host origin, and mapped to the 8733580 cucumber genome . Through this analysis, we found that 
there was no significant difference in the total number of combined reads from different time points; however, the number of Ps. cubensis genes expressed at each time point was significantly different for all time point 11885967” comparisons. To assess the experimental variation attributable to biological variation, we compared the gene expression pattern of the genes expressed in both of our biological replicates. In total, our experiments showed very high levels of correlation for biological replicates .0.94; mRNA-Seq transcriptome profiles In concordance with our visual assessment of pathogen growth throughout the time course, our analyses showed a diversity of transcriptional changes in Ps. cubensis, as well as a correlation between gene expression levels and similar stages of pathogen growth. In support of this, we identified 7,821 genes expressed at different time points of infection and 129 of those genes, mostly housekeeping, were expressed throughout all time points. Analyses of the top 20 highly expressed genes showed that genes expressed at earlier time points have substantially higher FPKM values than the genes expressed at later time points, consistent with the fewer numbers of genes expressed in the early stages of expression and saturation of detection of Ps. cubensis expression with our sampling depth. For all time points analyzed, the minimum FPKM value was zero but the maximum FPKM values ranoefficient values for comparisons of different time points ranged from 0.26 to 0.79 . Corresponding with our visual assessment of pathogen infection stages showing similar growth at 2 and 3 dpi, gene expression patterns at 2 dpi are strongly associated with that of 3 dpi. MedChemExpress Tangeritin Similarly, genes expressed at 6 dpi showed high correlation with the genes from 8 dpi, which represent comparable stages of pathogen growth and proliferation in the mesophyll. Additionally, at 1 dpi when encystment of zoospores is occurring, we observed a poor correlation between expression at that time point with any other time point, likely due to the unique set of genes that would be involved in this process. Interestingly, gene expression at 3 dpi was highly correlated with other time points, suggesting that events occurring at 3 dpi may represent a transition phase between early and late infection. Differential gene expression To identify genes specifically involved in distinct stages of pathogen infection and development, and to assess gene expression mRNA-seq Analysis of Cucurbit Downy Mildew pattern changes over the course of infection, we next evaluated differentially expressed genes between all time points. To provide context for the differential expression, we included expression data from mRNA-Seq analysis of sporangia in which 8,254 Ps. cubensis genes were expressed. In concordance with the similarities observed during our visualization of pathogen growth, comparisons with the least number of differentially expressed genes are those between early time points, with only 147 genes differentially expressed between 1 and 2 dpi. Additionally, 1 and 2 dpi had fewer differentially expressed genes compared to sporangia than the later time points. Of all the combinations tested, 1 dpi had the highest percentage of differentially expressed genes across all pair-wise comparisons, despite having the lowest number of genes expressed, indicating that the events occurring at this stage of in