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Genome sequencing and transcriptome analysis of the hop downy mildew pathogen Pseudoperonospora humuli reveal species-specific genes for diagnostics

Alamgir Rahman: NCSU

<div><em>Pseudoperonospora humuli</em> is an obligate oomycete pathogen of hop (<em>Humulus lupulus</em>) that causes downy mildew, an important disease in most production regions in the world. The pathogen can cause a systemic infection in hop, overwinter in the rhizomes, and infect propagation material. Nonetheless, no species-specific diagnostic assays or genome sequence are available for <em>P. humuli</em>. The genome of the isolate <em>P. humuli</em> OR502AA was 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 <em>P. humuli</em> isolates. Bioinformatics analysis of next-generation sequencing (NGS) reads of <em>P. humuli</em> and <em>P. cubensis</em> (a closely related sister species) identified 242 candidate species-specific <em>P. humuli</em> genes that could be used as diagnostic molecular markers. These candidate genes were validated using PCR against a diverse collection of isolates from <em>P. humuli</em>, <em>P. cubensis</em>, and other oomycetes. Overall four diagnostic markers were found to be uniquely present only in <em>P. humuli</em>. These candidate markers identified through comparative genomics can be used for pathogen diagnostics or adapted for biosurveillance of airborne sporangia, another important source of inoculum in hop downy mildew epidemics.</div>