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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

Workflow of secretome prediction using bioinformatics tools for the comprehensive characterization of proteins secreted at spore development stages or during the in-planta mycelium growth stage in infected stems of western white pine
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Fig2: Workflow of secretome prediction using bioinformatics tools for the comprehensive characterization of proteins secreted at spore development stages or during the in-planta mycelium growth stage in infected stems of western white pine

Mentions: Because secreted proteins have potential roles in plant-microbe interactions, we analyzed the Cri secretome based on transcript assemblies (Fig. 2). Secreted proteins were encoded by 629 transcripts in the Cri reference transcriptome that originated from rust fungal spores and 1,427 transcripts in the Cri-associated transcripts that originated from cankered WWP stems. Following CAP3 alignment of the complete ORFs of these secreted protein-encoding transcripts, a total of 734 unique proteins were identified as secreted proteins. A BLASTp search against a dataset of candidate effectors with 23,516 proteins from the other four rust pathogens [13] showed that 301 (41 % of the total) Cri secreted proteins were Cronartium-specific, as they showed no significant homology to candidate effectors reported on other rust fungi (E values ˃ e−5) (Additional file 1: Table S3). Because a large number of pathogenic effectors share features as secreted, small and cysteine-rich proteins (SSPs) that lack homology to proteins in other species, we examined the Cri secretome and manual curation found that it contained 466 proteins with lengths shorter than 300 amino acids and 155 of them had at least four cysteine residues in the mature proteins. As anticipated, most of these Cri SSPs (82 %) had no functional annotation as shown by BLAST2GO analysis.Fig. 2


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)

Workflow of secretome prediction using bioinformatics tools for the comprehensive characterization of proteins secreted at spore development stages or during the in-planta mycelium growth stage in infected stems of western white pine
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig2: Workflow of secretome prediction using bioinformatics tools for the comprehensive characterization of proteins secreted at spore development stages or during the in-planta mycelium growth stage in infected stems of western white pine
Mentions: Because secreted proteins have potential roles in plant-microbe interactions, we analyzed the Cri secretome based on transcript assemblies (Fig. 2). Secreted proteins were encoded by 629 transcripts in the Cri reference transcriptome that originated from rust fungal spores and 1,427 transcripts in the Cri-associated transcripts that originated from cankered WWP stems. Following CAP3 alignment of the complete ORFs of these secreted protein-encoding transcripts, a total of 734 unique proteins were identified as secreted proteins. A BLASTp search against a dataset of candidate effectors with 23,516 proteins from the other four rust pathogens [13] showed that 301 (41 % of the total) Cri secreted proteins were Cronartium-specific, as they showed no significant homology to candidate effectors reported on other rust fungi (E values ˃ e−5) (Additional file 1: Table S3). Because a large number of pathogenic effectors share features as secreted, small and cysteine-rich proteins (SSPs) that lack homology to proteins in other species, we examined the Cri secretome and manual curation found that it contained 466 proteins with lengths shorter than 300 amino acids and 155 of them had at least four cysteine residues in the mature proteins. As anticipated, most of these Cri SSPs (82 %) had no functional annotation as shown by BLAST2GO analysis.Fig. 2

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