Limits...
A novel workflow correlating RNA-seq data to Phythophthora infestans resistance levels in wild Solanum species and potato clones.

Frades I, Abreha KB, Proux-Wéra E, Lankinen Å, Andreasson E, Alexandersson E - Front Plant Sci (2015)

Bottom Line: More transcript families were expanded in the resistant clones and species and the enriched functions of these were associated to expected gene ontology (GO) terms for resistance mechanisms such as hypersensitive response, host programmed cell death and endopeptidase activity.However, no differences in numbers of susceptibility (S-)gene homologs were seen between species and clones.In addition, we identified P. infestans transcripts including effectors in the early stages of P. infestans-Solanum interactions.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Protection Biology, Swedish University of Agricultural Sciences Alnarp, Sweden.

ABSTRACT
Comparative transcriptomics between species can provide valuable understanding of plant-pathogen interactions. Here, we focus on wild Solanum species and potato clones with varying degree of resistance against Phytophthora infestans, which causes the devastating late blight disease in potato. The transcriptomes of three wild Solanum species native to Southern Sweden, Solanum dulcamara, Solanum nigrum, and Solanum physalifolium were compared to three potato clones, Desiree (cv.), SW93-1015 and Sarpo Mira. Desiree and S. physalifolium are susceptible to P. infestans whereas the other four have different degrees of resistance. By building transcript families based on de novo assembled RNA-seq across species and clones and correlating these to resistance phenotypes, we created a novel workflow to identify families with expanded or depleted number of transcripts in relation to the P. infestans resistance level. Analysis was facilitated by inferring functional annotations based on the family structure and semantic clustering. More transcript families were expanded in the resistant clones and species and the enriched functions of these were associated to expected gene ontology (GO) terms for resistance mechanisms such as hypersensitive response, host programmed cell death and endopeptidase activity. However, a number of unexpected functions and transcripts were also identified, for example transmembrane transport and protein acylation expanded in the susceptible group and a cluster of Zinc knuckle family proteins expanded in the resistant group. Over 400 expressed putative resistance (R-)genes were identified and resistant clones Sarpo Mira and SW93-1015 had ca 25% more expressed putative R-genes than susceptible cultivar Desiree. However, no differences in numbers of susceptibility (S-)gene homologs were seen between species and clones. In addition, we identified P. infestans transcripts including effectors in the early stages of P. infestans-Solanum interactions.

No MeSH data available.


Related in: MedlinePlus

Overview the workflow used to identify resistance and susceptible factors in the host and effectors of the infecting pathogen based on RNA-seq. (A) Phenotypic analysis and RNA Sequencing (RNA-Seq). (B) Bioinformatic analysis of the RNA-seq data and transcriptomes.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4585127&req=5

Figure 1: Overview the workflow used to identify resistance and susceptible factors in the host and effectors of the infecting pathogen based on RNA-seq. (A) Phenotypic analysis and RNA Sequencing (RNA-Seq). (B) Bioinformatic analysis of the RNA-seq data and transcriptomes.

Mentions: In order to capture lineage-specific events reflecting adaptive evolution and conferring resistance, we used a novel workflow incorporating a correlation-based method to identify clusters either expanded or depleted in transcript numbers dependent on the level of P. infestans resistance of the wild Solanum and potato clones studied. An overview of the workflow used is presented in Figure 1. We used class vectors describing the level of plant resistance either qualitatively, i.e., resistant vs. susceptible, or quantitatively, i.e., based on an experimentally determined resistance gradient. Clusters were analyzed functionally by gene ontology (GO) and clusters populated with R-genes studied in more detail. We also identified 100's of putative R-genes in the three wild Solanum species and three potato clones. Furthermore, P. infestans transcripts representing RXLR effectors, Crinklers (CRN) and elicitins were detected.


A novel workflow correlating RNA-seq data to Phythophthora infestans resistance levels in wild Solanum species and potato clones.

Frades I, Abreha KB, Proux-Wéra E, Lankinen Å, Andreasson E, Alexandersson E - Front Plant Sci (2015)

Overview the workflow used to identify resistance and susceptible factors in the host and effectors of the infecting pathogen based on RNA-seq. (A) Phenotypic analysis and RNA Sequencing (RNA-Seq). (B) Bioinformatic analysis of the RNA-seq data and transcriptomes.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4585127&req=5

Figure 1: Overview the workflow used to identify resistance and susceptible factors in the host and effectors of the infecting pathogen based on RNA-seq. (A) Phenotypic analysis and RNA Sequencing (RNA-Seq). (B) Bioinformatic analysis of the RNA-seq data and transcriptomes.
Mentions: In order to capture lineage-specific events reflecting adaptive evolution and conferring resistance, we used a novel workflow incorporating a correlation-based method to identify clusters either expanded or depleted in transcript numbers dependent on the level of P. infestans resistance of the wild Solanum and potato clones studied. An overview of the workflow used is presented in Figure 1. We used class vectors describing the level of plant resistance either qualitatively, i.e., resistant vs. susceptible, or quantitatively, i.e., based on an experimentally determined resistance gradient. Clusters were analyzed functionally by gene ontology (GO) and clusters populated with R-genes studied in more detail. We also identified 100's of putative R-genes in the three wild Solanum species and three potato clones. Furthermore, P. infestans transcripts representing RXLR effectors, Crinklers (CRN) and elicitins were detected.

Bottom Line: More transcript families were expanded in the resistant clones and species and the enriched functions of these were associated to expected gene ontology (GO) terms for resistance mechanisms such as hypersensitive response, host programmed cell death and endopeptidase activity.However, no differences in numbers of susceptibility (S-)gene homologs were seen between species and clones.In addition, we identified P. infestans transcripts including effectors in the early stages of P. infestans-Solanum interactions.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Protection Biology, Swedish University of Agricultural Sciences Alnarp, Sweden.

ABSTRACT
Comparative transcriptomics between species can provide valuable understanding of plant-pathogen interactions. Here, we focus on wild Solanum species and potato clones with varying degree of resistance against Phytophthora infestans, which causes the devastating late blight disease in potato. The transcriptomes of three wild Solanum species native to Southern Sweden, Solanum dulcamara, Solanum nigrum, and Solanum physalifolium were compared to three potato clones, Desiree (cv.), SW93-1015 and Sarpo Mira. Desiree and S. physalifolium are susceptible to P. infestans whereas the other four have different degrees of resistance. By building transcript families based on de novo assembled RNA-seq across species and clones and correlating these to resistance phenotypes, we created a novel workflow to identify families with expanded or depleted number of transcripts in relation to the P. infestans resistance level. Analysis was facilitated by inferring functional annotations based on the family structure and semantic clustering. More transcript families were expanded in the resistant clones and species and the enriched functions of these were associated to expected gene ontology (GO) terms for resistance mechanisms such as hypersensitive response, host programmed cell death and endopeptidase activity. However, a number of unexpected functions and transcripts were also identified, for example transmembrane transport and protein acylation expanded in the susceptible group and a cluster of Zinc knuckle family proteins expanded in the resistant group. Over 400 expressed putative resistance (R-)genes were identified and resistant clones Sarpo Mira and SW93-1015 had ca 25% more expressed putative R-genes than susceptible cultivar Desiree. However, no differences in numbers of susceptibility (S-)gene homologs were seen between species and clones. In addition, we identified P. infestans transcripts including effectors in the early stages of P. infestans-Solanum interactions.

No MeSH data available.


Related in: MedlinePlus