Comparative RNA-Seq Analysis of Early-Infected Peach Leaves by the Invasive Phytopathogen Xanthomonas arboricola pv. pruni

Abstract

Xanthomonas arboricola pv. pruni is a quarantine bacterial pathogen that threatens peach production by causing necrotic spots on leaves and fruits, thus with the potential of severely reducing yields. The current understanding of the host plant defense responses to the pathogen is very limited. Using whole transcriptome sequencing, differential gene expression was analyzed at two time points, 2 h and 12 h post inoculation (hpi), by comparing the inoculated samples to their respective controls. On the total of 19,781 known peach genes that were expressed in all time points and conditions, 34 and 263 were differentially expressed at 2 and 12 hpi, respectively. Of those, 82% and 40% were up-regulated, respectively; and 18% and 60% were down-regulated, respectively. The functional annotation based on gene ontology (GO) analysis highlighted that genes involved in metabolic process and response to stress were particularly represented at 2 hpi whereas at 12 hpi cellular and metabolic processes were the categories with the highest number of genes differentially expressed. Of particular interest among the differentially expressed genes identified were several pathogen-associated molecular pattern (PAMP) receptors, disease resistance genes including several RPM1-like and pathogenesis related thaumatin encoding genes. Other genes involved in photosynthesis, in cell wall reorganization, in hormone signaling pathways or encoding cytochrome were also differentially expressed. In addition, novel transcripts were identified, providing another basis for further characterization of plant defense-related genes. Overall, this study gives a first insight of the peach defense mechanisms during the very early stages of infection with a bacterial disease in the case of a compatible interaction.

Dual RNA-seq of pathogen and host

“…The ubiquitous polyadenylation of eukaryotic mRNAs and the sequence similarity of ribosomal transcripts facilitates the experimental protocol as it enables the poly(A) enrichment or ribosomal depletion for host and pathogen in a single step. Recently a few publications have reported the application of RNA-seq to a model of bacterial infection of plant leaves (Asai et al, 2014;Socquet-Juglard et al, 2013), porcine enterocytes (Vannucci et al, 2013), or human epithelial carcinoma cells (Humphrys et al, 2013). However, these suffered from the lack of an enrichment of invaded cells, resulting in a low bacterial transcriptome coverage, and/or from a shallow sequencing depth, hampering an in-depth profiling of the host response.…”

RNA-seq Transcriptome Response of Flax (Linum usitatissimum L.) to the Pathogenic Fungus Fusarium oxysporum f. sp. lini

“…RNA-seq studies of plant responses to fungal pathogens have been performed in numerous pathosystems including: lettuce infected by Botrytis cinerea (De Cremer et al, 2013), Arabidopsis thaliana after treatment with Pseudomonas syringae (Howard et al, 2013) chrysanthemum leaf after infection with Alternaria tenuissima (Li et al, 2014), a wheat resistant variety affected by Fusarium graminearum (Xiao et al, 2013), and the early infection of peach leaves by Xanthomonas arboricola (Socquet-Juglard et al, 2013). Specifically for the interaction with Fusarium oxysporum , studies were made in A. thaliana (Zhu et al, 2013b), banana roots (Li et al, 2012, 2013; Wang et al, 2012b), and cabbage (Xing et al, 2016); and additional research was made on the interaction of F. graminearum with wheat (Xiao et al, 2013; Erayman et al, 2015).…”

Identification and Expression Analysis of Candidate Genes Associated with Defense Responses to Phytophthora capsici in Pepper Line “PI 201234”

“…In recent years, RNA-seq technology has been widely used to provide precise gene expression measurements by mapping short reads to a reference genome [24,25,26,27,28]. In this study, Illumina paired-end sequencing technology was used to analyze root transcriptome changes in the highly resistant “PI 201234” line following P. capsici inoculation.…”