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Lv B, Guo Y, Zhao X, Li S, Sun M. Glucose-6-phosphate 1-Epimerase CrGlu6 Contributes to Development and Biocontrol Efficiency in Clonostachys chloroleuca. J Fungi (Basel) 2023; 9:764. [PMID: 37504752 PMCID: PMC10381721 DOI: 10.3390/jof9070764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/15/2023] [Accepted: 07/17/2023] [Indexed: 07/29/2023] Open
Abstract
Clonostachys chloroleuca (formerly classified as C. rosea) is an important mycoparasite active against various plant fungal pathogens. Mitogen-activated protein kinase (MAPK) signaling pathways are vital in mycoparasitic interactions; they participate in responses to diverse stresses and mediate fungal development. In previous studies, the MAPK-encoding gene Crmapk has been proven to be involved in mycoparasitism and the biocontrol processes of C. chloroleuca, but its regulatory mechanisms remain unclear. Aldose 1-epimerases are key enzymes in filamentous fungi that generate energy for fungal growth and development. By protein-protein interaction assays, the glucose-6-phosphate 1-epimerase CrGlu6 was found to interact with Crmapk, and expression of the CrGlu6 gene was significantly upregulated when C. chloroleuca colonized Sclerotinia sclerotiorum sclerotia. Gene deletion and complementation analyses showed that CrGlu6 deficiency caused abnormal morphology of hyphae and cells, and greatly reduced conidiation. Moreover, deletion mutants presented much lower antifungal activities and mycoparasitic ability, and control efficiency against sclerotinia stem rot was markedly decreased. When the CrGlu6 gene was reinserted, all biological characteristics and biocontrol activities were recovered. These findings provide new insight into the mechanisms of glucose-6-phosphate 1-epimerase in mycoparasitism and help to further reveal the regulation of MAPK and its interacting proteins in the biocontrol of C. chloroleuca.
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Affiliation(s)
- Binna Lv
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yan Guo
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xue Zhao
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Shidong Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Manhong Sun
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Song X, Zhao Q, Zhou A, Wen X, Li M, Li R, Liao X, Xu T. The Antifungal Effects of Citral on Magnaporthe oryzae Occur via Modulation of Chitin Content as Revealed by RNA-Seq Analysis. J Fungi (Basel) 2021; 7:jof7121023. [PMID: 34947005 PMCID: PMC8704549 DOI: 10.3390/jof7121023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/21/2021] [Accepted: 11/26/2021] [Indexed: 12/13/2022] Open
Abstract
The natural product citral has previously been demonstrated to possess antifungal activity against Magnaporthe oryzae. The purpose of this study was to screen and annotate genes that were differentially expressed (DEGs) in M. oryzae after treatment with citral using RNA sequencing (RNA-seq). Thereafter, samples were reprepared for quantitative real-time PCR (RT-qPCR) analysis verification of RNA-seq data. The results showed that 649 DEGs in M. oryzae were significantly affected after treatment with citral (100 μg/mL) for 24 h. Kyoto Encyclopedia of Genes and Genomes (KEGG) and a gene ontology (GO) analysis showed that DEGs were mainly enriched in amino sugar and nucleotide sugar metabolic pathways, including the chitin synthesis pathway and UDP sugar synthesis pathway. The results of the RT-qPCR analysis also showed that the chitin present in M. oryzae might be degraded to chitosan, chitobiose, N-acetyl-D-glucosamine, and β-D-fructose-6-phosphate following treatment with citral. Chitin degradation was indicated by damaged cell-wall integrity. Moreover, the UDP glucose synthesis pathway was involved in glycolysis and gluconeogenesis, providing precursors for the synthesis of polysaccharides. Galactose-1-phosphate uridylyltransferase, which is involved in the regulation of UDP-α-D-galactose and α-D-galactose-1-phosphate, was downregulated. This would result in the inhibition of UDP glucose (UDP-Glc) synthesis, a reduction in cell-wall glucan content, and the destruction of cell-wall integrity.
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Affiliation(s)
- Xingchen Song
- Institute of Crop Protection, Guizhou University, Guiyang 550025, China; (X.S.); (Q.Z.); (A.Z.); (X.W.); (M.L.); (X.L.); (T.X.)
- College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Qijun Zhao
- Institute of Crop Protection, Guizhou University, Guiyang 550025, China; (X.S.); (Q.Z.); (A.Z.); (X.W.); (M.L.); (X.L.); (T.X.)
- College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Aiai Zhou
- Institute of Crop Protection, Guizhou University, Guiyang 550025, China; (X.S.); (Q.Z.); (A.Z.); (X.W.); (M.L.); (X.L.); (T.X.)
- College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Xiaodong Wen
- Institute of Crop Protection, Guizhou University, Guiyang 550025, China; (X.S.); (Q.Z.); (A.Z.); (X.W.); (M.L.); (X.L.); (T.X.)
- College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Ming Li
- Institute of Crop Protection, Guizhou University, Guiyang 550025, China; (X.S.); (Q.Z.); (A.Z.); (X.W.); (M.L.); (X.L.); (T.X.)
- College of Agriculture, Guizhou University, Guiyang 550025, China
- The Provincial Key Laboratory for Agricultural Pest Management in Mountainous Region, Guiyang 550025, China
| | - Rongyu Li
- Institute of Crop Protection, Guizhou University, Guiyang 550025, China; (X.S.); (Q.Z.); (A.Z.); (X.W.); (M.L.); (X.L.); (T.X.)
- College of Agriculture, Guizhou University, Guiyang 550025, China
- The Provincial Key Laboratory for Agricultural Pest Management in Mountainous Region, Guiyang 550025, China
- Correspondence: ; Tel.: +86-151-8514-8063
| | - Xun Liao
- Institute of Crop Protection, Guizhou University, Guiyang 550025, China; (X.S.); (Q.Z.); (A.Z.); (X.W.); (M.L.); (X.L.); (T.X.)
- College of Agriculture, Guizhou University, Guiyang 550025, China
- The Provincial Key Laboratory for Agricultural Pest Management in Mountainous Region, Guiyang 550025, China
| | - Tengzhi Xu
- Institute of Crop Protection, Guizhou University, Guiyang 550025, China; (X.S.); (Q.Z.); (A.Z.); (X.W.); (M.L.); (X.L.); (T.X.)
- College of Agriculture, Guizhou University, Guiyang 550025, China
- The Provincial Key Laboratory for Agricultural Pest Management in Mountainous Region, Guiyang 550025, China
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Mahesh HB, Shirke MD, Wang GL, Gowda M. In planta transcriptome analysis reveals tissue-specific expression of pathogenicity genes and microRNAs during rice-Magnaporthe interactions. Genomics 2020; 113:265-275. [PMID: 33326830 DOI: 10.1016/j.ygeno.2020.12.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/23/2020] [Accepted: 12/10/2020] [Indexed: 12/17/2022]
Abstract
Transcriptional re-programming in host and pathogen upon leaf and neck infection is an evolving area of research for the rice blast community. Analysis of in planta rice transcriptome in leaf and neck tissues revealed tissue-specific and infection-specific expression of rice and Magnaporthe oryzae genes in host and pathogen. The glycosyl hydrolase, isocitrate lyase, cupin domain containing protein, TF2, CMPG1, CHIT17 and OsCML14 genes were uniquely expressed in leaf infection. Genes like cytochrome P450, inhibitor I family protein, GSTU6, abscisic stress ripening, and cupin domain containing protein were up-regulated during neck infection. In our microRNA sequencing study, Osa-miR166n-3p was highly expressed in upon Magnaporthe leaf infection, whereas osa-miR1661-3p, osa-miR166n-3p and osa-miR159b were overexpressed in neck infection. Here we report several transcripts being targeted by up and down regulated microRNAs during infection. The putative genes expressed upon infection in leaf and neck could be used in understanding the dual-epidemics of blast disease.
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Affiliation(s)
- H B Mahesh
- Genomics Laboratory, Centre for Cellular and Molecular Platforms (C-CAMP), National Centre for Biological Sciences (NCBS), Bengaluru 560065, India; Department of Genetics and Plant Breeding, College of Agriculture, V. C. Farm, Mandya, University of Agricultural Sciences, Bengaluru 560065, India; Centre for Functional Genomics and Bioinformatics, The University of Trans-disciplinary Health Science and Technology, Bengaluru 560064, India.
| | - Meghana Deepak Shirke
- Centre for Functional Genomics and Bioinformatics, The University of Trans-disciplinary Health Science and Technology, Bengaluru 560064, India
| | - Guo-Liang Wang
- Department of Genetics and Plant Breeding, College of Agriculture, V. C. Farm, Mandya, University of Agricultural Sciences, Bengaluru 560065, India
| | - Malali Gowda
- Department of Plant Pathology, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Columbus 43210, USA; Centre for Functional Genomics and Bioinformatics, The University of Trans-disciplinary Health Science and Technology, Bengaluru 560064, India.
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Nguyen Q, Iritani A, Ohkita S, Vu BV, Yokoya K, Matsubara A, Ikeda KI, Suzuki N, Nakayashiki H. A fungal Argonaute interferes with RNA interference. Nucleic Acids Res 2019; 46:2495-2508. [PMID: 29309640 PMCID: PMC5946944 DOI: 10.1093/nar/gkx1301] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 12/19/2017] [Indexed: 11/25/2022] Open
Abstract
Small RNA (sRNA)-mediated gene silencing phenomena, exemplified by RNA interference (RNAi), require a unique class of proteins called Argonautes (AGOs). An AGO protein typically forms a protein–sRNA complex that contributes to gene silencing using the loaded sRNA as a specificity determinant. Here, we show that MoAGO2, one of the three AGO genes in the fungus Pyricularia oryzae (Magnaporthe oryzae) interferes with RNAi. Gene knockout (KO) studies revealed that MoAGO1 and MoAGO3 additively or redundantly played roles in hairpin RNA- and retrotransposon (MAGGY)-triggered RNAi while, surprisingly, the KO mutants of MoAGO2 (Δmoago2) showed elevated levels of gene silencing. Consistently, transcript levels of MAGGY and mycoviruses were drastically reduced in Δmoago2, supporting the idea that MoAGO2 impeded RNAi against the parasitic elements. Deep sequencing analysis revealed that repeat- and mycovirus-derived small interfering RNAs were mainly associated with MoAGO2 and MoAGO3, and their populations were very similar based on their size distribution patterns and positional base preference. Site-directed mutagenesis studies indicated that sRNA binding but not slicer activity of MoAGO2 was essential for the ability to diminish the efficacy of RNAi. Overall, these results suggest a possible interplay between distinct sRNA-mediated gene regulation pathways through a competition for sRNA.
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Affiliation(s)
- Quyet Nguyen
- Laboratory of Cell Function and Structure, Graduate School of Agricultural Science, Kobe University, Nada Kobe 657-8501, Japan
| | - Akihide Iritani
- Laboratory of Cell Function and Structure, Graduate School of Agricultural Science, Kobe University, Nada Kobe 657-8501, Japan
| | - Shuhei Ohkita
- Laboratory of Cell Function and Structure, Graduate School of Agricultural Science, Kobe University, Nada Kobe 657-8501, Japan
| | - Ba V Vu
- Laboratory of Cell Function and Structure, Graduate School of Agricultural Science, Kobe University, Nada Kobe 657-8501, Japan
| | - Kana Yokoya
- Laboratory of Cell Function and Structure, Graduate School of Agricultural Science, Kobe University, Nada Kobe 657-8501, Japan
| | - Ai Matsubara
- Laboratory of Cell Function and Structure, Graduate School of Agricultural Science, Kobe University, Nada Kobe 657-8501, Japan
| | - Ken-Ichi Ikeda
- Laboratory of Cell Function and Structure, Graduate School of Agricultural Science, Kobe University, Nada Kobe 657-8501, Japan
| | - Nobuhiro Suzuki
- Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - Hitoshi Nakayashiki
- Laboratory of Cell Function and Structure, Graduate School of Agricultural Science, Kobe University, Nada Kobe 657-8501, Japan
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Shao J, Chen H, Yang D, Jiang M, Zhang H, Wu B, Li J, Yuan L, Liu C. Genome-wide Identification and Characterization of Natural Antisense Transcripts by Strand-specific RNA Sequencing in Ganoderma lucidum. Sci Rep 2017; 7:5711. [PMID: 28720793 PMCID: PMC5515960 DOI: 10.1038/s41598-017-04303-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 05/12/2017] [Indexed: 12/13/2022] Open
Abstract
Ganoderma lucidum is a white-rot fungus best-known for its medicinal and ligninolytic activities. To discover the underlying genes responsible for these activities, we identified and characterized the natural antisense transcripts (NATs) using strand-specific (ss) RNA-seq data obtained from the mycelia, primordia and fruiting bodies. NATs were identified using a custom pipeline and then subjected to functional enrichment and differential expression analyses. A total of 1613 cis- and 244 trans- sense and antisense transcripts were identified. Mapping to GO terms and KEGG pathways revealed that NATs were frequently associated with genes of particular functional categories in particular stages. ssRT-qPCR experiments showed that the expression profiles of 30 of 50 (60%) transcripts were highly correlated with those of the RNA-seq results (r ≥ 0.9). Expression profiles of 22 of 25 (88%) pairs of NATs and STs were highly correlated (p ≤ 0.01), with 15 having r ≥ 0.8 and 4 having r ≤ -0.8. Six lignin-modifying genes and their NATs were analyzed in detail. Diverse patterns of differential expression among different stages and positive and negative correlations were observed. These results suggested that NATs were implicated in gene expression regulation in a function-group and developmental-stage specific manner through complex mechanisms.
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Affiliation(s)
- Junjie Shao
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P.R. China
| | - Haimei Chen
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P.R. China
| | - Dan Yang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P.R. China
| | - Mei Jiang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P.R. China
| | - Hui Zhang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P.R. China
| | - Bin Wu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P.R. China
| | - Jianqin Li
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P.R. China
| | - Lichai Yuan
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P.R. China
| | - Chang Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P.R. China.
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Using Network Extracted Ontologies to Identify Novel Genes with Roles in Appressorium Development in the Rice Blast Fungus Magnaporthe oryzae. Microorganisms 2017; 5:microorganisms5010003. [PMID: 28106722 PMCID: PMC5374380 DOI: 10.3390/microorganisms5010003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 01/04/2017] [Accepted: 01/07/2017] [Indexed: 11/17/2022] Open
Abstract
Magnaporthe oryzae is the causal agent of rice blast disease, the most important infection of rice worldwide. Half the world's population depends on rice for its primary caloric intake and, as such, rice blast poses a serious threat to food security. The stages of M. oryzae infection are well defined, with the formation of an appressorium, a cell type that allows penetration of the plant cuticle, particularly well studied. However, many of the key pathways and genes involved in this disease stage are yet to be identified. In this study, I have used network-extracted ontologies (NeXOs), hierarchical structures inferred from RNA-Seq data, to identify pathways involved in appressorium development, which in turn highlights novel genes with potential roles in this process. This study illustrates the use of NeXOs for pathway identification from large-scale genomics data and also identifies novel genes with potential roles in disease. The methods presented here will be useful to study disease processes in other pathogenic species and these data represent predictions of novel targets for intervention in M. oryzae.
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Ismail IA, Able AJ. Secretome analysis of virulent Pyrenophora teres f. teres isolates. Proteomics 2016; 16:2625-2636. [PMID: 27402336 DOI: 10.1002/pmic.201500498] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Revised: 06/24/2016] [Accepted: 07/07/2016] [Indexed: 11/11/2022]
Abstract
Pyrenophora teres f. teres (Ptt) causes net form net blotch disease of barley, partially by producing necrosis-inducing proteins. The protein profiles of the culture filtrates of 28 virulent isolates were compared by a combination of 2DE and 1D-PAGE with 105 spots and 51 bands chosen for analysis by liquid chromatography electrospray ionization tandem mass spectrometry. A total of 259 individual proteins were identified with 63 of these proteins being common to the selected virulent isolates. Ptt secretes a broad spectrum of proteins including cell wall degrading enzymes; virulence factors and effectors; proteins associated with fungal pathogenesis and development; and proteins related to oxidation-reduction processes. Potential virulence factors and effectors identified included proteins with glucosidase activity, ricin B and concanavalin A-like lectins, glucanases, spherulin, cutinase, pectin lyase, leucine-rich repeat protein, and ceratoplatanin. Small proteins with unknown function but cysteine-rich, common to effectors, were also identified. Differences in the secretion profile of the Ptt isolates have also provided important insight into the different mechanisms contributing to virulence and the development of net form net blotch symptoms.
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Affiliation(s)
- Ismail A Ismail
- School of Agriculture, Food & Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, Australia
| | - Amanda J Able
- School of Agriculture, Food & Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, Australia.
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Mogga V, Delventhal R, Weidenbach D, Langer S, Bertram PM, Andresen K, Thines E, Kroj T, Schaffrath U. Magnaporthe oryzae effectors MoHEG13 and MoHEG16 interfere with host infection and MoHEG13 counteracts cell death caused by Magnaporthe-NLPs in tobacco. PLANT CELL REPORTS 2016; 35:1169-85. [PMID: 26883226 DOI: 10.1007/s00299-016-1943-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 01/24/2016] [Indexed: 05/21/2023]
Abstract
KEY MESSAGE Adapted pathogens are able to modulate cell responses of their hosts most likely due to the activity of secreted effector molecules thereby enabling colonisation by ostensible nonhost pathogens. It is postulated that host and nonhost pathogens of a given plant species differ in their repertoire of secreted effector molecules that are able to suppress plant resistance. We pursued the strategy of identifying novel effectors of Magnaporthe oryzae, the causal agent of blast disease, by comparing the infection process of closely related host vs. nonhost Magnaporthe species on barley (Hordeum vulgare L.). When both types of pathogen simultaneously attacked the same cell, the nonhost isolate became a successful pathogen possibly due to potent effectors secreted by the host isolate. Microarray studies led to a set of M. oryzae Hypothetical Effector Genes (MoHEGs) which were classified as Early- and LateMoHEGs according to the maximal transcript abundance during colonization of barley. Interestingly, orthologs of these MoHEGs from a nonhost pathogen were similarly regulated when investigated in a host situation, suggesting evolutionary conserved functions. Knockout mutants of MoHEG16 from the group of EarlyMoHEGs were less virulent on barley and microscopic studies revealed an attenuated transition from epidermal to mesophyll colonization. MoHEG13, a LateMoHEG, was shown to antagonize cell death induced by M. oryzae Necrosis-and ethylene-inducing-protein-1 (Nep1)-like proteins in Nicotiana benthamiana. MoHEG13 has a virulence function as a knockout mutant showed attenuated disease progression when inoculated on barley.
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Affiliation(s)
- Valerie Mogga
- Department of Plant Physiology, RWTH Aachen University, 52056, Aachen, Germany
| | - Rhoda Delventhal
- Department of Plant Physiology, RWTH Aachen University, 52056, Aachen, Germany
| | - Denise Weidenbach
- Department of Plant Physiology, RWTH Aachen University, 52056, Aachen, Germany
| | - Samantha Langer
- Department of Plant Physiology, RWTH Aachen University, 52056, Aachen, Germany
| | - Philipp M Bertram
- Department of Plant Physiology, RWTH Aachen University, 52056, Aachen, Germany
| | - Karsten Andresen
- Institute of Biotechnology and Drug Research, Erwin-Schrödinger-Strasse 56, 67663, Kaiserslautern, Germany
| | - Eckhard Thines
- Institute of Biotechnology and Drug Research, Erwin-Schrödinger-Strasse 56, 67663, Kaiserslautern, Germany
- Biotechnology, Johannes Gutenberg-University, 55099, Mainz, Germany
| | - Thomas Kroj
- INRA, UMR BGPI, Campus International de Baillarguet, TA A-54/K, 34398, Montpellier Cedex 5, France
| | - Ulrich Schaffrath
- Department of Plant Physiology, RWTH Aachen University, 52056, Aachen, Germany.
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Pham KTM, Inoue Y, Vu BV, Nguyen HH, Nakayashiki T, Ikeda KI, Nakayashiki H. MoSET1 (Histone H3K4 Methyltransferase in Magnaporthe oryzae) Regulates Global Gene Expression during Infection-Related Morphogenesis. PLoS Genet 2015; 11:e1005385. [PMID: 26230995 PMCID: PMC4521839 DOI: 10.1371/journal.pgen.1005385] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 06/23/2015] [Indexed: 12/18/2022] Open
Abstract
Here we report the genetic analyses of histone lysine methyltransferase (KMT) genes in the phytopathogenic fungus Magnaporthe oryzae. Eight putative M. oryzae KMT genes were targeted for gene disruption by homologous recombination. Phenotypic assays revealed that the eight KMTs were involved in various infection processes at varying degrees. Moset1 disruptants (Δmoset1) impaired in histone H3 lysine 4 methylation (H3K4me) showed the most severe defects in infection-related morphogenesis, including conidiation and appressorium formation. Consequently, Δmoset1 lost pathogenicity on wheat host plants, thus indicating that H3K4me is an important epigenetic mark for infection-related gene expression in M. oryzae. Interestingly, appressorium formation was greatly restored in the Δmoset1 mutants by exogenous addition of cAMP or of the cutin monomer, 16-hydroxypalmitic acid. The Δmoset1 mutants were still infectious on the super-susceptible barley cultivar Nigrate. These results suggested that MoSET1 plays roles in various aspects of infection, including signal perception and overcoming host-specific resistance. However, since Δmoset1 was also impaired in vegetative growth, the impact of MoSET1 on gene regulation was not infection specific. ChIP-seq analysis of H3K4 di- and tri-methylation (H3K4me2/me3) and MoSET1 protein during infection-related morphogenesis, together with RNA-seq analysis of the Δmoset1 mutant, led to the following conclusions: 1) Approximately 5% of M. oryzae genes showed significant changes in H3K4-me2 or -me3 abundance during infection-related morphogenesis. 2) In general, H3K4-me2 and -me3 abundance was positively associated with active transcription. 3) Lack of MoSET1 methyltransferase, however, resulted in up-regulation of a significant portion of the M. oryzae genes in the vegetative mycelia (1,491 genes), and during infection-related morphogenesis (1,385 genes), indicating that MoSET1 has a role in gene repression either directly or more likely indirectly. 4) Among the 4,077 differentially expressed genes (DEGs) between mycelia and germination tubes, 1,201 and 882 genes were up- and down-regulated, respectively, in a Moset1-dependent manner. 5) The Moset1-dependent DEGs were enriched in several gene categories such as signal transduction, transport, RNA processing, and translation. This paper provides two major contributions to the field of genetics. First, we systematically studied the biological roles of eight histone lysine methyltransferase (KMT) genes in the phytopathogenic fungus Magnaporthe oryzae. We investigated their roles, especially focusing on their involvement in infection-related morphogenesis and pathogenicity. The results showed that the eight KMTs were involved in various infection processes to varying degrees, and that MoSET1, one of the KMTs catalyzing methylation at histone H3 lysine 4 (H3K4), had the largest impact on the pathogenicity of the fungus. Second, we focused on the role of MoSET1 in global gene regulation. H3K4 methylation is generally believed to be an epigenetic mark for gene activation in higher eukaryotes. However, in Saccharomyces cerevisiae, SET1 was originally characterized as being required for transcriptional silencing of silent mating-type loci. We addressed this apparent discrepancy by examining genome-wide gene expression and H3K4 methylation during infection-related morphogenesis in M. oryzae. RNA-seq analysis of a MoSET1 deletion mutant revealed that MoSET1 was indeed required for proper gene activation and repression. ChIP-seq analyses of H3K4 methylation and MoSET1 suggested that MoSET1 could directly play a role in gene activation while MoSET1-dependent gene repression may be caused by indirect effects.
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Affiliation(s)
- Kieu Thi Minh Pham
- Laboratory of Cell Function and Structure, Graduate School of Agricultural Science, Kobe University, Nada Kobe, Japan
| | - Yoshihiro Inoue
- Laboratory of Cell Function and Structure, Graduate School of Agricultural Science, Kobe University, Nada Kobe, Japan
| | - Ba Van Vu
- Laboratory of Cell Function and Structure, Graduate School of Agricultural Science, Kobe University, Nada Kobe, Japan
| | - Hanh Hieu Nguyen
- Laboratory of Cell Function and Structure, Graduate School of Agricultural Science, Kobe University, Nada Kobe, Japan
| | - Toru Nakayashiki
- Laboratory of Cell Function and Structure, Graduate School of Agricultural Science, Kobe University, Nada Kobe, Japan
| | - Ken-ichi Ikeda
- Laboratory of Cell Function and Structure, Graduate School of Agricultural Science, Kobe University, Nada Kobe, Japan
| | - Hitoshi Nakayashiki
- Laboratory of Cell Function and Structure, Graduate School of Agricultural Science, Kobe University, Nada Kobe, Japan
- * E-mail:
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Gowda M, Shirke MD, Mahesh H, Chandarana P, Rajamani A, Chattoo BB. Genome analysis of rice-blast fungus Magnaporthe oryzae field isolates from southern India. GENOMICS DATA 2015; 5:284-91. [PMID: 26484270 PMCID: PMC4583678 DOI: 10.1016/j.gdata.2015.06.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 06/03/2015] [Indexed: 12/18/2022]
Abstract
The Indian subcontinent is the center of origin and diversity for rice (Oryza sativa L.). The O. sativa ssp. indica is a major food crop grown in India, which occupies the first and second position in area and production, respectively. Blast disease caused by Magnaporthe oryzae is a major constraint to rice production. Here, we report the analysis of genome architecture and sequence variation of two field isolates, B157 and MG01, of the blast fungus from southern India. The 40 Mb genome of B157 and 43 Mb genome of MG01 contained 11,344 and 11,733 predicted genes, respectively. Genomic comparisons unveiled a large set of SNPs and several isolate specific genes in the Indian blast isolates. Avr genes were analyzed in several sequenced Magnaporthe strains; this analysis revealed the presence of Avr-Pizt and Avr-Ace1 genes in all the sequenced isolates. Availability of whole genomes of field isolates from India will contribute to global efforts to understand genetic diversity of M. oryzae population and to track the emergence of virulent pathotypes. The first genomic study of Magnaporthe from Indian subcontinent Provided information about genomic variations in terms of SNPs, InDels and ICVs due to transposable elements Identified novel genes specific to Indian isolates Genome wide antisense transcripts identified from this study Identified Magnaporthe specific pathogenicity genes that are absent in non-pathogenic Ascomycetes fungi
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Affiliation(s)
- Malali Gowda
- Genomics Laboratory, Centre for Cellular and Molecular Platforms, Bangalore 560065, India
- Corresponding authors. Tel.: + 91 80 67185113.
| | - Meghana D. Shirke
- Genomics Laboratory, Centre for Cellular and Molecular Platforms, Bangalore 560065, India
| | - H.B. Mahesh
- Genomics Laboratory, Centre for Cellular and Molecular Platforms, Bangalore 560065, India
- Marker Assisted Selection Laboratory, Department of Genetics and Plant Breeding, University of Agricultural Sciences, Bangalore, India
| | - Pinal Chandarana
- Centre for Genome Research, Department of Microbiology and Biotechnology Centre, Faculty of Science, Maharaja Sayajirao University of Baroda, Vadodara 390002, India
| | | | - Bharat B. Chattoo
- Centre for Genome Research, Department of Microbiology and Biotechnology Centre, Faculty of Science, Maharaja Sayajirao University of Baroda, Vadodara 390002, India
- Corresponding authors. Tel.: + 91 80 67185113.
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Zhao B, Si HL, Sun ZY, Xu Z, Chen Z, Zhang JL, Xing JH, Dong JG. Identification of Development and Pathogenicity Related Gene in Botrytis cinerea via Digital Gene Expression Profile. Jundishapur J Microbiol 2015; 8:e22432. [PMID: 26034553 PMCID: PMC4449859 DOI: 10.5812/jjm.8(4)2015.22432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 12/12/2014] [Accepted: 01/02/2015] [Indexed: 11/16/2022] Open
Abstract
Background: Botrytis cinerea, a haploid Euascomycete fungus that infects numerous crops, has been used as a model system for studying molecular phytopathology. Botrytis cinerea adopts various modes of infection, which are mediated by a number of pathogenicity and virulence-related genes. Many of these genes have not been reported previously. Objectives: This study aimed to investigate development and pathogenicity-related genes between a novel nonpathogenic mutant and the Wild Type (WT) in B. cinerea. Materials and Methods: Digital Gene Expression (DGE) tag profiling can reveal novel genes that may be involved in development and pathogenicity of plant pathogen. A large volume of B. cinerea tag-seq was generated to identify differential expressed genes by the Illumina DGE tag profiling technology. Results: A total of 4,182,944 and 4,182,021 clean tags were obtained from the WT and a nonpathogenic mutant stain (BCt89), respectively, and 10,410 differentially expressed genes were identified. In addition, 84 genes were expressed in the WT only while 34 genes were expressed in the mutant only. A total of 664 differentially expressed genes were involved in 91 Kyoto Encyclopedia of Genes and Genome pathways, including signaling and metabolic pathways. Conclusions: Expression levels of 1,426 genes were significantly up-regulated in the mutant compared to WT. Furthermore, 301 genes were down-regulated with False Discovery Rates (FDR) of < 0.001 and absolute value of log2 Ratio of ≥ 1.
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Affiliation(s)
- Bin Zhao
- Mycotoxin and Molecular Plant Pathology Laboratory, Agricultural University of Hebei, Baoding, China
| | - He Long Si
- Mycotoxin and Molecular Plant Pathology Laboratory, Agricultural University of Hebei, Baoding, China
| | - Zhi Ying Sun
- Mycotoxin and Molecular Plant Pathology Laboratory, Agricultural University of Hebei, Baoding, China
| | - Zheng Xu
- Mycotoxin and Molecular Plant Pathology Laboratory, Agricultural University of Hebei, Baoding, China
| | - Zhan Chen
- Institute of Pomology, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Jin lin Zhang
- Mycotoxin and Molecular Plant Pathology Laboratory, Agricultural University of Hebei, Baoding, China
| | - Ji Hong Xing
- Mycotoxin and Molecular Plant Pathology Laboratory, Agricultural University of Hebei, Baoding, China
- Corresponding authors: Ji Hong Xing, Mycotoxin and Molecular Plant Pathology Laboratory, Agricultural University of Hebei, Baoding, China. Tel/Fax: +86-3127528142, E-mail: ; Jin Gao Dong, Mycotoxin and Molecular Plant Pathology Laboratory, Agricultural University of Hebei, Baoding, China, Tel/Fax: +86-3127528266, E-mail:
| | - Jin Gao Dong
- Mycotoxin and Molecular Plant Pathology Laboratory, Agricultural University of Hebei, Baoding, China
- Corresponding authors: Ji Hong Xing, Mycotoxin and Molecular Plant Pathology Laboratory, Agricultural University of Hebei, Baoding, China. Tel/Fax: +86-3127528142, E-mail: ; Jin Gao Dong, Mycotoxin and Molecular Plant Pathology Laboratory, Agricultural University of Hebei, Baoding, China, Tel/Fax: +86-3127528266, E-mail:
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12
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Meijueiro ML, Santoyo F, Ramirez L, Pisabarro AG. Transcriptome characteristics of filamentous fungi deduced using high-throughput analytical technologies. Brief Funct Genomics 2014; 13:440-50. [DOI: 10.1093/bfgp/elu033] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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13
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Aguilar-Pontes MV, de Vries RP, Zhou M. (Post-)genomics approaches in fungal research. Brief Funct Genomics 2014; 13:424-39. [PMID: 25037051 DOI: 10.1093/bfgp/elu028] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
To date, hundreds of fungal genomes have been sequenced and many more are in progress. This wealth of genomic information has provided new directions to study fungal biodiversity. However, to further dissect and understand the complicated biological mechanisms involved in fungal life styles, functional studies beyond genomes are required. Thanks to the developments of current -omics techniques, it is possible to produce large amounts of fungal functional data in a high-throughput fashion (e.g. transcriptome, proteome, etc.). The increasing ease of creating -omics data has also created a major challenge for downstream data handling and analysis. Numerous databases, tools and software have been created to meet this challenge. Facing such a richness of techniques and information, hereby we provide a brief roadmap on current wet-lab and bioinformatics approaches to study functional genomics in fungi.
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Venu RC, Ma J, Jia Y, Liu G, Jia MH, Nobuta K, Sreerekha MV, Moldenhauer K, McClung AM, Meyers BC, Wang GL. Identification of candidate genes associated with positive and negative heterosis in rice. PLoS One 2014; 9:e95178. [PMID: 24743656 PMCID: PMC3990613 DOI: 10.1371/journal.pone.0095178] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 03/24/2014] [Indexed: 12/25/2022] Open
Abstract
To identify the genes responsible for yield related traits, and heterosis, massively parallel signature sequencing (MPSS) libraries were constructed from leaves, roots and meristem tissues from the two parents, 'Nipponbare' and '93-11', and their F1 hybrid. From the MPSS libraries, 1-3 million signatures were obtained. Using cluster analysis, commonly and specifically expressed genes in the parents and their F1 hybrid were identified. To understand heterosis in the F1 hybrid, the differentially expressed genes in the F1 hybrid were mapped to yield related quantitative trait loci (QTL) regions using a linkage map constructed from 131 polymorphic simple sequence repeat markers with 266 recombinant inbred lines derived from a cross between Nipponbare and 93-11. QTLs were identified for yield related traits including days to heading, plant height, plant type, number of tillers, main panicle length, number of primary branches per main panicle, number of kernels per main panicle, total kernel weight per main panicle, 1000 grain weight and total grain yield per plant. Seventy one QTLs for these traits were mapped, of which 3 QTLs were novel. Many highly expressed chromatin-related genes in the F1 hybrid encoding histone demethylases, histone deacetylases, argonaute-like proteins and polycomb proteins were located in these yield QTL regions. A total of 336 highly expressed transcription factor (TF) genes belonging to 50 TF families were identified in the yield QTL intervals. These findings provide the starting genomic materials to elucidate the molecular basis of yield related traits and heterosis in rice.
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Affiliation(s)
- R. C. Venu
- Dale Bumpers National Rice Research Center (DB NRRC), Agricultural Research Service, United States Department of Agriculture (USDA-ARS), Stuttgart, Arkansas, United States of America
- Rice Research and Extension Center, University of Arkansas Division of Agriculture, Stuttgart, Arkansas, United States of America
- Department of Plant Pathology, Ohio State University, Columbus, Ohio, United States of America
| | - Jianbing Ma
- Dale Bumpers National Rice Research Center (DB NRRC), Agricultural Research Service, United States Department of Agriculture (USDA-ARS), Stuttgart, Arkansas, United States of America
- Rice Research and Extension Center, University of Arkansas Division of Agriculture, Stuttgart, Arkansas, United States of America
| | - Yulin Jia
- Dale Bumpers National Rice Research Center (DB NRRC), Agricultural Research Service, United States Department of Agriculture (USDA-ARS), Stuttgart, Arkansas, United States of America
- * E-mail:
| | - Guangjie Liu
- Dale Bumpers National Rice Research Center (DB NRRC), Agricultural Research Service, United States Department of Agriculture (USDA-ARS), Stuttgart, Arkansas, United States of America
- Rice Research and Extension Center, University of Arkansas Division of Agriculture, Stuttgart, Arkansas, United States of America
| | - Melissa H. Jia
- Dale Bumpers National Rice Research Center (DB NRRC), Agricultural Research Service, United States Department of Agriculture (USDA-ARS), Stuttgart, Arkansas, United States of America
| | - Kan Nobuta
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, United States of America
| | - M. V. Sreerekha
- Department of Plant Pathology, Ohio State University, Columbus, Ohio, United States of America
| | - Karen Moldenhauer
- Rice Research and Extension Center, University of Arkansas Division of Agriculture, Stuttgart, Arkansas, United States of America
| | - Anna M. McClung
- Dale Bumpers National Rice Research Center (DB NRRC), Agricultural Research Service, United States Department of Agriculture (USDA-ARS), Stuttgart, Arkansas, United States of America
| | - Blake C. Meyers
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, United States of America
| | - Guo-Liang Wang
- Department of Plant Pathology, Ohio State University, Columbus, Ohio, United States of America
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Traeger S, Altegoer F, Freitag M, Gabaldon T, Kempken F, Kumar A, Marcet-Houben M, Pöggeler S, Stajich JE, Nowrousian M. The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution. PLoS Genet 2013; 9:e1003820. [PMID: 24068976 PMCID: PMC3778014 DOI: 10.1371/journal.pgen.1003820] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 08/07/2013] [Indexed: 11/26/2022] Open
Abstract
Fungi are a large group of eukaryotes found in nearly all ecosystems. More than 250 fungal genomes have already been sequenced, greatly improving our understanding of fungal evolution, physiology, and development. However, for the Pezizomycetes, an early-diverging lineage of filamentous ascomycetes, there is so far only one genome available, namely that of the black truffle, Tuber melanosporum, a mycorrhizal species with unusual subterranean fruiting bodies. To help close the sequence gap among basal filamentous ascomycetes, and to allow conclusions about the evolution of fungal development, we sequenced the genome and assayed transcriptomes during development of Pyronema confluens, a saprobic Pezizomycete with a typical apothecium as fruiting body. With a size of 50 Mb and ∼13,400 protein-coding genes, the genome is more characteristic of higher filamentous ascomycetes than the large, repeat-rich truffle genome; however, some typical features are different in the P. confluens lineage, e.g. the genomic environment of the mating type genes that is conserved in higher filamentous ascomycetes, but only partly conserved in P. confluens. On the other hand, P. confluens has a full complement of fungal photoreceptors, and expression studies indicate that light perception might be similar to distantly related ascomycetes and, thus, represent a basic feature of filamentous ascomycetes. Analysis of spliced RNA-seq sequence reads allowed the detection of natural antisense transcripts for 281 genes. The P. confluens genome contains an unusually high number of predicted orphan genes, many of which are upregulated during sexual development, consistent with the idea of rapid evolution of sex-associated genes. Comparative transcriptomics identified the transcription factor gene pro44 that is upregulated during development in P. confluens and the Sordariomycete Sordaria macrospora. The P. confluens pro44 gene (PCON_06721) was used to complement the S. macrospora pro44 deletion mutant, showing functional conservation of this developmental regulator. Fungi are a morphologically and physiologically diverse group of organisms with huge impacts on nearly all ecosystems. In recent years, genomes of many fungal species have been sequenced and have greatly improved our understanding of fungal biology. Ascomycetes are the largest fungal group with the highest number of sequenced genomes; however, for the Pezizales, an early-diverging lineage of filamentous ascomycetes, only one genome has been sequence to date, namely that of the black truffle. While truffles are among the most valuable edible fungi, they have a specialized life style as plant symbionts producing belowground fruiting bodies; thus it is difficult to draw conclusions about basal ascomycetes from one truffle genome alone. Therefore, we have sequenced the genome and several transcriptomes of the basal ascomycete Pyronema confluens, which has a saprobic life style typical of many ascomycetes. Comparisons with other fungal genomes showed that P. confluens has two conserved mating type genes, but that the genomic environment of the mating type genes is different from that of higher ascomycetes. We also found that a high number of orphan genes, i.e. genes without homologs in other fungi, are upregulated during sexual development. This is consistent with rapid evolution of sex-associated genes.
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Affiliation(s)
- Stefanie Traeger
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, Bochum, Germany
| | - Florian Altegoer
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, Bochum, Germany
| | - Michael Freitag
- Center for Genome Research and Biocomputing, Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, United States of America
| | - Toni Gabaldon
- Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Frank Kempken
- Abteilung Botanische Genetik und Molekularbiologie, Botanisches Institut und Botanischer Garten, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Abhishek Kumar
- Abteilung Botanische Genetik und Molekularbiologie, Botanisches Institut und Botanischer Garten, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Marina Marcet-Houben
- Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Stefanie Pöggeler
- Institute of Microbiology and Genetics, Department of Genetics of Eukaryotic Microorganisms, Georg-August University, Göttingen, Germany
| | - Jason E. Stajich
- Department of Plant Pathology and Microbiology, University of California Riverside, Riverside, California, United States of America
| | - Minou Nowrousian
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, Bochum, Germany
- * E-mail:
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16
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Substrate-induced transcriptional activation of the MoCel7C cellulase gene is associated with methylation of histone H3 at lysine 4 in the rice blast fungus Magnaporthe oryzae. Appl Environ Microbiol 2013; 79:6823-32. [PMID: 23995923 DOI: 10.1128/aem.02082-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The mechanisms involved in substrate-dependent regulation of a Magnaporthe oryzae gene encoding a cellulase which we designate MoCel7C (MGG_14954) were investigated. The levels of MoCel7C transcript were dramatically increased more than 1,000-fold, 16 to 24 h after transfer to a medium containing 2% carboxymethylcellulose (CMC), while levels were very low or undetectable in conventional rich medium. Green fluorescent protein reporter assays showed that the MoCel7C promoter was activated by cello-oligosaccharides larger than a pentamer. CMC-induced activation of the MoCel7C promoter was suppressed by glucose and cellobiose. Chromatin immunoprecipitation assays revealed that histone H3 methylation on lysine 4 (H3K4) at the MoCel7C locus was associated with activation of the gene by CMC. Consistently, CMC-induced MoCel7C gene activation was drastically diminished in a knockout (KO) mutant of the MoSET1 gene, which encodes a histone lysine methyltransferase that catalyzes H3K4 methylation in M. oryzae. Interestingly, however, MoCel7C transcript levels under noninducing conditions were significantly increased in the MoSET1 KO mutant, suggesting that MoSET1 directly or indirectly plays a role in both activation and suppression of the MoCel7C gene in response to environmental signals. In addition, gene expression and silencing vectors using the MoCel7C promoter were constructed.
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Donaldson ME, Saville BJ. Ustilago maydis natural antisense transcript expression alters mRNA stability and pathogenesis. Mol Microbiol 2013; 89:29-51. [PMID: 23650872 PMCID: PMC3739942 DOI: 10.1111/mmi.12254] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2013] [Indexed: 11/29/2022]
Abstract
Ustilago maydis infection of Zea mays leads to the production of thick-walled diploid teliospores that are the dispersal agent for this pathogen. Transcriptome analyses of this model biotrophic basidiomycete fungus identified natural antisense transcripts (NATs) complementary to 247 open reading frames. The U. maydis NAT cDNAs were fully sequenced and annotated. Strand-specific RT-PCR screens confirmed expression and identified NATs preferentially expressed in the teliospore. Targeted screens revealed four U. maydis NATs that are conserved in a related fungus. Expression of NATs in haploid cells, where they are not naturally occurring, resulted in increased steady-state levels of some complementary mRNAs. The expression of one NAT, as-um02151, in haploid cells resulted in a twofold increase in complementary mRNA levels, the formation of sense-antisense double-stranded RNAs, and unchanged Um02151 protein levels. This led to a model for NAT function in the maintenance and expression of stored teliospore mRNAs. In testing this model by deletion of the regulatory region, it was determined that alteration in NAT expression resulted in decreased pathogenesis in both cob and seedling infections. This annotation and functional analysis supports multiple roles for U. maydis NATs in controlling gene expression and influencing pathogenesis.
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Affiliation(s)
- Michael E Donaldson
- Environmental and Life Sciences Graduate ProgramPeterborough, ON, Canada, K9J 7B8
| | - Barry J Saville
- Environmental and Life Sciences Graduate ProgramPeterborough, ON, Canada, K9J 7B8
- Forensic Science Program, Trent UniversityPeterborough, ON, Canada, K9J 7B8
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Chen S, Songkumarn P, Venu RC, Gowda M, Bellizzi M, Hu J, Liu W, Ebbole D, Meyers B, Mitchell T, Wang GL. Identification and characterization of in planta-expressed secreted effector proteins from Magnaporthe oryzae that induce cell death in rice. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2013; 26:191-202. [PMID: 23035914 DOI: 10.1094/mpmi-05-12-0117-r] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Interactions between rice and Magnaporthe oryzae involve the recognition of cellular components and the exchange of complex molecular signals from both partners. How these interactions occur in rice cells is still elusive. We employed robust-long serial analysis of gene expression, massively parallel signature sequencing, and sequencing by synthesis to examine transcriptome profiles of infected rice leaves. A total of 6,413 in planta-expressed fungal genes, including 851 genes encoding predicted effector proteins, were identified. We used a protoplast transient expression system to assess 42 of the predicted effector proteins for the ability to induce plant cell death. Ectopic expression assays identified five novel effectors that induced host cell death only when they contained the signal peptide for secretion to the extracellular space. Four of them induced cell death in Nicotiana benthamiana. Although the five effectors are highly diverse in their sequences, the physiological basis of cell death induced by each was similar. This study demonstrates that our integrative genomic approach is effective for the identification of in planta-expressed cell death-inducing effectors from M. oryzae that may play an important role facilitating colonization and fungal growth during infection.
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Affiliation(s)
- Songbiao Chen
- State Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Antal Z, Rascle C, Cimerman A, Viaud M, Billon-Grand G, Choquer M, Bruel C. The homeobox BcHOX8 gene in Botrytis cinerea regulates vegetative growth and morphology. PLoS One 2012; 7:e48134. [PMID: 23133556 PMCID: PMC3485016 DOI: 10.1371/journal.pone.0048134] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Accepted: 09/27/2012] [Indexed: 11/19/2022] Open
Abstract
Filamentous growth and the capacity at producing conidia are two critical aspects of most fungal life cycles, including that of many plant or animal pathogens. Here, we report on the identification of a homeobox transcription factor encoding gene that plays a role in these two particular aspects of the development of the phytopathogenic fungus Botrytis cinerea. Deletion of the BcHOX8 gene in both the B. cinerea B05-10 and T4 strains causes similar phenotypes, among which a curved, arabesque-like, hyphal growth on hydrophobic surfaces; the mutants were hence named Arabesque. Expression of the BcHOX8 gene is higher in conidia and infection cushions than in developing appressorium or mycelium. In the Arabesque mutants, colony growth rate is reduced and abnormal infection cushions are produced. Asexual reproduction is also affected with abnormal conidiophore being formed, strongly reduced conidia production and dramatic changes in conidial morphology. Finally, the mutation affects the fungus ability to efficiently colonize different host plants. Analysis of the B. cinerea genome shows that BcHOX8 is one member of a nine putative homeobox genes family. Available gene expression data suggest that these genes are functional and sequence comparisons indicate that two of them would be specific to B. cinerea and its close relative Sclerotinia sclerotiorum.
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Affiliation(s)
- Zsuzsanna Antal
- Unité Mixte de Recherche 5240 - Microbiologie, Adaptation et Pathogénie; Université Lyon 1, CNRS, Bayer CropScience, Villeurbanne, France
| | - Christine Rascle
- Unité Mixte de Recherche 5240 - Microbiologie, Adaptation et Pathogénie; Université Lyon 1, CNRS, Bayer CropScience, Villeurbanne, France
| | - Agnès Cimerman
- Biologie et Gestion des Risques en Agriculture - Champignons Pathogènes des Plantes, INRA 1290, Thiverval-Grignon, France
| | - Muriel Viaud
- Biologie et Gestion des Risques en Agriculture - Champignons Pathogènes des Plantes, INRA 1290, Thiverval-Grignon, France
| | - Geneviève Billon-Grand
- Unité Mixte de Recherche 5240 - Microbiologie, Adaptation et Pathogénie; Université Lyon 1, CNRS, Bayer CropScience, Villeurbanne, France
| | - Mathias Choquer
- Unité Mixte de Recherche 5240 - Microbiologie, Adaptation et Pathogénie; Université Lyon 1, CNRS, Bayer CropScience, Villeurbanne, France
| | - Christophe Bruel
- Unité Mixte de Recherche 5240 - Microbiologie, Adaptation et Pathogénie; Université Lyon 1, CNRS, Bayer CropScience, Villeurbanne, France
- * E-mail:
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Uncovering the genome-wide transcriptional responses of the filamentous fungus Aspergillus niger to lignocellulose using RNA sequencing. PLoS Genet 2012; 8:e1002875. [PMID: 22912594 PMCID: PMC3415456 DOI: 10.1371/journal.pgen.1002875] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 06/23/2012] [Indexed: 12/19/2022] Open
Abstract
A key challenge in the production of second generation biofuels is the conversion of lignocellulosic substrates into fermentable sugars. Enzymes, particularly those from fungi, are a central part of this process, and many have been isolated and characterised. However, relatively little is known of how fungi respond to lignocellulose and produce the enzymes necessary for dis-assembly of plant biomass. We studied the physiological response of the fungus Aspergillus niger when exposed to wheat straw as a model lignocellulosic substrate. Using RNA sequencing we showed that, 24 hours after exposure to straw, gene expression of known and presumptive plant cell wall-degrading enzymes represents a huge investment for the cells (about 20% of the total mRNA). Our results also uncovered new esterases and surface interacting proteins that might form part of the fungal arsenal of enzymes for the degradation of plant biomass. Using transcription factor deletion mutants (xlnR and creA) to study the response to both lignocellulosic substrates and low carbon source concentrations, we showed that a subset of genes coding for degradative enzymes is induced by starvation. Our data support a model whereby this subset of enzymes plays a scouting role under starvation conditions, testing for available complex polysaccharides and liberating inducing sugars, that triggers the subsequent induction of the majority of hydrolases. We also showed that antisense transcripts are abundant and that their expression can be regulated by growth conditions.
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Dean R, Van Kan JAL, Pretorius ZA, Hammond-Kosack KE, Di Pietro A, Spanu PD, Rudd JJ, Dickman M, Kahmann R, Ellis J, Foster GD. The Top 10 fungal pathogens in molecular plant pathology. MOLECULAR PLANT PATHOLOGY 2012. [PMID: 22471698 DOI: 10.1111/j.1364-3703.2012.2011.00783.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The aim of this review was to survey all fungal pathologists with an association with the journal Molecular Plant Pathology and ask them to nominate which fungal pathogens they would place in a 'Top 10' based on scientific/economic importance. The survey generated 495 votes from the international community, and resulted in the generation of a Top 10 fungal plant pathogen list for Molecular Plant Pathology. The Top 10 list includes, in rank order, (1) Magnaporthe oryzae; (2) Botrytis cinerea; (3) Puccinia spp.; (4) Fusarium graminearum; (5) Fusarium oxysporum; (6) Blumeria graminis; (7) Mycosphaerella graminicola; (8) Colletotrichum spp.; (9) Ustilago maydis; (10) Melampsora lini, with honourable mentions for fungi just missing out on the Top 10, including Phakopsora pachyrhizi and Rhizoctonia solani. This article presents a short resumé of each fungus in the Top 10 list and its importance, with the intent of initiating discussion and debate amongst the plant mycology community, as well as laying down a bench-mark. It will be interesting to see in future years how perceptions change and what fungi will comprise any future Top 10.
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Affiliation(s)
- Ralph Dean
- Department of Plant Pathology, Fungal Genomics Laboratory, North Carolina State University, Raleigh, NC 27695, USA
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Dean R, Van Kan JAL, Pretorius ZA, Hammond-Kosack KE, Di Pietro A, Spanu PD, Rudd JJ, Dickman M, Kahmann R, Ellis J, Foster GD. The Top 10 fungal pathogens in molecular plant pathology. MOLECULAR PLANT PATHOLOGY 2012; 13:414-30. [PMID: 22471698 PMCID: PMC6638784 DOI: 10.1111/j.1364-3703.2011.00783.x] [Citation(s) in RCA: 2085] [Impact Index Per Article: 173.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The aim of this review was to survey all fungal pathologists with an association with the journal Molecular Plant Pathology and ask them to nominate which fungal pathogens they would place in a 'Top 10' based on scientific/economic importance. The survey generated 495 votes from the international community, and resulted in the generation of a Top 10 fungal plant pathogen list for Molecular Plant Pathology. The Top 10 list includes, in rank order, (1) Magnaporthe oryzae; (2) Botrytis cinerea; (3) Puccinia spp.; (4) Fusarium graminearum; (5) Fusarium oxysporum; (6) Blumeria graminis; (7) Mycosphaerella graminicola; (8) Colletotrichum spp.; (9) Ustilago maydis; (10) Melampsora lini, with honourable mentions for fungi just missing out on the Top 10, including Phakopsora pachyrhizi and Rhizoctonia solani. This article presents a short resumé of each fungus in the Top 10 list and its importance, with the intent of initiating discussion and debate amongst the plant mycology community, as well as laying down a bench-mark. It will be interesting to see in future years how perceptions change and what fungi will comprise any future Top 10.
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Affiliation(s)
- Ralph Dean
- Department of Plant Pathology, Fungal Genomics Laboratory, North Carolina State University, Raleigh, NC 27695, USA
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Singh K, Nizam S, Sinha M, Verma PK. Comparative transcriptome analysis of the necrotrophic fungus Ascochyta rabiei during oxidative stress: insight for fungal survival in the host plant. PLoS One 2012; 7:e33128. [PMID: 22427966 PMCID: PMC3299738 DOI: 10.1371/journal.pone.0033128] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Accepted: 02/10/2012] [Indexed: 11/18/2022] Open
Abstract
Localized cell death, known as the hypersensitive response (HR), is an important defense mechanism for neutralizing phytopathogens. The hallmark of the HR is an oxidative burst produced by the host plant. We aimed to identify genes of the necrotrophic chickpea blight fungus Ascochyta rabiei that are involved in counteracting oxidative stress. A subtractive cDNA library was constructed after menadione treatment, which resulted in the isolation of 128 unigenes. A reverse northern blot was used to compare transcript profiles after H(2)O(2), menadione and sodium nitroprusside treatments. A total of 70 unigenes were found to be upregulated by more than two-fold following menadione treatment at different time intervals. A large number of genes not previously associated with oxidative stress were identified, along with many stress-responsive genes. Differential expression patterns of several genes were validated by quantitative real-time PCR (qRT-PCR) and northern blotting. In planta qRT-PCR of several selected genes also showed differential expression patterns during infection and disease progression. These data shed light on the molecular responses of the phytopathogen A. rabiei to overcome oxidative and nitrosative stresses and advance the understanding of necrotrophic fungal pathogen survival mechanisms.
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Affiliation(s)
- Kunal Singh
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Shadab Nizam
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Manisha Sinha
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Praveen K. Verma
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
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Soanes DM, Chakrabarti A, Paszkiewicz KH, Dawe AL, Talbot NJ. Genome-wide transcriptional profiling of appressorium development by the rice blast fungus Magnaporthe oryzae. PLoS Pathog 2012; 8:e1002514. [PMID: 22346750 PMCID: PMC3276559 DOI: 10.1371/journal.ppat.1002514] [Citation(s) in RCA: 125] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Accepted: 12/16/2011] [Indexed: 11/19/2022] Open
Abstract
The rice blast fungus Magnaporthe oryzae is one of the most significant pathogens affecting global food security. To cause rice blast disease the fungus elaborates a specialised infection structure called an appressorium. Here, we report genome wide transcriptional profile analysis of appressorium development using next generation sequencing (NGS). We performed both RNA-Seq and High-Throughput SuperSAGE analysis to compare the utility of these procedures for identifying differential gene expression in M. oryzae. We then analysed global patterns of gene expression during appressorium development. We show evidence for large-scale gene expression changes, highlighting the role of autophagy, lipid metabolism and melanin biosynthesis in appressorium differentiation. We reveal the role of the Pmk1 MAP kinase as a key global regulator of appressorium-associated gene expression. We also provide evidence for differential expression of transporter-encoding gene families and specific high level expression of genes involved in quinate uptake and utilization, consistent with pathogen-mediated perturbation of host metabolism during plant infection. When considered together, these data provide a comprehensive high-resolution analysis of gene expression changes associated with cellular differentiation that will provide a key resource for understanding the biology of rice blast disease.
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Affiliation(s)
- Darren M. Soanes
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Apratim Chakrabarti
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Konrad H. Paszkiewicz
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Angus L. Dawe
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, United States of America
| | - Nicholas J. Talbot
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
- * E-mail:
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Nunes CC, Gowda M, Sailsbery J, Xue M, Chen F, Brown DE, Oh Y, Mitchell TK, Dean RA. Diverse and tissue-enriched small RNAs in the plant pathogenic fungus, Magnaporthe oryzae. BMC Genomics 2011; 12:288. [PMID: 21635781 PMCID: PMC3132168 DOI: 10.1186/1471-2164-12-288] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Accepted: 06/02/2011] [Indexed: 01/16/2023] Open
Abstract
Background Emerging knowledge of the impact of small RNAs as important cellular regulators has prompted an explosion of small transcriptome sequencing projects. Although significant progress has been made towards small RNA discovery and biogenesis in higher eukaryotes and other model organisms, knowledge in simple eukaryotes such as filamentous fungi remains limited. Results Here, we used 454 pyrosequencing to present a detailed analysis of the small RNA transcriptome (~ 15 - 40 nucleotides in length) from mycelia and appressoria tissues of the rice blast fungal pathogen, Magnaporthe oryzae. Small RNAs mapped to numerous nuclear and mitochondrial genomic features including repetitive elements, tRNA loci, rRNAs, protein coding genes, snRNAs and intergenic regions. For most elements, small RNAs mapped primarily to the sense strand with the exception of repetitive elements to which small RNAs mapped in the sense and antisense orientation in near equal proportions. Inspection of the small RNAs revealed a preference for U and suppression of C at position 1, particularly for antisense mapping small RNAs. In the mycelia library, small RNAs of the size 18 - 23 nt were enriched for intergenic regions and repetitive elements. Small RNAs mapping to LTR retrotransposons were classified as LTR retrotransposon-siRNAs (LTR-siRNAs). Conversely, the appressoria library had a greater proportion of 28 - 35 nt small RNAs mapping to tRNA loci, and were classified as tRNA-derived RNA fragments (tRFs). LTR-siRNAs and tRFs were independently validated by 3' RACE PCR and northern blots, respectively. Conclusions Our findings suggest M. oryzae small RNAs differentially accumulate in vegetative and specialized-infection tissues and may play an active role in genome integrity and regulating growth and development.
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Affiliation(s)
- Cristiano C Nunes
- Fungal Genomics Laboratory, Center for Integrated Fungal Research, Department of Plant Pathology, North Carolina State University, Raleigh, NC 27606, USA
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de Vries RP, Benoit I, Doehlemann G, Kobayashi T, Magnuson JK, Panisko EA, Baker SE, Lebrun MH. Post-genomic approaches to understanding interactions between fungi and their environment. IMA Fungus 2011; 2:81-6. [PMID: 22679591 PMCID: PMC3317359 DOI: 10.5598/imafungus.2011.02.01.11] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 05/18/2011] [Indexed: 01/22/2023] Open
Abstract
Fungi inhabit every natural and anthropogenic environment on Earth. They have highly varied life-styles including saprobes (using only dead biomass as a nutrient source), pathogens (feeding on living biomass), and symbionts (co-existing with other organisms). These distinctions are not absolute as many species employ several life styles (e.g. saprobe and opportunistic pathogen, saprobe and mycorrhiza). To efficiently survive in these different and often changing environments, fungi need to be able to modify their physiology and in some cases will even modify their local environment. Understanding the interaction between fungi and their environments has been a topic of study for many decades. However, recently these studies have reached a new dimension. The availability of fungal genomes and development of post-genomic technologies for fungi, such as transcriptomics, proteomics and metabolomics, have enabled more detailed studies into this topic resulting in new insights. Based on a Special Interest Group session held during IMC9, this paper provides examples of the recent advances in using (post-)genomic approaches to better understand fungal interactions with their environments.
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Affiliation(s)
- Ronald P de Vries
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
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Venu R, Sreerekha M, Nobuta K, Beló A, Ning Y, An G, Meyers BC, Wang GL. Deep sequencing reveals the complex and coordinated transcriptional regulation of genes related to grain quality in rice cultivars. BMC Genomics 2011; 12:190. [PMID: 21492454 PMCID: PMC3098810 DOI: 10.1186/1471-2164-12-190] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Accepted: 04/14/2011] [Indexed: 11/12/2022] Open
Abstract
Background Milling yield and eating quality are two important grain quality traits in rice. To identify the genes involved in these two traits, we performed a deep transcriptional analysis of developing seeds using both massively parallel signature sequencing (MPSS) and sequencing-by-synthesis (SBS). Five MPSS and five SBS libraries were constructed from 6-day-old developing seeds of Cypress (high milling yield), LaGrue (low milling yield), Ilpumbyeo (high eating quality), YR15965 (low eating quality), and Nipponbare (control). Results The transcriptomes revealed by MPSS and SBS had a high correlation co-efficient (0.81 to 0.90), and about 70% of the transcripts were commonly identified in both types of the libraries. SBS, however, identified 30% more transcripts than MPSS. Among the highly expressed genes in Cypress and Ilpumbyeo, over 100 conserved cis regulatory elements were identified. Numerous specifically expressed transcription factor (TF) genes were identified in Cypress (282), LaGrue (312), Ilpumbyeo (363), YR15965 (260), and Nipponbare (357). Many key grain quality-related genes (i.e., genes involved in starch metabolism, aspartate amino acid metabolism, storage and allergenic protein synthesis, and seed maturation) that were expressed at high levels underwent alternative splicing and produced antisense transcripts either in Cypress or Ilpumbyeo. Further, a time course RT-PCR analysis confirmed a higher expression level of genes involved in starch metabolism such as those encoding ADP glucose pyrophosphorylase (AGPase) and granule bound starch synthase I (GBSS I) in Cypress than that in LaGrue during early seed development. Conclusion This study represents the most comprehensive analysis of the developing seed transcriptome of rice available to date. Using two high throughput sequencing methods, we identified many differentially expressed genes that may affect milling yield or eating quality in rice. Many of the identified genes are involved in the biosynthesis of starch, aspartate family amino acids, and storage proteins. Some of the differentially expressed genes could be useful for the development of molecular markers if they are located in a known QTL region for milling yield or eating quality in the rice genome. Therefore, our comprehensive and deep survey of the developing seed transcriptome in five rice cultivars has provided a rich genomic resource for further elucidating the molecular basis of grain quality in rice.
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Affiliation(s)
- Rc Venu
- Department of Plant Pathology, The Ohio State University, Columbus OH-43210, USA
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Tisserant E, Da Silva C, Kohler A, Morin E, Wincker P, Martin F. Deep RNA sequencing improved the structural annotation of the Tuber melanosporum transcriptome. THE NEW PHYTOLOGIST 2011; 189:883-891. [PMID: 21223284 DOI: 10.1111/j.1469-8137.2010.03597.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
• The functional complexity of the Tuber melanosporum transcriptome has not yet been fully elucidated. Here, we applied high-throughput Illumina RNA-sequencing (RNA-Seq) to the transcriptome of T. melanosporum at different major developmental stages, that is free-living mycelium, fruiting body and ectomycorrhiza. • Sequencing of cDNA libraries generated a total of c. 24 million sequence reads representing > 882 Mb of sequence data. To construct a coverage signal profile across the genome, all reads were then aligned to the reference genome assembly of T. melanosporum Mel28. • We were able to identify a substantial number of novel transcripts, antisense transcripts, new exons, untranslated regions (UTRs), alternative upstream initiation codons and upstream open reading frames. • This RNA-Seq analysis allowed us to improve the genome annotation. It also provided us with a genome-wide view of the transcriptional and post-transcriptional mechanisms generating an increased number of transcript isoforms during major developmental transitions in T. melanosporum.
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Affiliation(s)
- E Tisserant
- INRA, UMR INRA/Nancy Université'Interactions Arbres/Micro-Organismes', INRA-Nancy, 54280 Champenoux, France
| | - C Da Silva
- CEA, IG, Genoscope, 2 rue Gaston Crémieux CP5702, F-91057 Evry, France
| | - A Kohler
- INRA, UMR INRA/Nancy Université'Interactions Arbres/Micro-Organismes', INRA-Nancy, 54280 Champenoux, France
| | - E Morin
- INRA, UMR INRA/Nancy Université'Interactions Arbres/Micro-Organismes', INRA-Nancy, 54280 Champenoux, France
| | - P Wincker
- CEA, IG, Genoscope, 2 rue Gaston Crémieux CP5702, F-91057 Evry, France
| | - F Martin
- INRA, UMR INRA/Nancy Université'Interactions Arbres/Micro-Organismes', INRA-Nancy, 54280 Champenoux, France
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Gowda M, Nunes CC, Sailsbery J, Xue M, Chen F, Nelson CA, Brown DE, Oh Y, Meng S, Mitchell T, Hagedorn CH, Dean RA. Genome-wide characterization of methylguanosine-capped and polyadenylated small RNAs in the rice blast fungus Magnaporthe oryzae. Nucleic Acids Res 2010; 38:7558-69. [PMID: 20660015 PMCID: PMC2995040 DOI: 10.1093/nar/gkq583] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Small RNAs are well described in higher eukaryotes such as mammals and plants; however, knowledge in simple eukaryotes such as filamentous fungi is limited. In this study, we discovered and characterized methylguanosine-capped and polyadenylated small RNAs (CPA-sRNAs) by using differential RNA selection, full-length cDNA cloning and 454 transcriptome sequencing of the rice blast fungus Magnaporthe oryzae. This fungus causes blast, a devastating disease on rice, the principle food staple for over half the world’s population. CPA-sRNAs mapped primarily to the transcription initiation and termination sites of protein-coding genes and were positively correlated with gene expression, particularly for highly expressed genes including those encoding ribosomal proteins. Numerous CPA-sRNAs also mapped to rRNAs, tRNAs, snRNAs, transposable elements and intergenic regions. Many other 454 sequence reads could not be mapped to the genome; however, inspection revealed evidence for non-template additions and chimeric sequences. CPA-sRNAs were independently confirmed using a high affinity variant of eIF-4E to capture 5′-methylguanosine-capped RNA followed by 3′-RACE sequencing. These results expand the repertoire of small RNAs in filamentous fungi.
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Affiliation(s)
- Malali Gowda
- Fungal Genomics Laboratory, Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC 27606, USA
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Genome sequence of the model mushroom Schizophyllum commune. Nat Biotechnol 2010; 28:957-63. [PMID: 20622885 DOI: 10.1038/nbt.1643] [Citation(s) in RCA: 350] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Accepted: 05/12/2010] [Indexed: 11/08/2022]
Abstract
Much remains to be learned about the biology of mushroom-forming fungi, which are an important source of food, secondary metabolites and industrial enzymes. The wood-degrading fungus Schizophyllum commune is both a genetically tractable model for studying mushroom development and a likely source of enzymes capable of efficient degradation of lignocellulosic biomass. Comparative analyses of its 38.5-megabase genome, which encodes 13,210 predicted genes, reveal the species's unique wood-degrading machinery. One-third of the 471 genes predicted to encode transcription factors are differentially expressed during sexual development of S. commune. Whereas inactivation of one of these, fst4, prevented mushroom formation, inactivation of another, fst3, resulted in more, albeit smaller, mushrooms than in the wild-type fungus. Antisense transcripts may also have a role in the formation of fruiting bodies. Better insight into the mechanisms underlying mushroom formation should affect commercial production of mushrooms and their industrial use for producing enzymes and pharmaceuticals.
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Samolski I, de Luis A, Vizcaíno JA, Monte E, Suárez MB. Gene expression analysis of the biocontrol fungus Trichoderma harzianum in the presence of tomato plants, chitin, or glucose using a high-density oligonucleotide microarray. BMC Microbiol 2009; 9:217. [PMID: 19825185 PMCID: PMC2768740 DOI: 10.1186/1471-2180-9-217] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Accepted: 10/13/2009] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND It has recently been shown that the Trichoderma fungal species used for biocontrol of plant diseases are capable of interacting with plant roots directly, behaving as symbiotic microorganisms. With a view to providing further information at transcriptomic level about the early response of Trichoderma to a host plant, we developed a high-density oligonucleotide (HDO) microarray encompassing 14,081 Expressed Sequence Tag (EST)-based transcripts from eight Trichoderma spp. and 9,121 genome-derived transcripts of T. reesei, and we have used this microarray to examine the gene expression of T. harzianum either alone or in the presence of tomato plants, chitin, or glucose. RESULTS Global microarray analysis revealed 1,617 probe sets showing differential expression in T. harzianum mycelia under at least one of the culture conditions tested as compared with one another. Hierarchical clustering and heat map representation showed that the expression patterns obtained in glucose medium clustered separately from the expression patterns observed in the presence of tomato plants and chitin. Annotations using the Blast2GO suite identified 85 of the 257 transcripts whose probe sets afforded up-regulated expression in response to tomato plants. Some of these transcripts were predicted to encode proteins related to Trichoderma-host (fungus or plant) associations, such as Sm1/Elp1 protein, proteases P6281 and PRA1, enchochitinase CHIT42, or QID74 protein, although previously uncharacterized genes were also identified, including those responsible for the possible biosynthesis of nitric oxide, xenobiotic detoxification, mycelium development, or those related to the formation of infection structures in plant tissues. CONCLUSION The effectiveness of the Trichoderma HDO microarray to detect different gene responses under different growth conditions in the fungus T. harzianum strongly indicates that this tool should be useful for further assays that include different stages of plant colonization, as well as for expression studies in other Trichoderma spp. represented on it. Using this microarray, we have been able to define a number of genes probably involved in the transcriptional response of T. harzianum within the first hours of contact with tomato plant roots, which may provide new insights into the mechanisms and roles of this fungus in the Trichoderma-plant interaction.
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Affiliation(s)
- Ilanit Samolski
- Centro Hispano-Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca. Campus de Villamayor-Parque Científico, 37185 Villamayor, Salamanca, Spain
| | - Alberto de Luis
- Centro de Investigación Biomédica de La Rioja (CIBIR). Piqueras 98, 26006 Logroño, La Rioja, Spain
| | - Juan Antonio Vizcaíno
- EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Enrique Monte
- Centro Hispano-Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca. Campus de Villamayor-Parque Científico, 37185 Villamayor, Salamanca, Spain
| | - M Belén Suárez
- Centro Hispano-Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca. Campus de Villamayor-Parque Científico, 37185 Villamayor, Salamanca, Spain
- Current address: Instituto de Microbiología Bioquímica, CSIC/Universidad de Salamanca. Campus Miguel de Unamuno, 37007 Salamanca, Spain
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Takahara H, Dolf A, Endl E, O'Connell R. Flow cytometric purification of Colletotrichum higginsianum biotrophic hyphae from Arabidopsis leaves for stage-specific transcriptome analysis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 59:672-683. [PMID: 19392696 DOI: 10.1111/j.1365-313x.2009.03896.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Generation of stage-specific cDNA libraries is a powerful approach to identify pathogen genes that are differentially expressed during plant infection. Biotrophic pathogens develop specialized infection structures inside living plant cells, but sampling the transcriptome of these structures is problematic due to the low ratio of fungal to plant RNA, and the lack of efficient methods to isolate them from infected plants. Here we established a method, based on fluorescence-activated cell sorting (FACS), to purify the intracellular biotrophic hyphae of Colletotrichum higginsianum from homogenates of infected Arabidopsis leaves. Specific selection of viable hyphae using a fluorescent vital marker provided intact RNA for cDNA library construction. Pilot-scale sequencing showed that the library was enriched with plant-induced and pathogenicity-related fungal genes, including some encoding small, soluble secreted proteins that represent candidate fungal effectors. The high purity of the hyphae (94%) prevented contamination of the library by sequences derived from host cells or other fungal cell types. RT-PCR confirmed that genes identified in the FACS-purified hyphae were also expressed in planta. The method has wide applicability for isolating the infection structures of other plant pathogens, and will facilitate cell-specific transcriptome analysis via deep sequencing and microarray hybridization, as well as proteomic analyses.
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Affiliation(s)
- Hiroyuki Takahara
- Department of Plant-Microbe Interactions, Max-Planck-Institute for Plant Breeding Research, 50829 Köln, Germany
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Thakur S, Jha S, Roy-Barman S, Chattoo B. Genomic resources of Magnaporthe oryzae (GROMO): a comprehensive and integrated database on rice blast fungus. BMC Genomics 2009; 10:316. [PMID: 19604367 PMCID: PMC2721851 DOI: 10.1186/1471-2164-10-316] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Accepted: 07/15/2009] [Indexed: 11/27/2022] Open
Abstract
Background Magnaporthe oryzae, rice blast fungus, is the most devastating pathogen of rice. It has emerged as a model phytopathogen for the study of host-pathogen interactions. A large body of data has been generated on different aspects of biology of this fungus and on host-pathogen interactions. However, most of the data is scattered and is not available as a single resource for researchers in this field. Description Genomic Resources of Magnaporthe oyzae (GROMO), is a specialized, and comprehensive database for rice blast fungus, integrating information from several resources. GROMO contains information on genomic sequence, mutants available, gene expression, localization of proteins obtained from a variety of repositories, as primary data. In addition, prediction of domains, pathways, protein-protein interactions, sumolyation sites and biochemical properties that were obtained after computational analysis of protein sequences have also been included as derived data. This database has an intuitive user interface that shall prompt the user to explore various possible information resources available on a given gene or a protein, from a single source. Conclusion Currently, information on M. oryzae is available from different resources like BROAD MIT Magnaporthe database, Agrobacterium tumefaciens-mediated transformation (ATMT) M. oryzae database, Magnaporthe grisea – Oryza sativa (MGOS) and Massive Parallel Signature Sequencing (MPSS) databases. In the GROMO project, an effort has been made to integrate information from all these databases, derive some new data based on the available information analyzed by relevant programs and make more insightful predictions to better understand the biology of M. oryzae. The database is currently available at:
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Affiliation(s)
- Shalabh Thakur
- Centre for Genome Research, Department of Microbiology and Biotechnology Centre, Faculty of Science, The M, S, University of Baroda, Vadodara - 390002, India.
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Mosquera G, Giraldo MC, Khang CH, Coughlan S, Valent B. Interaction transcriptome analysis identifies Magnaporthe oryzae BAS1-4 as Biotrophy-associated secreted proteins in rice blast disease. THE PLANT CELL 2009; 21:1273-90. [PMID: 19357089 PMCID: PMC2685627 DOI: 10.1105/tpc.107.055228] [Citation(s) in RCA: 243] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2007] [Revised: 02/12/2009] [Accepted: 03/18/2009] [Indexed: 05/18/2023]
Abstract
Biotrophic invasive hyphae (IH) of the blast fungus Magnaporthe oryzae secrete effectors to alter host defenses and cellular processes as they successively invade living rice (Oryza sativa) cells. However, few blast effectors have been identified. Indeed, understanding fungal and rice genes contributing to biotrophic invasion has been difficult because so few plant cells have encountered IH at the earliest infection stages. We developed a robust procedure for isolating infected-rice sheath RNAs in which approximately 20% of the RNA originated from IH in first-invaded cells. We analyzed these IH RNAs relative to control mycelial RNAs using M. oryzae oligoarrays. With a 10-fold differential expression threshold, we identified known effector PWL2 and 58 candidate effectors. Four of these candidates were confirmed to be fungal biotrophy-associated secreted (BAS) proteins. Fluorescently labeled BAS proteins were secreted into rice cells in distinct patterns in compatible, but not in incompatible, interactions. BAS1 and BAS2 proteins preferentially accumulated in biotrophic interfacial complexes along with known avirulence effectors, BAS3 showed additional localization near cell wall crossing points, and BAS4 uniformly outlined growing IH. Analysis of the same infected-tissue RNAs with rice oligoarrays identified putative effector-induced rice susceptibility genes, which are highly enriched for sensor-transduction components rather than typically identified defense response genes.
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Affiliation(s)
- Gloria Mosquera
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66506, USA
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Meng S, Brown DE, Ebbole DJ, Torto-Alalibo T, Oh YY, Deng J, Mitchell TK, Dean RA. Gene Ontology annotation of the rice blast fungus, Magnaporthe oryzae. BMC Microbiol 2009; 9 Suppl 1:S8. [PMID: 19278556 PMCID: PMC2654668 DOI: 10.1186/1471-2180-9-s1-s8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Background Magnaporthe oryzae, the causal agent of blast disease of rice, is the most destructive disease of rice worldwide. The genome of this fungal pathogen has been sequenced and an automated annotation has recently been updated to Version 6 . However, a comprehensive manual curation remains to be performed. Gene Ontology (GO) annotation is a valuable means of assigning functional information using standardized vocabulary. We report an overview of the GO annotation for Version 5 of M. oryzae genome assembly. Methods A similarity-based (i.e., computational) GO annotation with manual review was conducted, which was then integrated with a literature-based GO annotation with computational assistance. For similarity-based GO annotation a stringent reciprocal best hits method was used to identify similarity between predicted proteins of M. oryzae and GO proteins from multiple organisms with published associations to GO terms. Significant alignment pairs were manually reviewed. Functional assignments were further cross-validated with manually reviewed data, conserved domains, or data determined by wet lab experiments. Additionally, biological appropriateness of the functional assignments was manually checked. Results In total, 6,286 proteins received GO term assignment via the homology-based annotation, including 2,870 hypothetical proteins. Literature-based experimental evidence, such as microarray, MPSS, T-DNA insertion mutation, or gene knockout mutation, resulted in 2,810 proteins being annotated with GO terms. Of these, 1,673 proteins were annotated with new terms developed for Plant-Associated Microbe Gene Ontology (PAMGO). In addition, 67 experiment-determined secreted proteins were annotated with PAMGO terms. Integration of the two data sets resulted in 7,412 proteins (57%) being annotated with 1,957 distinct and specific GO terms. Unannotated proteins were assigned to the 3 root terms. The Version 5 GO annotation is publically queryable via the GO site . Additionally, the genome of M. oryzae is constantly being refined and updated as new information is incorporated. For the latest GO annotation of Version 6 genome, please visit our website . The preliminary GO annotation of Version 6 genome is placed at a local MySql database that is publically queryable via a user-friendly interface Adhoc Query System. Conclusion Our analysis provides comprehensive and robust GO annotations of the M. oryzae genome assemblies that will be solid foundations for further functional interrogation of M. oryzae.
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Affiliation(s)
- Shaowu Meng
- Center for Integrated Fungal Research, North Carolina State University, Raleigh NC 27695, USA.
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Hornshøj H, Bendixen E, Conley LN, Andersen PK, Hedegaard J, Panitz F, Bendixen C. Transcriptomic and proteomic profiling of two porcine tissues using high-throughput technologies. BMC Genomics 2009; 10:30. [PMID: 19152685 PMCID: PMC2633351 DOI: 10.1186/1471-2164-10-30] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2008] [Accepted: 01/19/2009] [Indexed: 02/03/2023] Open
Abstract
Background The recent development within high-throughput technologies for expression profiling has allowed for parallel analysis of transcriptomes and proteomes in biological systems such as comparative analysis of transcript and protein levels of tissue regulated genes. Until now, such studies of have only included microarray or short length sequence tags for transcript profiling. Furthermore, most comparisons of transcript and protein levels have been based on absolute expression values from within the same tissue and not relative expression values based on tissue ratios. Results Presented here is a novel study of two porcine tissues based on integrative analysis of data from expression profiling of identical samples using cDNA microarray, 454-sequencing and iTRAQ-based proteomics. Sequence homology identified 2.541 unique transcripts that are detectable by both microarray hybridizations and 454-sequencing of 1.2 million cDNA tags. Both transcript-based technologies showed high reproducibility between sample replicates of the same tissue, but the correlation across these two technologies was modest. Thousands of genes being differentially expressed were identified with microarray. Out of the 306 differentially expressed genes, identified by 454-sequencing, 198 (65%) were also found by microarray. The relationship between the regulation of transcript and protein levels was analyzed by integrating iTRAQ-based proteomics data. Protein expression ratios were determined for 354 genes, of which 148 could be mapped to both microarray and 454-sequencing data. A comparison of the expression ratios from the three technologies revealed that differences in transcript and protein levels across heart and muscle tissues are positively correlated. Conclusion We show that the reproducibility within cDNA microarray and 454-sequencing is high, but that the agreement across these two technologies is modest. We demonstrate that the regulation of transcript and protein levels across identical tissue samples is positively correlated when the tissue expression ratios are used for comparison. The results presented are of interest in systems biology research in terms of integration and analysis of high-throughput expression data from mammalian tissues.
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Affiliation(s)
- Henrik Hornshøj
- Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, Aarhus University, Tjele, Denmark.
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Wang W, Meng B, Ge X, Song S, Yang Y, Yu X, Wang L, Hu S, Liu S, Yu J. Proteomic profiling of rice embryos from a hybrid rice cultivar and its parental lines. Proteomics 2008; 8:4808-21. [DOI: 10.1002/pmic.200701164] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Veerappan CS, Avramova Z, Moriyama EN. Evolution of SET-domain protein families in the unicellular and multicellular Ascomycota fungi. BMC Evol Biol 2008; 8:190. [PMID: 18593478 PMCID: PMC2474616 DOI: 10.1186/1471-2148-8-190] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2008] [Accepted: 07/01/2008] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The evolution of multicellularity is accompanied by the occurrence of differentiated tissues, of organismal developmental programs, and of mechanisms keeping the balance between proliferation and differentiation. Initially, the SET-domain proteins were associated exclusively with regulation of developmental genes in metazoa. However, finding of SET-domain genes in the unicellular yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe suggested that SET-domain proteins regulate a much broader variety of biological programs. Intuitively, it is expected that the numbers, types, and biochemical specificity of SET-domain proteins of multicellular versus unicellular forms would reflect the differences in their biology. However, comparisons across the unicellular and multicellular domains of life are complicated by the lack of knowledge of the ancestral SET-domain genes. Even within the crown group, different biological systems might use the epigenetic 'code' differently, adapting it to organism-specific needs. Simplifying the model, we undertook a systematic phylogenetic analysis of one monophyletic fungal group (Ascomycetes) containing unicellular yeasts, Saccharomycotina (hemiascomycetes), and a filamentous fungal group, Pezizomycotina (euascomycetes). RESULTS Systematic analysis of the SET-domain genes across an entire eukaryotic phylum has outlined clear distinctions in the SET-domain gene collections in the unicellular and in the multicellular (filamentous) relatives; diversification of SET-domain gene families has increased further with the expansion and elaboration of multicellularity in animal and plant systems. We found several ascomycota-specific SET-domain gene groups; each was unique to either Saccharomycotina or Pezizomycotina fungi. Our analysis revealed that the numbers and types of SET-domain genes in the Saccharomycotina did not reflect the habitats, pathogenicity, mechanisms of sexuality, or the ability to undergo morphogenic transformations. However, novel genes have appeared for functions associated with the transition to multicellularity. Descendents of most of the SET-domain gene families found in the filamentous fungi could be traced in the genomes of extant animals and plants, albeit as more complex structural forms. CONCLUSION SET-domain genes found in the filamentous species but absent from the unicellular sister group reflect two alternative evolutionary events: deletion from the yeast genomes or appearance of novel structures in filamentous fungal groups. There were no Ascomycota-specific SET-domain gene families (i.e., absent from animal and plant genomes); however, plants and animals share SET-domain gene subfamilies that do not exist in the fungi. Phylogenetic and gene-structure analyses defined several animal and plant SET-domain genes as sister groups while those of fungal origin were basal to them. Plants and animals also share SET-domain subfamilies that do not exist in fungi.
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Nygaard V, Liu F, Holden M, Kuo WP, Trimarchi J, Ohno-Machado L, Cepko CL, Frigessi A, Glad IK, Wiel MAVD, Hovig E, Lyng H. Validation of oligoarrays for quantitative exploration of the transcriptome. BMC Genomics 2008; 9:258. [PMID: 18513391 PMCID: PMC2430212 DOI: 10.1186/1471-2164-9-258] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2007] [Accepted: 05/30/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Oligoarrays have become an accessible technique for exploring the transcriptome, but it is presently unclear how absolute transcript data from this technique compare to the data achieved with tag-based quantitative techniques, such as massively parallel signature sequencing (MPSS) and serial analysis of gene expression (SAGE). By use of the TransCount method we calculated absolute transcript concentrations from spotted oligoarray intensities, enabling direct comparisons with tag counts obtained with MPSS and SAGE. The tag counts were converted to number of transcripts per cell by assuming that the sum of all transcripts in a single cell was 5.105. Our aim was to investigate whether the less resource demanding and more widespread oligoarray technique could provide data that were correlated to and had the same absolute scale as those obtained with MPSS and SAGE. RESULTS A number of 1,777 unique transcripts were detected in common for the three technologies and served as the basis for our analyses. The correlations involving the oligoarray data were not weaker than, but, similar to the correlation between the MPSS and SAGE data, both when the entire concentration range was considered and at high concentrations. The data sets were more strongly correlated at high transcript concentrations than at low concentrations. On an absolute scale, the number of transcripts per cell and gene was generally higher based on oligoarrays than on MPSS and SAGE, and ranged from 1.6 to 9,705 for the 1,777 overlapping genes. The MPSS data were on same scale as the SAGE data, ranging from 0.5 to 3,180 (MPSS) and 9 to1,268 (SAGE) transcripts per cell and gene. The sum of all transcripts per cell for these genes was 3.8.105 (oligoarrays), 1.1.105 (MPSS) and 7.6.104 (SAGE), whereas the corresponding sum for all detected transcripts was 1.1.106 (oligoarrays), 2.8.105 (MPSS) and 3.8.105 (SAGE). CONCLUSION The oligoarrays and TransCount provide quantitative transcript concentrations that are correlated to MPSS and SAGE data, but, the absolute scale of the measurements differs across the technologies. The discrepancy questions whether the sum of all transcripts within a single cell might be higher than the number of 5.105 suggested in the literature and used to convert tag counts to transcripts per cell. If so, this may explain the apparent higher transcript detection efficiency of the oligoarrays, and has to be clarified before absolute transcript concentrations can be interchanged across the technologies. The ability to obtain transcript concentrations from oligoarrays opens up the possibility of efficient generation of universal transcript databases with low resource demands.
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Affiliation(s)
- Vigdis Nygaard
- Department of Tumor Biology, Institute for Cancer Research, Norwegian Radium Hospital, Montebello, Oslo, Norway.
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Robust-LongSAGE (RL-SAGE): an improved LongSAGE method for high-throughput transcriptome analysis. Methods Mol Biol 2008; 387:25-38. [PMID: 18287620 DOI: 10.1007/978-1-59745-454-4_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Serial analysis of gene expression (SAGE) is a powerful technique for large-scale transcriptome analysis in eukaryotes. However, technical difficulties in the SAGE library construction, such as low concatemer cloning efficiency, small concatemer size, and a high level of empty clones, has prohibited its widespread use as a routine technique for expression profiling in many laboratories. We recently improved the LongSAGE library construction method considerably and developed a modified version called Robust-LongSAGE, or RL-SAGE. In RL-SAGE, concatemer cloning efficiency and clone insert size were increased significantly. About 20 PCR reactions are sufficient to make a library with more than 150,000 clones. Using RL-SAGE, we have made 10 libraries of rice, maize, and the rice blast fungus Magnaporthe grisea.
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Gainetdinov IV, Azhikina TL, Sverdlov ED. Use of short representative sequences for structural and functional genomic studies. BIOCHEMISTRY. BIOKHIMIIA 2007; 72:1179-1186. [PMID: 18205599 DOI: 10.1134/s0006297907110028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Existing approaches to direct genomic studies are costly and time-consuming. To overcome these problems, a series of tag-based methods utilizing short fragments uniquely representing full-length transcripts/genes from which they originate has been developed. This review summarizes basic principles underlying these methods and their numerous modifications designed for studying transcriptome profiles, searching for unidentified expressed loci, characterization of promoter regions, and high-throughput mapping of various genomic sites, such as hypo- and hypermethylated CpGs, and chromatin-binding and DNase I cleavage sites.
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Affiliation(s)
- I V Gainetdinov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
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Gowda M, Venu RC, Li H, Jantasuriyarat C, Chen S, Bellizzi M, Pampanwar V, Kim H, Dean RA, Stahlberg E, Wing R, Soderlund C, Wang GL. Magnaporthe grisea infection triggers RNA variation and antisense transcript expression in rice. PLANT PHYSIOLOGY 2007; 144:524-33. [PMID: 17351054 PMCID: PMC1913787 DOI: 10.1104/pp.107.095653] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2007] [Accepted: 02/15/2007] [Indexed: 05/14/2023]
Abstract
Rice blast disease, caused by the fungal pathogen Magnaporthe grisea, is an excellent model system to study plant-fungal interactions and host defense responses. In this study, comprehensive analysis of the rice (Oryza sativa) transcriptome after M. grisea infection was conducted using robust-long serial analysis of gene expression. A total of 83,382 distinct 21-bp robust-long serial analysis of gene expression tags were identified from 627,262 individual tags isolated from the resistant (R), susceptible (S), and control (C) libraries. Sequence analysis revealed that the tags in the R and S libraries had a significant reduced matching rate to the rice genomic and expressed sequences in comparison to the C library. The high level of one-nucleotide mismatches of the R and S library tags was due to nucleotide conversions. The A-to-G and U-to-C nucleotide conversions were the most predominant types, which were induced in the M. grisea-infected plants. Reverse transcription-polymerase chain reaction analysis showed that expression of the adenine deaminase and cytidine deaminase genes was highly induced after inoculation. In addition, many antisense transcripts were induced in infected plants and expression of four antisense transcripts was confirmed by strand-specific reverse transcription-polymerase chain reaction. These results demonstrate that there is a series of dynamic and complex transcript modifications and changes in the rice transcriptome at the M. grisea early infection stages.
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Affiliation(s)
- Malali Gowda
- Department of Plant Pathology, Ohio State University, Columbus, OH 43212, USA
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Ebbole DJ. Magnaporthe as a model for understanding host-pathogen interactions. ANNUAL REVIEW OF PHYTOPATHOLOGY 2007; 45:437-56. [PMID: 17489691 DOI: 10.1146/annurev.phyto.45.062806.094346] [Citation(s) in RCA: 270] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The rice blast pathosystem has been the subject of intense interest in part because of the importance of the disease to world agriculture, but also because both Magnaporthe oryzae and its host are amenable to advanced experimental approaches. The goal of this review is to provide an overview of the system and to point out recent significant studies that update our understanding of the biology of M. oryzae. The genome sequence of M. oryzae has provided insight into how genome structure and pathogen population genetic variability has been shaped by transposable elements. The sequence allows systematic approaches to long-standing areas of investigation, including pathogen development and the molecular basis of compatible and incompatible interactions with its host. Rice blast provides an integrated system to illustrate most of the important concepts governing fungal/plant interactions and serves as an excellent starting point for gaining a broad perspective of issues in plant pathology.
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Affiliation(s)
- Daniel J Ebbole
- Program for the Biology of Filamentous Fungi, Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843-2132, USA.
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Gowda M, Li H, Wang GL. Robust analysis of 5'-transcript ends: a high-throughput protocol for characterization of sequence diversity of transcription start sites. Nat Protoc 2007; 2:1622-32. [PMID: 17585303 DOI: 10.1038/nprot.2007.242] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The structure and diversity at the 3' ends of mRNA transcripts have been extensively characterized using several tag-based techniques in eukaryotes. However, the 5' ends of mRNA transcripts are not well understood, owing to a lack of efficient experimental approaches. We developed a new gene expression profiling method, called robust analysis of 5'-transcript ends (5' RATE), to rapidly isolate the 5' ends of mRNA transcripts. After ligating RNA oligo linkers to the 5' regions of decapped mRNA, cDNA is synthesized and digested with the restriction enzyme NlaIII. Ditags are formed by ligating two individual NlaIII tags, and are then PCR-amplified, purified and sequenced using a pyrosequencing approach. The 5'-RATE procedure is simple, fast and cost-effective because the complicated steps in comparative methods such as serial analysis of gene expression (including the formation of concatemers and their subsequent cloning and sequencing) have been eliminated. The longer 5'-RATE tags (>80 bp) provide more accurate matching to reference sequences for gene annotation and allow in-depth analysis of sequence diversity at the 5' regions of mRNA transcripts. Using our procedure, a 5'-RATE library with about 180,000 end sequences can be generated within a week. We have successfully applied the 5'-RATE method to characterize the transcriptome of various plant species including maize, rice and soybean. This method can be easily adapted to other eukaryotic organisms using the detailed procedures described in this protocol.
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Affiliation(s)
- Malali Gowda
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio 43210, USA.
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