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

Detached leaves from plants of three wild Solanum species, (S. nigrum, Sn 4:3; S. dulcamara, Sd 3:6; and S. physalifolium, Sp 2:4), and potato clones (Sarpo Mira, SW93-1015, and Desiree) inoculated with Phytophthora infestans. The pathogen grew on the susceptible Desiree and Sp 2:4 (gray bars) whilst its growth was restricted to the inoculation site on the resistant ones (white bars). Pictures were taken at 7 days after inoculation (dpi). Error bars indicate standard error of the mean. Bars that are not connected by the same letter are significantly different (P < 0.05).
© Copyright Policy
Related In: Results  -  Collection

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

Figure 2: Detached leaves from plants of three wild Solanum species, (S. nigrum, Sn 4:3; S. dulcamara, Sd 3:6; and S. physalifolium, Sp 2:4), and potato clones (Sarpo Mira, SW93-1015, and Desiree) inoculated with Phytophthora infestans. The pathogen grew on the susceptible Desiree and Sp 2:4 (gray bars) whilst its growth was restricted to the inoculation site on the resistant ones (white bars). Pictures were taken at 7 days after inoculation (dpi). Error bars indicate standard error of the mean. Bars that are not connected by the same letter are significantly different (P < 0.05).

Mentions: We were only able to detect visible macroscopic symptom of the P. infestans inoculation after 48 hai as noted for potato in a review by Fry (2008). The 45 hai is referred as biotrophic phase (Vleeshouwers et al., 2000) whilst the 72 hai is considered the start of the necrotrophic phase of the pathogen (Birch et al., 2003). Consequently, RNA was isolated either up to 24 hpi (potato clones) or 48 hpi (wild Solanum species) before macroscopic lesions occurred in any of the species or clones and before the onset of the necrotrophic phase. Therefore, the samples in this study cover only the biotrophic phase of the P. infestans infection. Although our analysis groups the samples as either as susceptible or resistant to make general findings, the samples should not be regarded as proper biological replications. That sort of comparison is difficult, if not impossible, to accomplish, since progression of infection inevitably varies between species and clones with varying resistance levels. Based on the resistance assay using detached leaves a resistant to susceptible gradient was established in the following order: Sarpo Mira, SW93-1015, S. nigrum, S. dulcamara, Desiree, and S. physalifolium (Figure 2). Applying the Kruskal-Wallis test on mean rank of the lesion size [, P < 0.01] showed a resistance difference and the grouping was in line with the gradient.


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)

Detached leaves from plants of three wild Solanum species, (S. nigrum, Sn 4:3; S. dulcamara, Sd 3:6; and S. physalifolium, Sp 2:4), and potato clones (Sarpo Mira, SW93-1015, and Desiree) inoculated with Phytophthora infestans. The pathogen grew on the susceptible Desiree and Sp 2:4 (gray bars) whilst its growth was restricted to the inoculation site on the resistant ones (white bars). Pictures were taken at 7 days after inoculation (dpi). Error bars indicate standard error of the mean. Bars that are not connected by the same letter are significantly different (P < 0.05).
© Copyright Policy
Related In: Results  -  Collection

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

Figure 2: Detached leaves from plants of three wild Solanum species, (S. nigrum, Sn 4:3; S. dulcamara, Sd 3:6; and S. physalifolium, Sp 2:4), and potato clones (Sarpo Mira, SW93-1015, and Desiree) inoculated with Phytophthora infestans. The pathogen grew on the susceptible Desiree and Sp 2:4 (gray bars) whilst its growth was restricted to the inoculation site on the resistant ones (white bars). Pictures were taken at 7 days after inoculation (dpi). Error bars indicate standard error of the mean. Bars that are not connected by the same letter are significantly different (P < 0.05).
Mentions: We were only able to detect visible macroscopic symptom of the P. infestans inoculation after 48 hai as noted for potato in a review by Fry (2008). The 45 hai is referred as biotrophic phase (Vleeshouwers et al., 2000) whilst the 72 hai is considered the start of the necrotrophic phase of the pathogen (Birch et al., 2003). Consequently, RNA was isolated either up to 24 hpi (potato clones) or 48 hpi (wild Solanum species) before macroscopic lesions occurred in any of the species or clones and before the onset of the necrotrophic phase. Therefore, the samples in this study cover only the biotrophic phase of the P. infestans infection. Although our analysis groups the samples as either as susceptible or resistant to make general findings, the samples should not be regarded as proper biological replications. That sort of comparison is difficult, if not impossible, to accomplish, since progression of infection inevitably varies between species and clones with varying resistance levels. Based on the resistance assay using detached leaves a resistant to susceptible gradient was established in the following order: Sarpo Mira, SW93-1015, S. nigrum, S. dulcamara, Desiree, and S. physalifolium (Figure 2). Applying the Kruskal-Wallis test on mean rank of the lesion size [, P < 0.01] showed a resistance difference and the grouping was in line with the gradient.

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