Abstract
Key message
Host perception of Phytophthora nicotianae switching to necrotrophy is fundamental for disease tolerance of citrus. It involves an HR-like response, strengthening of the cell wall structure and hormonal signaling.
Abstract
Stem rot caused by P. nicotianae is a worldwide disease of several important crops, including citrus. Given the growing awareness of chemical fungicides drawbacks, genetic improvement of citrus rootstocks remains the best alternative. However, the molecular basis underlying the successful response of resistant and/or tolerant genotypes remains poorly understood. Therefore, we performed a transcriptomic analysis to examine the differential defense response to P. nicotianae of two germplasms—tolerant sour orange (SO, Citrus aurantium) and susceptible Madam Vinous (MV, C. sinensis)—in both the biotrophic and necrotrophic phases of host–pathogen interaction. Our results revealed the necrotrophic phase as a decisive turning point, since it included stronger modulation of a number of genes implicated in pathogen perception, signal transduction, HR-like response, transcriptional reprogramming, hormone signaling, and cell wall modifications. In particular, the pathogen perception category reflected the ability of SO to perceive the pathogen even after its switch to necrotrophy, and thus to cope successfully with the infection, while MV failed. The concomitant changes in genes involved in the remaining functional categories seemed to prevent pathogen spread. This investigation provided further understanding of the successful defense mechanisms of C. aurantium against P. nicotianae, which might be exploited in post-genomic strategies to develop resistant Citrus genotypes.
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Acknowledgements
The NGS activity was conducted by the Illumina platform of “Rete di laboratori pubblici di ricerca SELGE-Regione Puglia (cod. 14)” (http://www.selge.uniba.it). Arwa Ajengui was supported by a mobility grant from the Tunisian Ministry of Higher Education and Scientific Research. We thank Dr. Sarah Jane Christopher for her critical English revision.
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ESM_1
. RNA-sequencing adapters, number of trimmed and mapped reads on Citrus sinensis genome. (DOCX 13 KB)
ESM_2
. Comparison of RT-qPCR relative expression values and RNA-seq data of a selection of DEGs from in the tolerant (SO) and susceptible (MV) rootstocks inoculated by Phytophthora nicotianae at 24 (1) and 168 (2) HPI. Values (reported as log2 fold change) are mean ± SEM of two biological and technical replicates. Primers used in RT-qPCR validation assay are reported. (XLSX 15 KB)
ESM_3
. A) Percentage of mapped reads against the reference genome Citrus sinensis. X-axis represents the two plant germplasms used in the experiment. Each RNA-seq library is represented by a dot within the boxplot. Y-axis represents the percentage of mapped reads. B) Heatmap representing the sample distance of the dataset. (PPTX 228 KB)
ESM_4
. MA-plots of genes modulated in: A) the tolerant (SO) vs. susceptible (MV) germplasm at 24 and 168 HPI by Phytophthora nicotianae (biotrophic and necrotrophic phases, respectively); B) at 24 vs. 168 HPI by P. nicotianae in SO and MV germplasms. (PPTX 1135 KB)
ESM_5
. List of DEGs MV1 vs. SO1 included in the Functional categories of Table 2. DEGs with FDR<0.1 were grouped based on MAPMAN distribution and literature evaluation. (XLSX 192 KB)
ESM_6
. List of DEGs MV2 vs. SO2 included in the Functional categories of Table 2. DEGs with FDR<0.1 were grouped based on MAPMAN distribution and literature evaluation. (XLSX 787 KB)
ESM_7
. List of DEGs MV1vs. MV2 included in the Functional categories of Table 3. DEGs with FDR<0.1 were grouped based on MAPMAN distribution and literature evaluation. (XLSX 848 KB)
ESM_8
. List of DEGs SO1 vs. SO2 included in the Functional categories of Table 3. DEGs with FDR<0.1 were grouped based on MAPMAN distribution and literature evaluation. (XLSX 827 KB)
ESM_9
. List of DEGs in the tolerant (SO) vs. susceptible (MV) germplasm, during the biotrophic (24 HPI) and necrotrophic (168 HPI) phases of Phytophthora nicotianae infection, associated with “pathogen perception and signalling” category and included in Figure 3. (XLSX 31 KB)
ESM_10
. List of DEGs in the tolerant (SO) vs. susceptible (MV) germplasm, during the biotrophic (24 HPI) and necrotrophic (168 HPI) phase of Phytophthora nicotianae infection, belonging to the “transcription factors” category and included in Figure 4. (XLSX 16 KB)
ESM_11
. List of DEGs in the tolerant (SO) vs. susceptible (MV) germplasm, during the biotrophic (24 HPI) and necrotrophic (168 HPI) phase of Phytophthora nicotianae infection, belonging to the “cell wall modifications” category and included in Figure 5. (XLSX 17 KB)
ESM_12
. List of DEGs in the tolerant (SO) vs. susceptible (MV) germplasm, during the biotrophic (24 HPI) and necrotrophic (168 HPI) phase of Phytophthora nicotianae infection, related to A) “proteasome functioning” and B) “response to auxin” categories and included in Figure 6. (XLSX 22 KB)
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Ajengui, A., Bertolini, E., Ligorio, A. et al. Comparative transcriptome analysis of two citrus germplasms with contrasting susceptibility to Phytophthora nicotianae provides new insights into tolerance mechanisms. Plant Cell Rep 37, 483–499 (2018). https://doi.org/10.1007/s00299-017-2244-7
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DOI: https://doi.org/10.1007/s00299-017-2244-7