The Effector Repertoire of the Hop Downy Mildew Pathogen Pseudoperonospora humuli.

Megan J. Bowman,Savithri Purayannur,Kevin L. Childs,Liliana M. Cano,David H. Gent,Lina M. Quesada-Ocampo

doi:10.3389/fgene.2020.00910

Abstract

Pseudoperonospora humuli is an obligate biotrophic oomycete that causes downy mildew (DM), one of the most destructive diseases of cultivated hop that can lead to 100% crop loss in susceptible cultivars. We used the published genome of P. humuli to predict the secretome and effectorome and analyze the transcriptome variation among diverse isolates and during infection of hop leaves. Mining the predicted coding genes of the sequenced isolate OR502AA of P. humuli revealed a secretome of 1,250 genes. We identified 296 RXLR and RXLR-like effector-encoding genes in the secretome. Among the predicted RXLRs, there were several WY-motif-containing effectors that lacked canonical RXLR domains. Transcriptome analysis of sporangia from 12 different isolates collected from various hop cultivars revealed 754 secreted proteins and 201 RXLR effectors that showed transcript evidence across all isolates with reads per kilobase million (RPKM) values > 0. RNA-seq analysis of OR502AA-infected hop leaf samples at different time points after infection revealed highly expressed effectors that may play a relevant role in pathogenicity. Quantitative RT-PCR analysis confirmed the differential expression of selected effectors. We identified a set of P. humuli core effectors that showed transcript evidence in all tested isolates and elevated expression during infection. These effectors are ideal candidates for functional analysis and effector-assisted breeding to develop DM resistant hop cultivars.

Highlights

Downy mildew (DM) pathogens are a group of obligate biotrophic oomycetes that belong to the Peronosporales lineage oomycetes and have caused epidemics in many agriculturally important plants including grapes (Gessler et al, 2011), spinach (Correll et al, 2011), cucumber (Holmes et al, 2015), and lettuce (Parra et al, 2016), to name a few
We generated a nuclear phylogenetic tree of P. humuli with the 10 other oomycete species listed in Section “Phylogenetic Analysis of Nuclear Genes” using 362 of the core eukaryotic housekeeping genes described by Parra et al (2007), P. humuli and its sister species P. cubensis were clustered in a group with maximum bootstrap support confirming their close relationship (Figure 1)
Other downy mildew (DM) pathogens such as P. tabacina, and the Arabidopsis DM H. arabidopsidis formed sister groups and separated themselves from the sunflower DM pathogen P. halstedii and Phytophthora species

Summary

Introduction

Downy mildew (DM) pathogens are a group of obligate biotrophic oomycetes that belong to the Peronosporales lineage oomycetes and have caused epidemics in many agriculturally important plants including grapes (Gessler et al, 2011), spinach (Correll et al, 2011), cucumber (Holmes et al, 2015), and lettuce (Parra et al, 2016), to name a few. Despite their economic importance, Pseudoperonospora humuli Effectors. This avirulence function of effectors can be used in plant improvement programs to search for genotypes that contain R genes against core in planta expressed pathogen effectors (Jones et al, 2014; Vleeshouwers and Oliver, 2014)

Methods

Results

Conclusion