Transcriptomic analysis of pea roots infected with Aphanomyces euteiches

The oomycete Aphanomyces euteiches causes root rot in pea (Pisum sativum) and various legume species. The objective of this study was to investigate the molecular basis of resistance to a highly (UK16) and lowly (SE51) virulent A. euteiches strain in susceptible ('Linnea') and resistant ('PI180693') pea genotypes. RNA from infected roots at time points 6, 20 and 48 hours post infection was sequenced and trimming of the 54 libraries was done using Bbduk. To avoid mismapping, a combined index of the P. sativum reference genome 'Caméor' and the A. euteiches strain ATCC201684 was generated using STAR.