Transcriptome responses to Ralstonia solanacearum infection in the roots of the wild potato Solanum commersonii
Zuluaga Cruz, Andrea Paola (Centre de Recerca en Agrigenòmica)
Solé Castellví, Montserrat (Centre de Recerca en Agrigenòmica)
Lu, Haibin (Centre de Recerca en Agrigenòmica)
Góngora-Castillo, Elsa (Michigan State University. Department of Plant Biology)
Vaillancourt, Brieanne (Michigan State University. Department of Plant Biology)
Sánchez Coll, Núria (Centre de Recerca en Agrigenòmica)
Buell, Robin (Michigan State University. Department of Plant Biology)
Valls, Marc (Centre de Recerca en Agrigenòmica)

Date:	2015
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.
Grants:	Ministerio de Economía y Competitividad AGL2010-21870 Agència de Gestió d'Ajuts Universitaris i de Recerca 2011/SGR-0052 Agència de Gestió d'Ajuts Universitaris i de Recerca 2010/CONES0030
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Subject:	Solanum commersonii ; Bacterial wilt ; Brown rot ; Ralstonia solanacearum ; RNA sequencing ; Transcriptome ; Disease resistance
Published in:	BMC genomics, Vol. 16, art. 246 (2015) , ISSN 1471-2164

DOI: 10.1186/s12864-015-1460-1
PMID: 25880642

16 p, 1.6 MB

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Research literature > UAB research groups literature > Research Centres and Groups (research output) > Experimental sciences > CRAG (Centre for Research in Agricultural Genomics)
Articles > Research articles
Articles > Published articles