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Damage caused by  Phytophthora cinnamomi  Rands remains an important concern on forest tree species. The pathogen causes root and collar rot, stem cankers, and dieback of various economically important  Eucalyptus  spp. In South Africa, susceptible cold tolerant  Eucalyptus  plantations have been affected by various  Phytophthora  spp. with  P. cinnamomi  considered one of the most virulent. The molecular basis of this compatible interaction is poorly understood. In this study, susceptible  Eucalyptus nitens  plants were stem inoculated with  P. cinnamomi  and tissue was harvested five days post inoculation. Dual RNA-sequencing, a technique which allows the concurrent detection of both pathogen and host transcripts during infection, was performed. Approximately 1% of the reads mapped to the draft genome of  P. cinnamomi  while 78% of the reads mapped to the  Eucalyptus grandis  genome. The highest expressed  P. cinnamomi  gene  in planta  was a putative crinkler effector ( CRN1 ). Phylogenetic analysis indicated the high similarity of this  P. cinnamomi CRN1  to that of  Phytophthora infestans . Some CRN effectors are known to target host nuclei to suppress defense. In the host, over 1400 genes were significantly differentially expressed in comparison to mock inoculated trees, including suites of pathogenesis related ( PR ) genes. In particular, a  PR-9  peroxidase gene with a high similarity to a  Carica papaya PR-9  ortholog previously shown to be suppressed upon infection by  Phytophthora palmivora  was down-regulated two-fold. This  PR-9  gene may represent a cross-species effector target during  P. cinnamomi  infection. This study identified pathogenicity factors, potential manipulation targets, and attempted host defense mechanisms activated by  E. nitens  that contributed to the susceptible outcome of the interaction.

Dual RNA-Sequencing of Eucalyptus nitens during Phytophthora cinnamomi Challenge Reveals Pathogen and Host Factors Influencing Compatibility