Dual RNA-seq of the plant pathogen Phytophthora ramorum and its tanoak host
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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.
KeywordsHemibiotroph 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.
- Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene Ontology: tool for the unification of biology. Nat Genet 25:25–29. doi: 10.1038/75556 PubMedCentralPubMedCrossRefGoogle Scholar
- Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B 57:289–300Google Scholar
- Croucher PJP, Mascheretti S, Garbelotto M (2013) Combining field epidemiological information and genetic data to comprehensively reconstruct the invasion history and the microevolution of the sudden oak death agent Phytophthora ramorum (Stramenopila: Oomycetes) in California. Biol Invasions 15:2281–2297. doi: 10.1007/s10530-013-0453-8Google Scholar
- Davidson J, Werres S, Garbelotto M, et al. (2003) Sudden Oak Death and associated diseases caused by Phytophthora ramorum. PHP. doi: 10.1094/PHP-2003-0707-01-DG
- Duran A, Gryzenhout M, Slippers B et al (2008) Phytophthora pinifolia sp nov associated with a serious needle disease of Pinus radiata in Chile. Plant Pathol 57:715–727. doi: 10.1111/j.1365-3059.2008.01893.x
- Erwin DC, Ribeiro OK (1996) Phytophthora diseases worldwide. APS, St. PaulGoogle Scholar
- Fung RWM, Gonzalo M, Fekete C, Kovacs LG, He Y, Marsh E, McIntyre LM, Schachtman DP, Qiu W (2008) Powdery mildew induces defense-oriented reprogramming of the transcriptome in a susceptible but not in a resistant grapevine. Plant Physiol 146:236–249. doi: 10.1104/pp. 107.108712 PubMedCentralPubMedCrossRefGoogle Scholar
- Hansen E, Reeser P, Davidson J et al (2003) Phytophthora nemorosa, a new species causing cankers and leaf blight of forest trees in California and Oregon, USA. Mycotaxon 88:129–138Google Scholar
- Hayden KJ, Garbelotto M, Dodd R, Wright JW (2013) Scaling up from greenhouse resistance to fitness in the field for a host of an emerging forest disease. Evol App. doi: 10.1111/eva.12080
- Kleemann J, Rincon-Rivera LJ, Takahara H et al (2012) Sequential delivery of host-induced virulence effectors by appressoria and intracellular hyphae of the phytopathogen Collectrotrichum higginsianum. PLoS Pathog 8:e1002643. doi: 10.1371/journal.ppat.1002643 PubMedCentralPubMedCrossRefGoogle Scholar
- Lee S-J, Rose JK (2010) Mediation of the transition from biotrophy to necrotrophy in hemibiotrophic plant pathogens by secreted effector proteins. Plant Signal Behav 5:769–772Google Scholar
- Pachter L (2011) Models for transcript quantification from RNA-Seq. arXiv.org arXiv:1104.3889v2 [q-bio.GN].Google Scholar
- Risso D, Schwartz K, Sherlock G, Dudoit S (2011) GC-Content normalization for RNA-seq data. BMC Bioinformatics 12:480. doi: 10.1186/1471-2105-12-480
- Roberts A, Pachter L (2013) Streaming fragment assignment for real-time analysis of sequencing experiments. Nat Meth 10:71–73. doi: 10.1038/nmeth.2251
- Stamm E, Parke J (2013) The effect of Phytophthora ramorum on the physiology and xylem function of young tanoak trees. Proceedings of the Fifth Sudden Oak Death Science Symposium, June 19–22, 2012, Petaluma, CA, USA GTR PSWXXXGoogle Scholar
- Ueno S, Provost GL, Léger V, et al (2010) Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak. BMC Genomics 11:650. doi: 10.1186/1471-2164-11-650