Cloning of Phytophthora capsici effector genes to guide the development of resistant pepper varieties.

As part of the project EffeCaps, we generated 8 transcriptomes from plant tissues from two pepper genotypes that differ in their level of resistance to Phytophthora capsici, infected each with 2 isolates of P. capsici which differ in their level of aggressiveness, and at 2 times after inoculation (24 and 72 hpi). These 8 observed conditions (2 host genotypes x 2 P. capsici isolates x 2 times) were independently repeated 3 times, bringing to 24 the number of biological samples sequenced. The construction of libraries and the HiSeq 2 sequencing were performed on transcriptomics platform of URGV INRA of Evry. The sequence data were acquired in September 213. The sequencing of the 24 biological samples delivered 46 billion sequences. The first bio-analysis showed the exceptional quality of the acquired data set. It has been shown that the samples sequenced contained many more sequences from the host than from the pathogene. This data sets were compared to a library of known P. capsici effectors to identify those that were expressed in our samples. Our data revealed that 641 known P. capsici genes encoding RXLR effectors were expressed. Similarly, we identified effectors that are expressed differentially between pepper genotypes, or between isolates of P. capsici, or else, between sampling times after inoculation.