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

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.

Common bean resistance to Xanthomonas is associated with upregulation of the salicylic acid pathway and downregulation of photosynthesis.

“…The speci c suppression of photosynthesis, sugar metabolism and other chloroplast-associated genes observed in BAT93 re ects a rather classical defense response. Indeed, similar trends have been described using transcriptomics in different interactions between plants and bacteria [91][92][93][94] and integration of transcriptomic data from different pathosystems led to the hypothesis that suppression of photosynthesis is part of the plant adaptive immunity [95]. In addition, several studies have shown that incompatible interaction is linked to a decrease in photosynthetic activity [96][97][98][99] and that inhibition of photosynthesis often leads to the accumulation of reactive oxygen species [100].…”

Common bean resistance to Xanthomonas is associated with upregulation of the salicylic acid pathway and downregulation of photosynthesis

“…The specific suppression of photosynthesis, sugar metabolism and other chloroplast-associated genes observed in BAT93 reflects a rather classical defense response. Indeed, similar trends have been described using transcriptomics in different interactions between plants and bacteria [83][84][85], and integration of transcriptomic data from different pathosystems led to the hypothesis that suppression of photosynthesis is part of the plant adaptive immunity [86]. In addition, several studies have shown that incompatible interaction is linked to a decrease in photosynthetic activity [87][88][89][90] and that inhibition of photosynthesis often leads to the accumulation of reactive oxygen species [91].…”

Time-series expression profiling of sugarcane leaves infected withPuccinia kuehniireveals an ineffective defense system leading to susceptibility

“…Additionally, we observed that 83 genes 505 were upregulated at 48 hai. Downregulation of genes associated with photosynthesis is a 506 general phenomenon that can support defense response initiation against biotic stresses 507 [113,114], which is evidenced in RNA-Seq of infected leaves of other species [34,37,100]. 508 Our data shows that this repression occurred for a majority of genes in the first 12 509 hours after inoculation with P.kuehnii, later restored to basal expression levels at 48 hai 510 (Fig 1-C).…”

“…Furthermore, this kind 462 of response can be delayed in compatible interactions [107]. Hence, high expression of 463 PAL-encoding genes is a common attribute of resistant cultivars [31,34], including 464 those of sugarcane [39,40,42]. In the P. kuehnii pathosystem the five DEGs annotated 465 as PAL were repressed at 12 hai, but three of them were upregulated in the next hours, 466 returning to the basal level at 5 dai (Fig 2-C).…”

“…A peroxiredoxin of defense response to bacterium was stimulated 549 at 48 hai, possibly as a result of the presence of ROS, because it is a sensor peroxidase 550 [81]. Amine oxidases collaborate in ROS production and are upregulated in resistant 551 apple and peach plants submitted to biotic stress [34,121]. These genes formed a large 552 group characterized by repression at 12 hai, with some members showing an LFC less 553 than -2.0 until 24 hai (S4 File-E).…”