Transcriptome responses to Ralstonia solanacearum infection in the roots of the wild potato Solanum commersonii
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 Ra...
| Autores: | , , , , , , , |
|---|---|
| Formato: | artículo |
| Fecha de publicación: | 2015 |
| País: | España |
| Recursos: | Universitat Autònoma de Barcelona |
| Repositorio: | Dipòsit Digital de Documents de la UAB |
| Idioma: | inglés |
| OAI Identifier: | oai:ddd.uab.cat:175934 |
| Acesso em linha: | https://ddd.uab.cat/record/175934 https://dx.doi.org/urn:doi:10.1186/s12864-015-1460-1 |
| Access Level: | acceso abierto |
| Palavra-chave: | Solanum commersonii Bacterial wilt Brown rot Ralstonia solanacearum RNA sequencing Transcriptome Disease resistance |
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Transcriptome responses to Ralstonia solanacearum infection in the roots of the wild potato Solanum commersoniiZuluaga Cruz, Andrea Paola|||0000-0002-3003-4856Solé Castellví, MontserratLu, Haibin|||0000-0002-0613-4697Góngora-Castillo, ElsaVaillancourt, BrieanneSánchez Coll, Núria|||0000-0002-8889-0399Buell, RobinValls, Marc|||0000-0003-2312-0091Solanum commersoniiBacterial wiltBrown rotRalstonia solanacearumRNA sequencingTranscriptomeDisease resistanceBackground: 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. 22015-01-0120152015-01-01Articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://ddd.uab.cat/record/175934https://dx.doi.org/urn:doi:10.1186/s12864-015-1460-1reponame:Dipòsit Digital de Documents de la UABinstname:Universitat Autònoma de BarcelonaInglésengMinisterio de Ciencia e Innovación https://doi.org/10.13039/501100004837 AGL2010-21870Agència de Gestió d'Ajuts Universitaris i de Recerca https://doi.org/10.13039/501100003030 2011/SGR-0052Agència de Gestió d'Ajuts Universitaris i de Recerca https://doi.org/10.13039/501100003030 2010/CONES0030open accesshttp://purl.org/coar/access_right/c_abf2Aquest 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.https://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:ddd.uab.cat:1759342026-06-06T12:50:31Z |
| dc.title.none.fl_str_mv |
Transcriptome responses to Ralstonia solanacearum infection in the roots of the wild potato Solanum commersonii |
| title |
Transcriptome responses to Ralstonia solanacearum infection in the roots of the wild potato Solanum commersonii |
| spellingShingle |
Transcriptome responses to Ralstonia solanacearum infection in the roots of the wild potato Solanum commersonii Zuluaga Cruz, Andrea Paola|||0000-0002-3003-4856 Solanum commersonii Bacterial wilt Brown rot Ralstonia solanacearum RNA sequencing Transcriptome Disease resistance |
| title_short |
Transcriptome responses to Ralstonia solanacearum infection in the roots of the wild potato Solanum commersonii |
| title_full |
Transcriptome responses to Ralstonia solanacearum infection in the roots of the wild potato Solanum commersonii |
| title_fullStr |
Transcriptome responses to Ralstonia solanacearum infection in the roots of the wild potato Solanum commersonii |
| title_full_unstemmed |
Transcriptome responses to Ralstonia solanacearum infection in the roots of the wild potato Solanum commersonii |
| title_sort |
Transcriptome responses to Ralstonia solanacearum infection in the roots of the wild potato Solanum commersonii |
| dc.creator.none.fl_str_mv |
Zuluaga Cruz, Andrea Paola|||0000-0002-3003-4856 Solé Castellví, Montserrat Lu, Haibin|||0000-0002-0613-4697 Góngora-Castillo, Elsa Vaillancourt, Brieanne Sánchez Coll, Núria|||0000-0002-8889-0399 Buell, Robin Valls, Marc|||0000-0003-2312-0091 |
| author |
Zuluaga Cruz, Andrea Paola|||0000-0002-3003-4856 |
| author_facet |
Zuluaga Cruz, Andrea Paola|||0000-0002-3003-4856 Solé Castellví, Montserrat Lu, Haibin|||0000-0002-0613-4697 Góngora-Castillo, Elsa Vaillancourt, Brieanne Sánchez Coll, Núria|||0000-0002-8889-0399 Buell, Robin Valls, Marc|||0000-0003-2312-0091 |
| author_role |
author |
| author2 |
Solé Castellví, Montserrat Lu, Haibin|||0000-0002-0613-4697 Góngora-Castillo, Elsa Vaillancourt, Brieanne Sánchez Coll, Núria|||0000-0002-8889-0399 Buell, Robin Valls, Marc|||0000-0003-2312-0091 |
| author2_role |
author author author author author author author |
| dc.subject.none.fl_str_mv |
Solanum commersonii Bacterial wilt Brown rot Ralstonia solanacearum RNA sequencing Transcriptome Disease resistance |
| topic |
Solanum commersonii Bacterial wilt Brown rot Ralstonia solanacearum RNA sequencing Transcriptome Disease resistance |
| description |
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. |
| publishDate |
2015 |
| dc.date.none.fl_str_mv |
2 2015-01-01 2015 2015-01-01 |
| dc.type.none.fl_str_mv |
Article http://purl.org/coar/resource_type/c_6501 VoR http://purl.org/coar/version/c_970fb48d4fbd8a85 |
| dc.type.openaire.fl_str_mv |
info:eu-repo/semantics/article |
| format |
article |
| dc.identifier.none.fl_str_mv |
https://ddd.uab.cat/record/175934 https://dx.doi.org/urn:doi:10.1186/s12864-015-1460-1 |
| url |
https://ddd.uab.cat/record/175934 https://dx.doi.org/urn:doi:10.1186/s12864-015-1460-1 |
| dc.language.none.fl_str_mv |
Inglés eng |
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Inglés |
| language |
eng |
| dc.relation.none.fl_str_mv |
Ministerio de Ciencia e Innovación https://doi.org/10.13039/501100004837 AGL2010-21870 Agència de Gestió d'Ajuts Universitaris i de Recerca https://doi.org/10.13039/501100003030 2011/SGR-0052 Agència de Gestió d'Ajuts Universitaris i de Recerca https://doi.org/10.13039/501100003030 2010/CONES0030 |
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open access http://purl.org/coar/access_right/c_abf2 https://creativecommons.org/licenses/by/4.0/ |
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info:eu-repo/semantics/openAccess |
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open access http://purl.org/coar/access_right/c_abf2 https://creativecommons.org/licenses/by/4.0/ |
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openAccess |
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