Fig_3_Type_II_MADS_genes_peach

Unrooted Bayesian consensus tree of Type II MADS-box proteins from peach and Arabidopsis. Bayesian posterior probabilities for all clades are given at their respective nodes

Fig_2_Type_I_MADS_genes_peach

Unrooted Bayesian consensus tree of Type I MADS-box proteins from peach and Arabidopsis. Bayesian posterior probabilities for all clades are given at their respective nodes

Fig_5_FLC_genes

Unrooted maximum likelihood phylogenetic tree of MADS-box proteins from the FLC subfamily in peach, Arabidopsis, grapevine, poplar, maize, sorghum, and rice. Bayesian posterior probabilities for all clades are given at their respective nodes

Fig_4_SVP_AGL24_genes

Unrooted Bayesian consensus tree of MADS-box proteins from the SVP/AGL24 subfamily in peach, Arabidopsis, grapevine, poplar, maize, sorghum, and rice. Bayesian posterior probabilities for all clades are given at their respective nodes

Transcriptome reprogramming of resistant and susceptible peach genotypes during <i>Xanthomonas arboricola</i> pv. <i>pruni</i> early leaf infection

<div><p>Bacterial spot caused by <i>Xanthomonas arboricola</i> pv. <i>pruni</i> (Xap) is a major threat to <i>Prunus</i> species worldwide. The molecular mechanisms of peach resistance to Xap during early leaf infection were investigated by RNA-Seq analysis of two <i>Prunus persica</i> 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 (<i>WRKY</i>-like, <i>CRK</i>-like, <i>Copper amine oxidase</i>-like, and <i>TIR-NBS-LRR</i>-like) are of interest for further functional characterization with the aim of elucidating their role in <i>Prunus</i> spp. resistance to Xap.</p></div

Distribution of frequency classes of gene expression levels (RPKM) after Xap inoculation on leaves of ‘JH Hale’ (susceptible) and ‘Redkist’ (resistant) peach cultivars.

<p>Distribution of frequency classes of gene expression levels (RPKM) after Xap inoculation on leaves of ‘JH Hale’ (susceptible) and ‘Redkist’ (resistant) peach cultivars.</p

RNA-Seq read statistics before mapping and after quality selection and trimming.

<p>RNA-Seq read statistics before mapping and after quality selection and trimming.</p

MA plot of genes differentially expressed (red dots) by two peach varieties during a time course after Xap infection.

<p>DEGs were selected by filtering based on log₂ (FC) > 2, or log₂ (FC) < -2, and FDR < 0.05.</p

Significantly enriched GO terms (Biological processes) in the susceptible cultivar ‘JH Hale’ at 30 mpi with Xap.

<p>Significantly enriched GO terms (Biological processes) in the susceptible cultivar ‘JH Hale’ at 30 mpi with Xap.</p

Relative fold change (FC) of expression levels of genes regulated in both ‘Redkist’ (resistant) and in ‘JH Hale’ (susceptible) peach cultivars after Xap infection; max FC = 2216, min FC = -49.

<p>Relative fold change (FC) of expression levels of genes regulated in both ‘Redkist’ (resistant) and in ‘JH Hale’ (susceptible) peach cultivars after Xap infection; max FC = 2216, min FC = -49.</p