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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

Enrichment analysis of gene ontology (GO) terms for up-regulated genes at three Cronartium ribicola life cycle stages: aeciospore, urediniospore and inplanta mycelium growth in infected Pinus monticola stem tissues. Fisher’s test was performed using Cri reference transcriptome as reference (p <0.05 with FDR correction). GO terms involved in biological process include: GO:0051716, cellular response to stimulus; GO:0044700, single organism signaling; GO:0050794, regulation of cellular process; GO:0007165, signal transduction; GO:0007154, cell communication; GO:0023052, signaling; GO:0009058, biosynthetic process; GO:0044249, cellular biosynthetic process; GO:0034645, cellular macromolecule biosynthetic process; GO:1901576, organic substance biosynthetic process; GO:0010467, gene expression; GO:0009059, macromolecule biosynthetic process; GO:0008152, metabolic process; GO:0071704, organic substance metabolic process; GO:0044238, primary metabolic process; GO:0019538, protein metabolic process; GO:0044267, cellular protein metabolic process; GO:0006412, translation; GO:0065007, biological regulation; GO:0022402, cell cycle process; GO:0051301, cell division; GO:0000910, cytokinesis; GO:0051234, establishment of localization; GO:0051179, localization; GO:0050789, regulation of biological process; GO:0044763, single-organism cellular process; GO:0044699, single-organism process; GO:0006810, transport
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Fig6: Enrichment analysis of gene ontology (GO) terms for up-regulated genes at three Cronartium ribicola life cycle stages: aeciospore, urediniospore and inplanta mycelium growth in infected Pinus monticola stem tissues. Fisher’s test was performed using Cri reference transcriptome as reference (p <0.05 with FDR correction). GO terms involved in biological process include: GO:0051716, cellular response to stimulus; GO:0044700, single organism signaling; GO:0050794, regulation of cellular process; GO:0007165, signal transduction; GO:0007154, cell communication; GO:0023052, signaling; GO:0009058, biosynthetic process; GO:0044249, cellular biosynthetic process; GO:0034645, cellular macromolecule biosynthetic process; GO:1901576, organic substance biosynthetic process; GO:0010467, gene expression; GO:0009059, macromolecule biosynthetic process; GO:0008152, metabolic process; GO:0071704, organic substance metabolic process; GO:0044238, primary metabolic process; GO:0019538, protein metabolic process; GO:0044267, cellular protein metabolic process; GO:0006412, translation; GO:0065007, biological regulation; GO:0022402, cell cycle process; GO:0051301, cell division; GO:0000910, cytokinesis; GO:0051234, establishment of localization; GO:0051179, localization; GO:0050789, regulation of biological process; GO:0044763, single-organism cellular process; GO:0044699, single-organism process; GO:0006810, transport

Mentions: To understand the potential roles of DEGs in biological process, Fisher’s test (FDR P < 0.05) for enrichment of GO terms was performed using the Cri reference transcriptome as a reference data set. Compared to either aeciospores or urediniospores, the infected stem showed up-regulated DEGs with enriched GO terms of biosynthetic process (five GO terms), metabolic process (five GO terms), gene expression and translation (two GO terms) (Fig. 6). The DEGs contributing to enriched biosynthetic processes include a large number of genes encoding various ribosomal proteins, histones, transcriptional factors, and enzymes for biosynthesis of macromolecules (DNA, RNA, and proteins), amino acids, fatty acids, lipids, steroids, sugar, ATP, and others (Additional file 1: Table S12). Protein synthesis from transcription to posttranslational modification seems to be a major process in the infected pine stem tissues. Among multiple families of up-regulated transcription factors, fork-head box (FOX) proteins are a family of transcription factors that play important roles in regulating the expression of genes involved in cell growth, proliferation, differentiation, and longevity. Active protein synthesis was further evidenced by the strong induction of many ribosomal proteins and other components in translation. The up-regulated metabolic genes were largely involved in DNA and carbohydrate metabolism. A number of transcripts associated with transposons and retrotransposons were also detected to be over-presented in infected stem tissues (Additional file 1: Table S12).Fig. 6


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)

Enrichment analysis of gene ontology (GO) terms for up-regulated genes at three Cronartium ribicola life cycle stages: aeciospore, urediniospore and inplanta mycelium growth in infected Pinus monticola stem tissues. Fisher’s test was performed using Cri reference transcriptome as reference (p <0.05 with FDR correction). GO terms involved in biological process include: GO:0051716, cellular response to stimulus; GO:0044700, single organism signaling; GO:0050794, regulation of cellular process; GO:0007165, signal transduction; GO:0007154, cell communication; GO:0023052, signaling; GO:0009058, biosynthetic process; GO:0044249, cellular biosynthetic process; GO:0034645, cellular macromolecule biosynthetic process; GO:1901576, organic substance biosynthetic process; GO:0010467, gene expression; GO:0009059, macromolecule biosynthetic process; GO:0008152, metabolic process; GO:0071704, organic substance metabolic process; GO:0044238, primary metabolic process; GO:0019538, protein metabolic process; GO:0044267, cellular protein metabolic process; GO:0006412, translation; GO:0065007, biological regulation; GO:0022402, cell cycle process; GO:0051301, cell division; GO:0000910, cytokinesis; GO:0051234, establishment of localization; GO:0051179, localization; GO:0050789, regulation of biological process; GO:0044763, single-organism cellular process; GO:0044699, single-organism process; GO:0006810, transport
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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Fig6: Enrichment analysis of gene ontology (GO) terms for up-regulated genes at three Cronartium ribicola life cycle stages: aeciospore, urediniospore and inplanta mycelium growth in infected Pinus monticola stem tissues. Fisher’s test was performed using Cri reference transcriptome as reference (p <0.05 with FDR correction). GO terms involved in biological process include: GO:0051716, cellular response to stimulus; GO:0044700, single organism signaling; GO:0050794, regulation of cellular process; GO:0007165, signal transduction; GO:0007154, cell communication; GO:0023052, signaling; GO:0009058, biosynthetic process; GO:0044249, cellular biosynthetic process; GO:0034645, cellular macromolecule biosynthetic process; GO:1901576, organic substance biosynthetic process; GO:0010467, gene expression; GO:0009059, macromolecule biosynthetic process; GO:0008152, metabolic process; GO:0071704, organic substance metabolic process; GO:0044238, primary metabolic process; GO:0019538, protein metabolic process; GO:0044267, cellular protein metabolic process; GO:0006412, translation; GO:0065007, biological regulation; GO:0022402, cell cycle process; GO:0051301, cell division; GO:0000910, cytokinesis; GO:0051234, establishment of localization; GO:0051179, localization; GO:0050789, regulation of biological process; GO:0044763, single-organism cellular process; GO:0044699, single-organism process; GO:0006810, transport
Mentions: To understand the potential roles of DEGs in biological process, Fisher’s test (FDR P < 0.05) for enrichment of GO terms was performed using the Cri reference transcriptome as a reference data set. Compared to either aeciospores or urediniospores, the infected stem showed up-regulated DEGs with enriched GO terms of biosynthetic process (five GO terms), metabolic process (five GO terms), gene expression and translation (two GO terms) (Fig. 6). The DEGs contributing to enriched biosynthetic processes include a large number of genes encoding various ribosomal proteins, histones, transcriptional factors, and enzymes for biosynthesis of macromolecules (DNA, RNA, and proteins), amino acids, fatty acids, lipids, steroids, sugar, ATP, and others (Additional file 1: Table S12). Protein synthesis from transcription to posttranslational modification seems to be a major process in the infected pine stem tissues. Among multiple families of up-regulated transcription factors, fork-head box (FOX) proteins are a family of transcription factors that play important roles in regulating the expression of genes involved in cell growth, proliferation, differentiation, and longevity. Active protein synthesis was further evidenced by the strong induction of many ribosomal proteins and other components in translation. The up-regulated metabolic genes were largely involved in DNA and carbohydrate metabolism. A number of transcripts associated with transposons and retrotransposons were also detected to be over-presented in infected stem tissues (Additional file 1: Table S12).Fig. 6

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