Genome and secretome analysis of the hemibiotrophic fungal pathogen, Moniliophthora roreri, which causes frosty pod rot disease of cacao: mechanisms of the biotrophic and necrotrophic phases

[1]  F. Faoro,et al.  Differential timing of defense-related responses induced by cerato-platanin and cerato-populin, two non-catalytic fungal elicitors. , 2013, Physiologia plantarum.

[2]  R. Berger,et al.  PfaH2: A novel hydrophobin from the ascomycete Paecilomyces farinosus , 2013, Biotechnology and applied biochemistry.

[3]  Y. Narusaka,et al.  Comparative genomic and transcriptomic analyses reveal the hemibiotrophic stage shift of Colletotrichum fungi. , 2013, The New phytologist.

[4]  G. Friedbacher,et al.  Self-assembly at Air/Water Interfaces and Carbohydrate Binding Properties of the Small Secreted Protein EPL1 from the fungus Trichoderma atroviride* , 2012, The Journal of Biological Chemistry.

[5]  N. Callewaert,et al.  A bacterial glycosidase enables mannose-6-phosphate modification and improved cellular uptake of yeast-produced recombinant human lysosomal enzymes , 2012, Nature Biotechnology.

[6]  P. Mieczkowski,et al.  The Fungal Pathogen Moniliophthora perniciosa Has Genes Similar to Plant PR-1 That Are Highly Expressed during Its Interaction with Cacao , 2012, PloS one.

[7]  L. H. Gomes,et al.  Genetic diversity of polysporic isolates of Moniliophthora perniciosa (Tricholomataceae). , 2012, Genetics and molecular research : GMR.

[8]  G. Tuskan,et al.  Characterization of Transposable Elements in the Ectomycorrhizal Fungus Laccaria bicolor , 2012, PloS one.

[9]  G. Pereira,et al.  The hemibiotrophic cacao pathogen Moniliophthora perniciosa depends on a mitochondrial alternative oxidase for biotrophic development , 2012, The New phytologist.

[10]  R. Sicher,et al.  The interaction of Theobroma cacao and Moniliophthora perniciosa, the causal agent of witches’ broom disease, during parthenocarpy , 2012, Tree Genetics & Genomes.

[11]  J. Guarro,et al.  A PR-1-like Protein of Fusarium oxysporum Functions in Virulence on Mammalian Hosts* , 2012, The Journal of Biological Chemistry.

[12]  J. Latgé,et al.  Hydrophobins—Unique Fungal Proteins , 2012, PLoS pathogens.

[13]  K. Hammond-Kosack,et al.  The Predicted Secretome of the Plant Pathogenic Fungus Fusarium graminearum: A Refined Comparative Analysis , 2012, PloS one.

[14]  G. Van den Ackerveken,et al.  Nontoxic Nep1-like proteins of the downy mildew pathogen Hyaloperonospora arabidopsidis: repression of necrosis-inducing activity by a surface-exposed region. , 2012, Molecular plant-microbe interactions : MPMI.

[15]  M. Ruocco,et al.  The expression of the cerato-platanin gene is related to hyphal growth and chlamydospores formation in Ceratocystis platani. , 2012, FEMS microbiology letters.

[16]  L. Holm,et al.  The Pfam protein families database , 2011, Nucleic Acids Res..

[17]  G. Pereira,et al.  The crystal structure of necrosis- and ethylene-inducing protein 2 from the causal agent of cacao's Witches' Broom disease reveals key elements for its activity. , 2011, Biochemistry.

[18]  S. Brunak,et al.  SignalP 4.0: discriminating signal peptides from transmembrane regions , 2011, Nature Methods.

[19]  G. Selvaraj,et al.  EST mining identifies proteins putatively secreted by the anthracnose pathogen Colletotrichum truncatum , 2011, BMC Genomics.

[20]  A. Spisni,et al.  The Structure of the Elicitor Cerato-platanin (CP), the First Member of the CP Fungal Protein Family, Reveals a Double ψβ-Barrel Fold and Carbohydrate Binding* , 2011, The Journal of Biological Chemistry.

[21]  L. Segovia,et al.  Loosenin, a novel protein with cellulose-disrupting activity from Bjerkandera adusta , 2011, Microbial cell factories.

[22]  W. Huber,et al.  which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets , 2011 .

[23]  Wei Li,et al.  Ectopic expression of MgSM1, a Cerato-platanin family protein from Magnaporthe grisea, confers broad-spectrum disease resistance in Arabidopsis. , 2009, Plant biotechnology journal.

[24]  A. Hernández-Ortega,et al.  Aryl-alcohol Oxidase Involved in Lignin Degradation , 2009, The Journal of Biological Chemistry.

[25]  S. Coughlan,et al.  Interaction Transcriptome Analysis Identifies Magnaporthe oryzae BAS1-4 as Biotrophy-Associated Secreted Proteins in Rice Blast Disease[W][OA] , 2009, The Plant Cell Online.

[26]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[27]  G. Volckaert,et al.  Structural analysis of a glycoside hydrolase family 43 arabinoxylan arabinofuranohydrolase in complex with xylotetraose reveals a different binding mechanism compared with other members of the same family. , 2009, The Biochemical journal.

[28]  M. Borodovsky,et al.  Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. , 2008, Genome research.

[29]  Helaine Carrer,et al.  A genome survey of Moniliophthora perniciosa gives new insights into Witches' Broom Disease of cacao , 2008, BMC Genomics.

[30]  G. Griffith,et al.  Moniliophthora perniciosa, the causal agent of witches' broom disease of cacao: what's new from this old foe? , 2008, Molecular plant pathology.

[31]  M. Carazzolle,et al.  Differential gene expression between the biotrophic-like and saprotrophic mycelia of the witches' broom pathogen Moniliophthora perniciosa. , 2008, Molecular plant-microbe interactions : MPMI.

[32]  Thomas D. Schmittgen,et al.  Analyzing real-time PCR data by the comparative CT method , 2008, Nature Protocols.

[33]  E. Birney,et al.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

[34]  I. Chet,et al.  Role of Swollenin, an Expansin-Like Protein from Trichoderma, in Plant Root Colonization1[W] , 2008, Plant Physiology.

[35]  W. Willats,et al.  Silencing of acidic pathogenesis-related PR-1 genes increases extracellular beta-(1->3)-glucanase activity at the onset of tobacco defence reactions. , 2008, Journal of experimental botany.

[36]  Jonathan E. Allen,et al.  Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments , 2007, Genome Biology.

[37]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[38]  R. Voegele,et al.  Secreted proteins of Uromyces fabae: similarities and stage specificity. , 2007, Molecular plant pathology.

[39]  T. Kumasaka,et al.  The 1.3 Å crystal structure of a novel endo‐β‐1,3‐glucanase of glycoside hydrolase family 16 from alkaliphilic Nocardiopsis sp. strain F96 , 2007, Proteins.

[40]  W. Phillips-Mora,et al.  Frosty pod of cacao: a disease with a limited geographic range but unlimited potential for damage. , 2007, Phytopathology.

[41]  Xin Chen,et al.  FragAnchor: A Large-Scale Predictor of Glycosylphosphatidylinositol Anchors in Eukaryote Protein Sequences by Qualitative Scoring , 2007, Genom. Proteom. Bioinform..

[42]  B. Epel,et al.  beta-1,3-Glucanases: Plasmodesmal Gate Keepers for Intercellular Communication. , 2007, Plant signaling & behavior.

[43]  Christina A. Cuomo,et al.  Comparative proteomics of extracellular proteins in vitro and in planta from the pathogenic fungus Fusarium graminearum , 2007, Proteomics.

[44]  R. Dean,et al.  The Magnaporthe grisea snodprot1 homolog, MSP1, is required for virulence. , 2007, FEMS microbiology letters.

[45]  G. Pereira,et al.  Characterization of necrosis and ethylene-inducing proteins (NEP) in the basidiomycete Moniliophthora perniciosa, the causal agent of witches' broom in Theobroma cacao. , 2007, Mycological research.

[46]  Mihai Pop,et al.  Minimus: a fast, lightweight genome assembler , 2007, BMC Bioinformatics.

[47]  J. Vervoort,et al.  Cladosporium fulvum Avr4 protects fungal cell walls against hydrolysis by plant chitinases accumulating during infection. , 2006, Molecular plant-microbe interactions : MPMI.

[48]  B. Morgenstern,et al.  AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome , 2006, Genome Biology.

[49]  Burkhard Morgenstern,et al.  AUGUSTUS: ab initio prediction of alternative transcripts , 2006, Nucleic Acids Res..

[50]  P. Dodds,et al.  Haustorially Expressed Secreted Proteins from Flax Rust Are Highly Enriched for Avirulence Elicitors[W] , 2005, The Plant Cell Online.

[51]  M. C. Aime,et al.  The causal agents of witches' broom and frosty pod rot of cacao (chocolate, Theobroma cacao) form a new lineage of Marasmiaceae. , 2005, Mycologia.

[52]  J. Jurka,et al.  Repbase Update, a database of eukaryotic repetitive elements , 2005, Cytogenetic and Genome Research.

[53]  Gertraud Burger,et al.  AutoFACT: An Automatic Functional Annotation and Classification Tool , 2005, BMC Bioinformatics.

[54]  Cathryn J. Rehmeyer,et al.  The genome sequence of the rice blast fungus Magnaporthe grisea , 2005, Nature.

[55]  G. Pereira,et al.  Biochemical changes during the development of witches' broom: the most important disease of cocoa in Brazil caused by Crinipellis perniciosa. , 2005, Journal of experimental botany.

[56]  Ewan Birney,et al.  Automated generation of heuristics for biological sequence comparison , 2005, BMC Bioinformatics.

[57]  M. Frieman,et al.  Multiple sequence signals determine the distribution of glycosylphosphatidylinositol proteins between the plasma membrane and cell wall in Saccharomyces cerevisiae. , 2004, Microbiology.

[58]  G. Salmond,et al.  The Nep1-like proteins-a growing family of microbial elicitors of plant necrosis. , 2004, Molecular plant pathology.

[59]  L. Tailford,et al.  Insights into the Molecular Determinants of Substrate Specificity in Glycoside Hydrolase Family 5 Revealed by the Crystal Structure and Kinetics of Cellvibrio mixtus Mannosidase 5A* , 2004, Journal of Biological Chemistry.

[60]  J. Epstein,et al.  Comparative , 2004, Research Methods in International Law.

[61]  S. Salzberg,et al.  Versatile and open software for comparing large genomes , 2004, Genome Biology.

[62]  M. Frieman,et al.  The ω‐site sequence of glycosylphosphatidylinositol‐anchored proteins in Saccharomyces cerevisiae can determine distribution between the membrane and the cell wall , 2003, Molecular microbiology.

[63]  B. Thomma.  Alternaria spp.: from general saprophyte to specific parasite. , 2003, Molecular plant pathology.

[64]  M. Chalot,et al.  Analysis of expressed sequence tags from the ectomycorrhizal basidiomycetes Laccaria bicolor and Pisolithus microcarpus. , 2003, The New phytologist.

[65]  Mark Borodovsky,et al.  Eukaryotic Gene Prediction Using GeneMark.hmm , 2003, Current protocols in bioinformatics.

[66]  John F. McDonald,et al.  LTR_STRUC: a novel search and identification program for LTR retrotransposons , 2003, Bioinform..

[67]  A. Mayer,et al.  Laccase: new functions for an old enzyme. , 2002, Phytochemistry.

[68]  J. Wöstemeyer,et al.  Repetitive DNA elements in fungi (Mycota): impact on genomic architecture and evolution , 2002, Current Genetics.

[69]  S. Salzberg,et al.  Fast algorithms for large-scale genome alignment and comparison. , 2002, Nucleic acids research.

[70]  Thomas D. Schmittgen,et al.  Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. , 2001, Methods.

[71]  H. Wösten,et al.  Hydrophobins: multipurpose proteins. , 2001, Annual review of microbiology.

[72]  Š. Janeček,et al.  Pectin degrading glycoside hydrolases of family 28: sequence-structural features, specificities and evolution. , 2001, Protein engineering.

[73]  A. Latunde-Dada.  Colletotrichum: tales of forcible entry, stealth, transient confinement and breakout. , 2001, Molecular plant pathology.

[74]  M. Pfaffl,et al.  A new mathematical model for relative quantification in real-time RT-PCR. , 2001, Nucleic acids research.

[75]  S. Perfect,et al.  Infection structures of biotrophic and hemibiotrophic fungal plant pathogens. , 2001, Molecular plant pathology.

[76]  A. Krogh,et al.  Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. , 2001, Journal of molecular biology.

[77]  Daniel J. Cosgrove,et al.  Loosening of plant cell walls by expansins , 2000, Nature.

[78]  Erik L. L. Sonnhammer,et al.  A Hidden Markov Model for Predicting Transmembrane Helices in Protein Sequences , 1998, ISMB.

[79]  N J Talbot,et al.  Hydrophobins and repellents: proteins with fundamental roles in fungal morphogenesis. , 1998, Fungal genetics and biology : FG & B.

[80]  B. Barrell,et al.  Life with 6000 Genes , 1996, Science.

[81]  B. Henrissat,et al.  Conserved catalytic machinery and the prediction of a common fold for several families of glycosyl hydrolases. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[82]  H. Deising,et al.  Chitin deacetylase activity of the rust Uromyces viciae-fabae is controlled by fungal morphogenesis , 1995 .

[83]  B Henrissat,et al.  A classification of glycosyl hydrolases based on amino acid sequence similarities. , 1991, The Biochemical journal.

[84]  P. Kersten.  Glyoxal oxidase of Phanerochaete chrysosporium: its characterization and activation by lignin peroxidase. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[85]  D. Roby,et al.  Chitin oligosaccharides as elicitors of chitinase activity in melon plants. , 1987, Biochemical and biophysical research communications.

[86]  J. Stalpers,et al.  On the taxonomy of Monilia roreri, an important pathogen of Theobroma cacao in South America , 1978 .

[87]  D. Adomako.  Cocoa pod husk pectin , 1972 .

[88]  A. Engel,et al.  PloS One 2012 , 2015 .

[89]  R. Sicher,et al.  Dynamic changes in pod and fungal physiology associated with the shift from biotrophy to necrotrophy during the infection of Theobroma cacao by Moniliophthora roreri. , 2013 .

[90]  G. Pereira,et al.  Identification of a second family of genes in Moniliophthora perniciosa, the causal agent of witches' broom disease in cacao, encoding necrosis-inducing proteins similar to cerato-platanins. , 2009, Mycological research.

[91]  M. Okazaki,et al.  Isolation and analysis of genes specifically expressed during fruiting body development in the basidiomycete Flammulina velutipes by fluorescence differential display. , 2006, FEMS microbiology letters.

[92]  Gang Wang,et al.  ConiferEST: an integrated bioinformatics system for data reprocessing and mining of conifer expressed sequence tags (ESTs) , 2007, BMC Genomics.

[93]  BIOINFORMATICS APPLICATIONS NOTE , 2005 .

[94]  R. I. P. O. Iver,et al.  Arabidopsis pathology breathes new life into the necrotrophs-vs .-biotrophs classification of fungal pathogens , 2004 .

[95]  P. De Wit,et al.  THE TOMATO-CLADOSPORIUM FULVUM INTERACTION: A Versatile Experimental System to Study Plant-Pathogen Interactions. , 1999, Annual review of phytopathology.

[96]  Hiroyuki Ogata,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..

[97]  H. Evans.  Pod rot of cacao caused by Moniliophthora (Monilia) roreri. , 1981 .

[98]  BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btm098 Databases and ontologies UniRef: comprehensive and non-redundant UniProt reference , 2022 .