Abstract
Bacterial spot caused by Xanthomonas arboricola pv. pruni (Xap) is a major threat to Prunus species worldwide. The molecular mechanisms of peach resistance to Xap during early leaf infection were investigated by RNA-Seq analysis of two Prunus persica cultivars, ‘Redkist’ (resistant), and ‘JH Hale’ (susceptible) at 30 minutes, 1 and 3 hours-post-infection (hpi). Both cultivars exhibited extensive modulation of gene expression at 30 mpi, which reduced significantly at 1 hpi, increasing again at 3 hpi. Overall, 714 differentially expressed genes (DEGs) were detected in ‘Redkist’ (12% at 30 mpi and 1 hpi and 88% at 3 hpi). In ‘JH Hale’, 821 DEGs were identified (47% at 30 mpi and 1 hpi and 53% at 3 hpi). Highly up-regulated genes (fold change > 100) at 3 hpi exhibited higher fold change values in ‘Redkist’ than in ‘JH Hale’. RNA-Seq bioinformatics analyses were validated by RT-qPCR. In both cultivars, DEGs included genes with putative roles in perception, signal transduction, secondary metabolism, and transcription regulation, and there were defense responses in both cultivars, with enrichment for the gene ontology terms, ‘immune system process’, ‘defense response’, and ‘cell death’. There were particular differences between the cultivars in the intensity and kinetics of modulation of expression of genes with putative roles in transcriptional activity, secondary metabolism, photosynthesis, and receptor and signaling processes. Analysis of differential exon usage (DEU) revealed that both cultivars initiated remodeling their transcriptomes at 30 mpi; however, ‘Redkist’ exhibited alternative exon usage for a greater number of genes at every time point compared with ‘JH Hale’. Candidate resistance genes (WRKY-like, CRK-like, Copper amine oxidase-like, and TIR-NBS-LRR-like) are of interest for further functional characterization with the aim of elucidating their role in Prunus spp. resistance to Xap.
Highlights
Xanthomonas arboricola pv. pruni (Xap) is the causal agent of bacterial spot on stone fruits and it is distributed widely across all continents. [1]
To explore the very early defense response of resistant (‘Redkist’) and susceptible (‘JH Hale’) peach cultivars to Xap, the transcriptomes of infected leaves at 30 mpi, 1, and 3 hpi were subjected to massively parallel sequencing using the Illumina NGS platform
After quality selection and trimming, an average of 68 million single reads were available for mapping per sample, which together (1.09 billion reads) provided an extensive snapshot of the defense response of peach to Xap (Table C, D, E in S1 File)
Summary
Xanthomonas arboricola pv. pruni (Xap) is the causal agent of bacterial spot on stone fruits and it is distributed widely across all continents. [1]. This bacterium affects all stone fruit crops, including Prunus davidiana and Prunus mume as well as the ornamental species Prunus laurocerasus, Prunus japonica and their derived hybrids [2,3]. Peach [Prunus persica (L.) Batsch] is one of the most important fruit crops in temperate regions with a global annual production of 25 million tonnes The P. persica genome sequence was obtained by an international consortium [5] and was recently improved [6], generating a high-quality genome sequence with a large portion of sequences mapped to chromosomes, high accuracy, and high contiguity, representing an important tool for functional and comparative genomics in the genus Prunus, as well as the Rosaceae family, due to its high quality [6,7]
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