Development of hop transcriptome to support research into host-viroid interactions

Area of Science:

• Plant Pathology
• Molecular Biology
• Genomics

Background:

• Viroids are small, protein-less pathogens causing significant plant diseases.
• Viroid pathogenicity is linked to host gene silencing via viroid-derived small RNAs (vd-sRNAs).
• Hop plants (Humulus lupulus) are susceptible to viroids like Hop Latent Viroid (HLVd) and Chrysanthemum Stunt Viroid (CSVd), exhibiting varied disease severity.

Purpose of the Study:

• To construct a comprehensive hop transcriptome for studying host-viroid interactions.
• To identify potential hop gene targets of vd-sRNAs from HLVd and CSVd using in-silico methods.
• To analyze the expression of candidate target genes and pathogenesis-related genes in infected hop plants.

Main Methods:

• Deep next-generation sequencing (NGS) of hop transcriptome (35 Gb data).
• Assembly of NGS data into hop contigs (over 74 Mb).
• In-silico prediction of vd-sRNA targets using two software tools.
• Expression analysis via RT-qPCR for selected transcripts and pathogenesis-related genes.

Main Results:

• A deep hop transcriptome was generated, serving as a resource for host-pathogen interaction studies.
• In-silico analysis predicted 1062 and 1387 hop transcripts as potential targets for HLVd- and CSVd-vd-sRNAs, respectively.
• Expression analysis indicated upregulation of pathogenesis-related genes and potential downregulation of specific host genes (GATA transcription factor, linoleate 13S-lipoxygenase) by vd-sRNAs.

Conclusions:

• The study provides a valuable hop transcriptome resource.
• It offers the first detailed insights into the molecular mechanisms of viroid-hop interactions, including potential gene silencing pathways.
• Findings highlight the role of vd-sRNAs in modulating host gene expression during viroid infection.