title: Transcriptome responses to Ralstonia solanacearum infection in the roots of the wild potato Solanum commersonii.
abstract: BACKGROUND
  Solanum commersonii is a wild potato species that exhibits high tolerance to both biotic and abiotic stresses and has been used as a source of genes for introgression into cultivated potato. Among the interesting features of S. commersonii is resistance to the bacterial wilt caused by Ralstonia solanacearum, one of the most devastating bacterial diseases of crops.
  
  
  RESULTS
  In this study, we used deep sequencing of S. commersonii RNA (RNA-seq) to analyze the below-ground plant transcriptional responses to R. solanacearum. While a majority of S. commersonii RNA-seq reads could be aligned to the Solanum tuberosum Group Phureja DM reference genome sequence, we identified 2,978 S. commersonii novel transcripts through assembly of unaligned S. commersonii RNA-seq reads. We also used RNA-seq to study gene expression in pathogen-challenged roots of S. commersonii accessions resistant (F118) and susceptible (F97) to the pathogen. Expression profiles obtained from read mapping to the S. tuberosum reference genome and the S. commersonii novel transcripts revealed a differential response to the pathogen in the two accessions, with 221 (F118) and 644 (F97) differentially expressed genes including S. commersonii novel transcripts in the resistant and susceptible genotypes. Interestingly, 22.6% of the F118 and 12.8% of the F97 differentially expressed genes had been previously identified as responsive to biotic stresses and half of those up-regulated in both accessions had been involved in plant pathogen responses. Finally, we compared two different methods to eliminate ribosomal RNA from the plant RNA samples in order to allow dual mapping of RNAseq reads to the host and pathogen genomes and provide insights on the advantages and limitations of each technique.
  
  
  CONCLUSIONS
  Our work catalogues the S. commersonii transcriptome and strengthens the notion that this species encodes specific genes that are differentially expressed to respond to bacterial wilt. In addition, a high proportion of S. commersonii-specific transcripts were altered by R. solanacearum only in F118 accession, while phythormone-related genes were highly induced in F97, suggesting a markedly different response to the pathogen in the two plant accessions studied.
authors.affiliation: Genetics Department, Universitat de Barcelona and Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB) Edifici CRAG, Campus UAB, Bellaterra, 08193, Catalonia, Spain. apd22@cornell.edu.
authors.forename: A Paola
authors.initials: AP
authors.lastname: Zuluaga
authors.affiliation: Genetics Department, Universitat de Barcelona and Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB) Edifici CRAG, Campus UAB, Bellaterra, 08193, Catalonia, Spain. montserrat.sole.castellvi@gmail.com.
authors.forename: Montserrat
authors.initials: M
authors.lastname: Solé
authors.affiliation: Genetics Department, Universitat de Barcelona and Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB) Edifici CRAG, Campus UAB, Bellaterra, 08193, Catalonia, Spain. haibin.lu@cragenomica.es.
authors.forename: Haibin
authors.initials: H
authors.lastname: Lu
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA. casti111@msu.edu.
authors.forename: Elsa
authors.initials: E
authors.lastname: Góngora-Castillo
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA. vaillan6@msu.edu.
authors.forename: Brieanne
authors.initials: B
authors.lastname: Vaillancourt
authors.affiliation: Genetics Department, Universitat de Barcelona and Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB) Edifici CRAG, Campus UAB, Bellaterra, 08193, Catalonia, Spain. nuria.sanchez-coll@cragenomica.es.
authors.forename: Nuria
authors.initials: N
authors.lastname: Coll
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA. buell@msu.edu.
authors.forename: C Robin
authors.initials: CR
authors.lastname: Buell
authors.affiliation: Genetics Department, Universitat de Barcelona and Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB) Edifici CRAG, Campus UAB, Bellaterra, 08193, Catalonia, Spain. marcvalls@ub.edu.
authors.forename: Marc
authors.initials: M
authors.lastname: Valls
mesh_terms: D060467:Disease Resistance / Q000235:genetics; D018745:Genome, Plant; D005838:Genotype; D054884:Host-Pathogen Interactions / Q000235:genetics; D010935:Plant Diseases / Q000382:microbiology; D010937:Plant Growth Regulators / Q000494:pharmacology; D018517:Plant Roots / Q000235:genetics / Q000382:microbiology; D043368:Ralstonia solanacearum / Q000502:physiology*; D017423:Sequence Analysis, RNA; D032322:Solanum / Q000235:genetics* / Q000382:microbiology; D059467:Transcriptome / Q000187:drug effects; D015854:Up-Regulation / Q000187:drug effects
chemical_list: D010937:Plant Growth Regulators