RT Journal Article
SR Electronic
T1 Time-resolved dual root-microbe transcriptomics reveals early induced <em>Nicotiana benthamiana</em> genes and conserved infection-promoting <em>Phytophthora palmivora</em> effectors
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 098855
DO 10.1101/098855
A1 Edouard Evangelisti
A1 Anna Gogleva
A1 Thomas Hainaux
A1 Mehdi Doumane
A1 Frej Tulin
A1 Clément Quan
A1 Temur Yunusov
A1 Kevin Floch
A1 Sebastian Schornack
YR 2017
UL http://biorxiv.org/content/early/2017/01/06/098855.abstract
AB Background Plant-pathogenic oomycetes are responsible for economically important losses on crops worldwide. Phytophthora palmivora, a broad-host-range tropical relative of the potato late blight pathogen, causes rotting diseases in many important tropical crops including papaya, cocoa, oil palm, black pepper, rubber, coconut, durian, mango, cassava and citrus.Transcriptomics have helped to identify repertoires of host-translocated microbial effector proteins which counteract defenses and reprogram the host in support of infection. As such, these studies have helped understanding of how pathogens cause diseases. Despite the importance of P. palmivora diseases, genetic resources to allow for disease resistance breeding and identification of microbial effectors are scarce.Results We employed the model plant N. benthamiana to study the P. palmivora root infections at the cellular and molecular level. Time-resolved dual transcriptomics revealed different pathogen and host transcriptome dynamics. De novo assembly of P. palmivora transcriptome and semi-automated prediction and annotation of the secretome enabled robust identification of conserved infection-promoting effectors. We show that one of them, REX3, suppresses plant secretion processes. In a survey for early transcriptionally activated plant genes we identified a N. benthamiana gene specifically induced at infected root tips that encodes a peptide with danger-associated molecular features.Conclusions These results constitute a major advance in our understanding of P. palmivora diseases and establish extensive resources for P. palmivora pathogenomics, effector-aided resistance breeding and the generation of induced resistance to Phytophthora root infections. Furthermore, our approach to find infection relevant secreted genes is transferable to other pathogen-host interactions and not restricted to plants.DEGdifferentially expressed genesCRNcrinkler effectorLFClog fold changeFDRfalse discovery rateORFopen reading frameTPMtranscripts per millionTMMtrimmed mean of m-valuesPCAprincipal component analysisBUSCObenchmarking universal single-copy orthologsREXputative RXLR-effector expressedNPPnecrosis-inducing Phytophthora proteinSCRsmall cysteine-rich peptidesPLTGPhytophthora palmivora transcribed genePIprotease inhibitorTMtransmembrane domainSPsignal peptideSESsymptoms extend stageaaamino acidhaihours after inoculationdaidays after inoculation