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Castanea root transcriptome in response to Phytophthora cinnamomi challenge

Abstract

The European chestnut, an important forest species for the economy of Southern Europe, covers an area of 2.53 million hectares, including 75,000 ha devoted to fruit production. Castanea sativa is declining due to ink disease caused by Phytophthora cinnamomi. To elucidate chestnut defense mechanisms to ink disease, we compared the root transcriptome of the susceptible species C. sativa and the resistant species C. crenata after P. cinnamomi inoculation. Four cDNA libraries were constructed, two of them included root samples from C. sativa, inoculated and non-inoculated and the other two libraries comprised samples from C. crenata at identical conditions. Pyrosequencing produced 771,030 reads and assembly set up 15,683 contigs for C. sativa and 16,828 for C. crenata. GO annotation revealed terms related to stress as “response to stimulus”, “transcription factor activity” or “signaling” for both transcriptomes. Differential gene expression analysis revealed that C. crenata involved more genes related with biotic stress upon pathogen inoculation than C. sativa. Those genes for both species are involved in regulation of plant immune response and stress adaptation and recovery. Furthermore, it is suggested that both species recognize the pathogen attack; however, the resistant species may involve more genes in the defense response than the susceptible species. RNA-seq enabled the selection of candidate genes for ink disease resistance in Castanea. The present data is a valuable contribution to the available Castanea genomic resources and constitutes the basis for further studies.

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Acknowledgments

We acknowledge Dr. Beatriz Cuenca (TRAGSA-SEPI) for providing the plant material used in this study. The authors are also grateful to Dr. Andreia Figueiredo (BioFIG) and Dr. Filipa Monteiro (BioFIG) for help on qRT-PCR, Dr. Conceição Egas (Next Gen Sequencing Unit, Biocant) for submitting raw data to NCBI, Dr. Dana Nelson (USDA Forest Service, MS, Unit of Forest genetics and Ecosystems Biology) for arrangements on submitting data to Fagaceae.org, and Prof. William Powell and Andrew Newhouse (SUNY College of Environmental Science and Forestry, NY, Department of Environmental and Forest Biology) for critical review of the manuscript. This work was funded by the Portuguese Foundation for Science and Technology (www.fct.pt) in the frame of the project Understanding Resistance to Pathogenic Fungi in Castanea sp (PTDC/AGR-CFL/101707/2008). Grant to SS (Investigador Ciência 2008) was also supported by FCT. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Data Archiving Statement

Raw data files can be accessed in the Short Read Archive at NCBI (http://www.ncbi.nlm.nih.gov/) with the reference PRJNA215368. Nucleotide and aminoacid sequences are publicly available in the Fagaceae Genomics Web (http://www.fagaceae.org/).

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Correspondence to Susana Serrazina.

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Mónica Sebastiana and Rita Costa contributed equally to this work.

Communicated by R. Sederoff.

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Serrazina, S., Santos, C., Machado, H. et al. Castanea root transcriptome in response to Phytophthora cinnamomi challenge. Tree Genetics & Genomes 11, 6 (2015). https://doi.org/10.1007/s11295-014-0829-7

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Keywords

  • Castanea sativa
  • Castanea crenata
  • Phytophthora cinnamomi
  • RNA-seq
  • Differentially expressed genes
  • Biotic stress