Analysis of differentially expressed Sclerotinia sclerotiorum genes during the interaction with moderately resistant and highly susceptible chickpea lines
- Disruption of the S. - sclerotiorum CAZymes arabinofuranosidase/β-xylosidase and an endo-β-1, 4-xylanase showed reduced or lost virulence [18], an indication of their importance in the growth and virulence of the pathogen.. - (2) catalogue upregulated and downregulated genes in the S. - At 72 hpi, the average percentage of reads mapping to the fungal genome in the S line was higher (68.1%) than in the MR line (61.8. - The larger lesions found on the S line at the later stage of infection during the current study (re- sults not shown) and greater abundance of fungal RNA in the S line samples together suggest that it exhibited greater levels of fungal colonisation than the MR line.. - 72 hpi, an indication of the significant differences in the types of genes expressed at these time points.. - 2a) were similar to the expression observed in the RNA-seq data (Fig. - Based on the distinct differences between the in planta and in vitro samples demonstrated in the MDS plot (Fig.. - Comparing the transcription changes in the MR and S lines showed that there were also differences between lines in expression of some S. - sclerotiorum genes relative to in vitro, with 82 and 251 genes upregulated exclu- sively in the MR or S line, respectively (Figure S2, Table S4). - There were 42 genes with functional domains expressed either in the MR or S line only and these are involved in cell wall degradation, secondary metabolite biosynthesis, transport, detoxification, and signalling (Figure S2).. - A gene in- volved in the pentose-phosphate pathway (sscle_. - 01g005580) was upregulated in the MR line only. - Expression analysis of the MR versus S line at each time point showed that genes with different expression relative to in vitro in the two lines. - This included two genes downregulated in the MR relative to the S line (upregulated in the S line) at 6 hpi and the other two upregulated in the MR relative to the S line (downregu- lated in S line) at 48 hpi. - These four genes are predicted in the S. - The BPs highly enriched in the significantly upregulated set of genes, during the early stage of infection, included oxidation-reduction process (GO:0055114), protein meta- bolic process (GO:0019538), proteolysis (GO:0006508), cellular response to stimulus (GO:0051716) signal trans- duction (GO:0007165), carbohydrate metabolic process (GO:0005975) and metabolic processes (GO:0008152) (Table S5). - The BP category oxidation-reduction process (GO:0055114) was highly enriched exclusively in genes upregulated in the MR line at 6 hpi and 48 hpi, suggesting that S. - The most significantly enriched GO categories in the current study grouped into carbohydrate-active enZYmes (CAZymes), proteases, transporters, transcription factors and other secondary metabolites. - Genes involved in the degradation of the host cuticle The plant cuticle is the first physical barrier to pathogen invasion and is composed of lipid-derived polyester and cuticular waxes [32]. - In the current study, S. - Lipases were also reported to act as virulence factors in the fungal phytopathogen B.. - Genes involved in the degradation of the host cell wall As a necrotroph, degradation of the host cell wall is im- portant during S. - A portion of the numerous cell wall degrading en- zymes (CWDEs) identified in the S. - Another gene encoding an aspartyl protease, sscle_07g058540, was upregulated at all stages of infec- tion in the current study, with a peak expression relative to in vitro at 24 hpi (Table S7). - sclero- tiorum and make up to 47.2% of the upregulated SM biosynthesis clusters in the current study (Table S8).. - Glutathione S-transferases (GSTs) play critical roles in the detoxification of xenobiotic chemicals in fungi by. - sclerotiorum genes involved in the cell wall and cuticle degradation. - Substrate CWDE category Number of upregulated genes in the category. - Ssbgt1 plays a role in the degradation of the antimicrobial compound brassinin through glycosylation and is induced in response to the presence of a variety of plant phytoalexins [44].. - Other GSTs induced in planta in the current study were sscle_01g005000 (logFC in both lines and sscle_08g067590 (logFC in the MR line, at 24–72 hpi (Table 3). - Disruption of GST genes AbGSOT1 and AbUre2pB1 in the host generalist brassica pathogen Alternaria brassicicola led to reduced virulence [45].. - sclerotiorum transcription factors were upregulated in the current study (Table S9). - Pac1 was upregulated at 12 hpi in the S line only (LogFC = 2.8) during chickpea infection (Table S9). - sclerotiorum expressed genes with the 523 secreted proteins identified in the S. - Of these, 173 were upregulated in both varieties, and 148 downregu- lated, with nine of the upregulated genes observed in the MR variety only and 27 in the S variety only (Table S10).. - Of the identified S. - In the current study, SsSSVP1 was upregulated at 48 hpi in the MR line and 72 hpi in the S line (logFC = 5.1 and 5.7), respectively (Table S11). - The earlier induction SsSSVP1 of in the MR line (48 hpi) compared to the S line (72 hpi) may suggest that temporal regulation of ex- pression of SsSSVP1 may depend on host susceptibility level.. - In the current study, SsNEP1 (sscle_04g039420) was not differentially expressed, and SsNEP2 (sscle_12g090490) was upregu- lated at the later stages of infection (48 hpi in MR and at 48–72 hpi In S lines) relative to in vitro (Table S11).. - The pattern of sscle_09g069850 expression in the current study may suggest involvement in both the biotrophic and necrotic stages during chickpea interaction.. - 15g104430, were upregulated during the late stage of in- fection (48–72 hpi) in the MR and 72 hpi in the S line (Table 4). - The upregulation of catalases and peroxi- dases was observed at an early stage in the MR line and later stage in the S line during infection, suggesting S.. - The number of reads that mapped to each gene in the reference (read counts/gene counts) were generated using HTseq package v . - org/10.1186/s . - Primers used in the validation of RNA sequencing data.. - LogFC upregulated ≥ 2 and downregulated ≤ 2).The colours indicate the fold change with red = upregulated, black = regulated and green = downregulated genes.. - LogFC upregulated ≥ 2 and downregulated ≤ 2).The colours indicate the fold change with red. - sclerotiorum proteins that are available in the NCBI protein database.. - https://doi.org . - https://doi.org/10.1016/j.plantsci . - Changes in the Sclerotinia sclerotiorum transcriptome during infection of Brassica napus. - https://doi.org/10.1186/s . - https://doi.. - 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