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Transcriptome analysis of the white pine blister rust pathogen Cronartium ribicola: de novo assembly, expression profiling, and identification of candidate effectors.

Liu JJ, Sturrock RN, Sniezko RA, Williams H, Benton R, Zamany A - BMC Genomics (2015)

Bottom Line: This study further identified a repertoire of candidate effectors and other pathogenicity determinants.This comprehensive transcriptome profiling substantially improves our current understanding of molecular WP-BR interactions.The repertoire of candidate effectors and other putative pathogenicity determinants identified here are valuable for future functional analysis of Cri virulence and pathogenicity.

View Article: PubMed Central - PubMed

Affiliation: Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada. Jun-Jun.Liu@NRCan-RNCan.gc.ca.

ABSTRACT

Background: The fungus Cronartium ribicola (Cri) is an economically and ecologically important forest pathogen that causes white pine blister rust (WPBR) disease on five-needle pines. To cause stem cankers and kill white pine trees the fungus elaborates a life cycle with five stages of spore development on five-needle pines and the alternate host Ribes plants. To increase our understanding of molecular WP-BR interactions, here we report genome-wide transcriptional profile analysis of C. ribicola using RNA-seq.

Results: cDNA libraries were constructed from aeciospore, urediniospore, and western white pine (Pinus monticola) tissues post Cri infection. Over 200 million RNA-seq 100-bp paired-end (PE) reads from rust fungal spores were de novo assembled and a reference transcriptome was generated with 17,880 transcripts that were expressed from 13,629 unigenes. A total of 734 unique proteins were predicted as a part of the Cri secretome from complete open reading frames (ORFs), and 41 % of them were Cronartium-specific. This study further identified a repertoire of candidate effectors and other pathogenicity determinants. Differentially expressed genes (DEGs) were identified to gain an understanding of molecular events important during the WPBR fungus life cycle by comparing Cri transcriptomes at different infection stages. Large-scale changes of in planta gene expression profiles were observed, revealing that multiple fungal biosynthetic pathways were enhanced during mycelium growth inside infected pine stem tissues. Conversely, many fungal genes that were up-regulated at the urediniospore stage appeared to be signalling components and transporters. The secreted fungal protein genes that were up-regulated in pine needle tissues during early infection were primarily associated with cell wall modifications, possibly to mask the rust pathogen from plant defenses.

Conclusion: This comprehensive transcriptome profiling substantially improves our current understanding of molecular WP-BR interactions. The repertoire of candidate effectors and other putative pathogenicity determinants identified here are valuable for future functional analysis of Cri virulence and pathogenicity.

No MeSH data available.


Related in: MedlinePlus

Heatmaps of transcript expression based on normalized data of expression values (FPKM) in three functional categories. Only differentially expressed genes (DEGs) with minimum fold change of two with p <0.05 after adjustment using false discovery rate (FDR) are shown in the heatmaps. Overrepresented (red) and underrepresented transcripts (blue) are shown as relative to the expression values measured across four stages of the rust life cycle, infected pine needle (IfN) at 4 dpi, infected pine stems (IfS), aeciospore (Aec), and urediniospore (Ure) in infected Ribes leaves. a Secreted proteins; b Candidate effectors with functional annotation in the PHI database; c CAZymes
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Fig5: Heatmaps of transcript expression based on normalized data of expression values (FPKM) in three functional categories. Only differentially expressed genes (DEGs) with minimum fold change of two with p <0.05 after adjustment using false discovery rate (FDR) are shown in the heatmaps. Overrepresented (red) and underrepresented transcripts (blue) are shown as relative to the expression values measured across four stages of the rust life cycle, infected pine needle (IfN) at 4 dpi, infected pine stems (IfS), aeciospore (Aec), and urediniospore (Ure) in infected Ribes leaves. a Secreted proteins; b Candidate effectors with functional annotation in the PHI database; c CAZymes

Mentions: Based on normalized expression values calculated by RNA-seq analysis, hierarchical clustering of expression patterns by heatmap analysis revealed that in planta genome-wide transcriptional profiles were more similar to each other than to the profiles at the aeciospore and urediniospore stages; likewise, the latter two showed greater similar to each other. Similar patterns were observed among three categories of genes encoding secreted proteins, candidate effectors, and CAZymes (Fig. 5). These results demonstrate that the Cri transcriptome is extensively reprogrammed during pine stem infection.Fig. 5


Transcriptome analysis of the white pine blister rust pathogen Cronartium ribicola: de novo assembly, expression profiling, and identification of candidate effectors.

Liu JJ, Sturrock RN, Sniezko RA, Williams H, Benton R, Zamany A - BMC Genomics (2015)

Heatmaps of transcript expression based on normalized data of expression values (FPKM) in three functional categories. Only differentially expressed genes (DEGs) with minimum fold change of two with p <0.05 after adjustment using false discovery rate (FDR) are shown in the heatmaps. Overrepresented (red) and underrepresented transcripts (blue) are shown as relative to the expression values measured across four stages of the rust life cycle, infected pine needle (IfN) at 4 dpi, infected pine stems (IfS), aeciospore (Aec), and urediniospore (Ure) in infected Ribes leaves. a Secreted proteins; b Candidate effectors with functional annotation in the PHI database; c CAZymes
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4559923&req=5

Fig5: Heatmaps of transcript expression based on normalized data of expression values (FPKM) in three functional categories. Only differentially expressed genes (DEGs) with minimum fold change of two with p <0.05 after adjustment using false discovery rate (FDR) are shown in the heatmaps. Overrepresented (red) and underrepresented transcripts (blue) are shown as relative to the expression values measured across four stages of the rust life cycle, infected pine needle (IfN) at 4 dpi, infected pine stems (IfS), aeciospore (Aec), and urediniospore (Ure) in infected Ribes leaves. a Secreted proteins; b Candidate effectors with functional annotation in the PHI database; c CAZymes
Mentions: Based on normalized expression values calculated by RNA-seq analysis, hierarchical clustering of expression patterns by heatmap analysis revealed that in planta genome-wide transcriptional profiles were more similar to each other than to the profiles at the aeciospore and urediniospore stages; likewise, the latter two showed greater similar to each other. Similar patterns were observed among three categories of genes encoding secreted proteins, candidate effectors, and CAZymes (Fig. 5). These results demonstrate that the Cri transcriptome is extensively reprogrammed during pine stem infection.Fig. 5

Bottom Line: This study further identified a repertoire of candidate effectors and other pathogenicity determinants.This comprehensive transcriptome profiling substantially improves our current understanding of molecular WP-BR interactions.The repertoire of candidate effectors and other putative pathogenicity determinants identified here are valuable for future functional analysis of Cri virulence and pathogenicity.

View Article: PubMed Central - PubMed

Affiliation: Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada. Jun-Jun.Liu@NRCan-RNCan.gc.ca.

ABSTRACT

Background: The fungus Cronartium ribicola (Cri) is an economically and ecologically important forest pathogen that causes white pine blister rust (WPBR) disease on five-needle pines. To cause stem cankers and kill white pine trees the fungus elaborates a life cycle with five stages of spore development on five-needle pines and the alternate host Ribes plants. To increase our understanding of molecular WP-BR interactions, here we report genome-wide transcriptional profile analysis of C. ribicola using RNA-seq.

Results: cDNA libraries were constructed from aeciospore, urediniospore, and western white pine (Pinus monticola) tissues post Cri infection. Over 200 million RNA-seq 100-bp paired-end (PE) reads from rust fungal spores were de novo assembled and a reference transcriptome was generated with 17,880 transcripts that were expressed from 13,629 unigenes. A total of 734 unique proteins were predicted as a part of the Cri secretome from complete open reading frames (ORFs), and 41 % of them were Cronartium-specific. This study further identified a repertoire of candidate effectors and other pathogenicity determinants. Differentially expressed genes (DEGs) were identified to gain an understanding of molecular events important during the WPBR fungus life cycle by comparing Cri transcriptomes at different infection stages. Large-scale changes of in planta gene expression profiles were observed, revealing that multiple fungal biosynthetic pathways were enhanced during mycelium growth inside infected pine stem tissues. Conversely, many fungal genes that were up-regulated at the urediniospore stage appeared to be signalling components and transporters. The secreted fungal protein genes that were up-regulated in pine needle tissues during early infection were primarily associated with cell wall modifications, possibly to mask the rust pathogen from plant defenses.

Conclusion: This comprehensive transcriptome profiling substantially improves our current understanding of molecular WP-BR interactions. The repertoire of candidate effectors and other putative pathogenicity determinants identified here are valuable for future functional analysis of Cri virulence and pathogenicity.

No MeSH data available.


Related in: MedlinePlus