA was partially sequenced using Illumina technology and assembled with ABySS . The assembly had a minimum scaffold length of 500bp and a N50 of 19.2 Kbp. A total number of 18,656 genes were identified using MAKER-standard gene predictions. Additionally, transcriptome assemblies were generated using RNA-seq and Trinity for seven additional P. humuli isolates. Bioinformatics analyses of next-generation sequencing reads of P. humuli and P. cubensis (a closely related sister species) identified 242 candidate species-specific P. humuli genes that could be used as diagnostic molecular markers. These candidate genes were validated using PCR against a diverse collection of isolates from P. humuli, P. cubensis, and other oomycetes. Overall, four diagnostic markers were found to be uniquely present in P. humuli. These candidate markers identified through comparative genomics can be used for pathogen diagnostics in tissue and planting material or adapted for biosurveillance of airborne sporangia, an important source of inoculum in hop downy mildew epidemics.