We anchored the P. capsici transcriptome using its draft genome as a reference, investigated the global gene expression in three important life cycle stages and identified a large number of genes associated with specific stages and pathogenicity. We identified 13,901, 14,633 and 14,695 genes from the reads of the MY, ZO and GC libraries, respectively. We showed that about 70% of the P. capsici genes in LT1534 genome are represented in our study. The remaining 30% of conserved eukaryotic genes may not have been sampled because not all developmental and infection stages of P. capsici were represented in our material. Comparative analysis between two of samples showed major differences between the expressed gene content of MY, ZO and GC stages. A suite of genes associated with specific stages and pathogenicity were identified between two of samples. These transcriptional shifts generally agreed with the biological process of the pathogen. This was confirmed by the analysis of differentially expressed genes, which showed major transitional shifts between the libraries from the different groups. The distinction of ZO and GC from MY is probably due to its divergence from non-mycelium status. The GC was an especially distinct group with more differentially expressed genes detected, probably because the initial hostpathogen interaction Oxysophocarpine occurred during this stage can reasonably be expected to modify the pathogen’s expression profile. Additionally the GC stage is transitory between the ZO and MY stages. The results of KEGG pathway enrichment analysis lend support to the biological significance of gene expression profiles derived from the deep sequencing, which will assist in the discovery and annotation of P. capsici genes playing key roles in development and particularly in pre-infection stages. It is not surprising that the ��ribosome-related’pathways were the most Tubeimoside-I affected for the DEGs more common in ZO and GC libraries. This finding implies that the oomycete utilizes new ribosomes or changes in ribosome components to help synthesize additional proteins to facilitate its swimming towards potential host plants and subsequent germination on host surface. Sequencing of plant pathogenic oomycetes has revealed a variable number of effectors in different species. In the present study, 99 P. capsici effector genes were identified with known or putative roles in virulence. We predicted that these RXLRs, CRNs, NLPs and elicitins would be highly expressed during pre-infection and infection stages. Our results partially supported our hypothesis, in that these effectors were mostly induced in planta. A study by Haas et al., in which the authors examined genome-wide expression in P. infestans over four time points from 2 to 5 dpi of potato, revealed similar results that in general RXLRs showed early expression. Interestingly, the elicitin class 
showed the induction at GC and infection stages for P. capsici, whereas there were no elicitins induced at all during infection by P. infestans. DEG analysis showed that in contrast to ZO, only 3 CRNs showed increased expression at GC compared with MY. This implied that some CRNs were probably repressed at GC stage. In a recent study on P. capsici CRNs, based on contrasting gene expression profiles, Stam et al. defined two classes of CRN effectors. We noted from the RT-PCR result that two tested CRN genes fell into Class 1 featuring high levels of expression at the early time points, a decrease during subsequent biotrophic stages and expression in the later stages.