Comparative transcriptional analysis of hop responses to infection with Verticillium nonalfalfae

Abstract

Key Message Dynamic transcriptome profiling revealed excessive, yet ineffective, immune response to V. nonalfalfae infection in susceptible hop, global gene downregulation in shoots of resistant hop and only a few infection-associated genes in roots. AbstractHop (Humulus lupulus L.) production is hampered by Verticillium wilt, a disease predominantly caused by the soil-borne fungus Verticillium nonalfalfae. Only a few hop cultivars exhibit resistance towards it and mechanisms of this resistance have not been discovered. In this study, we compared global transcriptional responses in roots and shoots of resistant and susceptible hop plants infected by a lethal strain of V. nonalfalfae. Time-series differential gene expression profiles between infected and mock inoculated plants were determined and subjected to network-based analysis of functional enrichment. In the resistant hop cultivar, a remarkably low number of genes were differentially expressed in roots in response to V. nonalfalfae infection, while the majority of differentially expressed genes were down-regulated in shoots. The most significantly affected genes were related to cutin biosynthesis, cell wall biogenesis, lateral root development and terpenoid biosynthesis. On the other hand, susceptible hop exhibited a strong defence response in shoots and roots, including increased expression of genes associated with plant responses, such as innate immunity, wounding, jasmonic acid pathway and chitinase activity. Strong induction of defence-associated genes in susceptible hop and a low number of infection-responsive genes in the roots of resistant hop are consistent with previous findings, confirming the pattern of excessive response of the susceptible cultivar, which ultimately fails to protect the plant from V. nonalfalfae. This research offers a multifaceted overview of transcriptional responses of susceptible and resistant hop cultivars to V. nonalfalfae infection and represents a valuable resource in the study of this plant-pathogen interaction.Electronic supplementary materialThe online version of this article (doi:10.1007/s00299-017-2177-1) contains supplementary material, which is available to authorized users.

Comprehensive analysis of Verticillium nonalfalfae in silico secretome uncovers putative effector proteins expressed during hop invasion

“…Genome-wide transcriptome analysis of the V . nonalfalfae interaction with hop [ 45 ] revealed that 766 (81%) transcripts in the V . nonalfalfae in silico secretome were expressed in infected hop samples.…”

“…nonalfalfae genomes [ 22 ], transcriptomic and proteomic research of fungal growth on xylem stimulating medium [ 44 ] and RNA-seq studies of V . nonalfalfae –hop interactions [ 45 ]. A customized bioinformatics platform was used to set up a pipeline for prediction and characterization of the V .…”

The invisibility cloak: Chitin binding protein ofVerticillium nonalfalfaedisguises fungus from plant chitinases

“…Proteins were classified into four groups: Lectin-like proteins (A), Chitinases (B), Chitin deacetlyases (C) and Xyloglucan endotransglucosylase (D). Gene expression is presented as a heatmap of log 2 CPM values determined by RNA sequencing of infected hop (Progar et al 2017).…”

“…RNA-Seq library preparation from V. nonalfalfae infected hop at 6, 12, 18 and 30 days post inoculation (dpi) and data processing have been previously described (Progar et al 2017). Fungal transcripts were filtered out and their gene expression profiles were generated using the Hierarchical clustering with Euclidean distance method in R language (R Core Team 2016).…”

Comparative Transcriptome Analysis Uncovers Genes and Pathways Relating to Downy Mildew Resistance in Isabgol (Plantago ovata Forsk.)

“…In the present study, maximum GO terms were assigned for cellular component indicating need for large number of CDS for cellular component activity. Maximum GO terms were assigned for cellular component category in plants such as Humulus lupulus, Brassica rapa, Oryza sativa, Bupleurum chinense, Cassia obtusifolia and Chrysanthemum[51][52][53][54][55][56]. In the cellular component category, highest number of CDS were associated with "membrane" followed by "cell" in infected and control leaf samples which indicates the need of large number of transcripts for…”