Tree Genetics & Genomes

, Volume 10, Issue 3, pp 489–502 | Cite as

Dual RNA-seq of the plant pathogen Phytophthora ramorum and its tanoak host

  • Katherine J. Hayden
  • Matteo Garbelotto
  • Brian J. Knaus
  • Richard C. Cronn
  • Hardeep Rai
  • Jessica W. Wright
Original Paper


Emergent diseases are an ever-increasing threat to forests and forest ecosystems and necessitate the development of research tools for species that often may have few pre-existing resources. We sequenced the mRNA expressed by the sudden oak death pathogen Phytophthora ramorum and its most susceptible forest host, tanoak, within the same tissue at two time points after inoculation, and in uninfected tanoak controls. Using the P. ramorum genome to differentiate host and pathogen transcripts, we detected more than 850 P. ramorum transcripts at 5 days post-inoculation and a concurrent upregulation of host genes usually associated with pathogenicity. At 1 day, in contrast, we did not detect pathogen expression or significant enrichment of functional categories of host transcripts relative to controls, highlighting the importance of sequencing depth for in planta studies of host–pathogen interactions. This study highlights processes in molecular host–pathogen interactions in forest trees and provides a first reference transcriptome for tanoak, allowing the preliminary identification of disease-related genes in this study and facilitating future work for this and other members of the family Fagaceae.


Hemibiotroph Host–pathogen interactions Oomycete Pathogenesis Sudden oak death 



We are grateful for funding provided by the Western Forest Transcriptome Survey of the USDA-Forest Service: Pacific Northwest Research Station, Pacific Southwest Research Station, and Rocky Mountain Research Stations; the Gordon and Betty Moore Foundation; and the National Science Foundation Ecology of Infectious Diseases Program. We thank Abdelali Barakat, Kenan Celtik, Tara Jennings, Alex Lundquist, Barb Rotz, and Chris Sullivan for generous assistance.

Data archiving statement

This Transcriptome Shotgun Assembly project has been deposited at DDBJ/EMBL/GenBank under the accession GAOS00000000. The version described in this paper is the first version, GAOS01000000.

Supplementary material

11295_2014_698_MOESM1_ESM.pdf (1.3 mb)
ESM 1 (PDF 1.32 MB)


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Copyright information

© Springer-Verlag Berlin Heidelberg (outside the USA) 2014

Authors and Affiliations

  • Katherine J. Hayden
    • 1
    • 5
    • 6
  • Matteo Garbelotto
    • 1
  • Brian J. Knaus
    • 2
  • Richard C. Cronn
    • 2
  • Hardeep Rai
    • 3
  • Jessica W. Wright
    • 4
  1. 1.Environmental Science, Policy, and ManagementUniversity of CaliforniaBerkeleyUSA
  2. 2.Pacific Northwest Research StationUSDA-Forest ServiceCorvallisUSA
  3. 3.Utah State UniversityLoganUSA
  4. 4.Pacific Southwest Research StationUSDA-Forest ServiceDavisUSA
  5. 5.Interactions Arbres-Microorganismes, UMR1136Université de LorraineVandoeuvre-lès-NancyFrance
  6. 6.Interactions Arbres-Microorganismes, UMR1136INRAChampenouxFrance

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