GSE23453
Global-gene expression of Phytophthora  phaseoli
Lima bean is an important vegetable processing crop to the Mid-Atlantic U.S. and is highly susceptible to the oomycete pathogen Phytophthora phaseoli, which causes downy mildew.  P. phaseoli resides in the same clade with the late blight pathogen, Phytophthora infestans.  Genetic resistance and fungicides are used to manage P. phaseoli and often fail.  Currently there are no molecular data on this pathosystem.  To rectify this situation and determine virulence mechanisms in P. phaseoli we performed a whole-transcriptome analysis using Illumina mRNA-Seq.  Six libraries were generated and compared, plate-grown and plant-grown.  Our data were normalized and were matched to the P. infestans gene models to obtain the abundance of the sequence reads.  This resulted in 10,427 P. phaseoli genes with homology to P. infestans and with expression in either one of the libraries.  Upon closer examination, 318 P. phaseoli-homologs matched either known or putative virulence genes in P. infestans.  We present data from the whole transcriptome as well as specifically chosen genes from this set of 318.  Interestingly, in six libraries from P. phaseoli we found a commonly expressed gene set of 66 out of 563 predicted RXLR genes in P. infestans.  The majority of the differentially expressed RxLR and elicitin-like were up-regulated in planta, while the reverse was true for crinkler homologs.  These results are discussed with respect to possible pathogenicity mechanisms in P. phaseoli and how they compare to P. infestans. Overall design: Examination of 3 different conditions of Phytophthora phaseoli