Genome assembly of the fungus Cochliobolus miyabeanus, and transcriptome analysis during early stages of infection on American wildrice (Zizania palustris L.)
Abstract
Here, the fungus Cochliobolus miyabeanus causes severe leaf spot disease on rice (Oryza sativa) and two North American specialty crops, American wildrice (Zizania palustris) and switchgrass (Panicum virgatu). Despite the importance of C. miyabeanus as a disease-causing agent in wildrice, little is known about either the mechanisms of pathogenicity or host defense responses. To start bridging these gaps, the genome of C. miyabeanus strain TG12bL2 was shotgun sequenced using Illumina technology. The genome assembly consists of 31.79 Mbp in 2,378 scaffolds with an N50 = 74,921. It contains 11,000 predicted genes of which 94.5% were annotated. Approximately 10% of total gene number is expected to be secreted. The C. miyabeanus genome is rich in carbohydrate active enzymes, and harbors 187 small secreted peptides (SSPs) and some fungal effector homologs. Detoxification systems were represented by a variety of enzymes that could offer protection against plant defense compounds. The non-ribosomal peptide synthetases and polyketide synthases (PKS) present were common to other Cochliobolus species. Additionally, the fungal transcriptome was analyzed at 48 hours after inoculation in planta. A total of 10,674 genes were found to be expressed, some of which are known to be involved in pathogenicity or response to host defenses includingmore »
- Authors:
-
- Univ. of Minnesota, St. Paul, MN (United States). Dept. of Plant Pathology
- Univ. of Minnesota, St. Paul, MN (United States). Dept. of Agronomy and Plant Genetics; USDA-ARS-Plant Science Research Unit, St. Paul, MN (United States)
- Mayo Clinic, Div. of Biomedical Statistics and Informatics, Rochester, MN (United States)
- Univ. of Minnesota, St. Paul, MN (United States). Dept. of Plant Biology
- Aix-Marseille Univ., Marseille (France). CNRS UMR 7257
- Aix-Marseille Univ., Marseille (France). CNRS UMR 7257; King Abdulaziz Univ., Jeddah (Saudi Arabia). Dept. of Biological Sciences
- Univ. of Minnesota, St. Paul, MN (United States). Dept. of Plant Pathology; USDA-ARS-Plant Science Research Unit, St. Paul, MN (United States)
- Publication Date:
- Research Org.:
- Univ. of Minnesota, St. Paul, MN (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1287181
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- PLoS ONE
- Additional Journal Information:
- Journal Volume: 11; Journal Issue: 6; Journal ID: ISSN 1932-6203
- Publisher:
- Public Library of Science
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; plant-pathogenic fungus; cyclic peptide biosynthesis; polyketide virulence factor; f-sp platani; functional-analysis; brown spot; t-toxin; hc-toxin; rna-seq; cytochrome-p450 monooxygenase; fungal genomics; protein domains; fungal genetics; transcriptome analysis; pathogenesis; genomic databases; plant genomics; fungi
Citation Formats
Castell-Miller, Claudia V., Gutierrez-Gonzalez, Juan J., Tu, Zheng Jin, Bushley, Kathryn E., Hainaut, Matthieu, Henrissat, Bernard, and Samac, Deborah A. Genome assembly of the fungus Cochliobolus miyabeanus, and transcriptome analysis during early stages of infection on American wildrice (Zizania palustris L.). United States: N. p., 2016.
Web. doi:10.1371/journal.pone.0154122.
Castell-Miller, Claudia V., Gutierrez-Gonzalez, Juan J., Tu, Zheng Jin, Bushley, Kathryn E., Hainaut, Matthieu, Henrissat, Bernard, & Samac, Deborah A. Genome assembly of the fungus Cochliobolus miyabeanus, and transcriptome analysis during early stages of infection on American wildrice (Zizania palustris L.). United States. https://doi.org/10.1371/journal.pone.0154122
Castell-Miller, Claudia V., Gutierrez-Gonzalez, Juan J., Tu, Zheng Jin, Bushley, Kathryn E., Hainaut, Matthieu, Henrissat, Bernard, and Samac, Deborah A. Thu .
"Genome assembly of the fungus Cochliobolus miyabeanus, and transcriptome analysis during early stages of infection on American wildrice (Zizania palustris L.)". United States. https://doi.org/10.1371/journal.pone.0154122. https://www.osti.gov/servlets/purl/1287181.
@article{osti_1287181,
title = {Genome assembly of the fungus Cochliobolus miyabeanus, and transcriptome analysis during early stages of infection on American wildrice (Zizania palustris L.)},
author = {Castell-Miller, Claudia V. and Gutierrez-Gonzalez, Juan J. and Tu, Zheng Jin and Bushley, Kathryn E. and Hainaut, Matthieu and Henrissat, Bernard and Samac, Deborah A.},
abstractNote = {Here, the fungus Cochliobolus miyabeanus causes severe leaf spot disease on rice (Oryza sativa) and two North American specialty crops, American wildrice (Zizania palustris) and switchgrass (Panicum virgatu). Despite the importance of C. miyabeanus as a disease-causing agent in wildrice, little is known about either the mechanisms of pathogenicity or host defense responses. To start bridging these gaps, the genome of C. miyabeanus strain TG12bL2 was shotgun sequenced using Illumina technology. The genome assembly consists of 31.79 Mbp in 2,378 scaffolds with an N50 = 74,921. It contains 11,000 predicted genes of which 94.5% were annotated. Approximately 10% of total gene number is expected to be secreted. The C. miyabeanus genome is rich in carbohydrate active enzymes, and harbors 187 small secreted peptides (SSPs) and some fungal effector homologs. Detoxification systems were represented by a variety of enzymes that could offer protection against plant defense compounds. The non-ribosomal peptide synthetases and polyketide synthases (PKS) present were common to other Cochliobolus species. Additionally, the fungal transcriptome was analyzed at 48 hours after inoculation in planta. A total of 10,674 genes were found to be expressed, some of which are known to be involved in pathogenicity or response to host defenses including hydrophobins, cutinase, cell wall degrading enzymes, enzymes related to reactive oxygen species scavenging, PKS, detoxification systems, SSPs, and a known fungal effector. This work will facilitate future research on C. miyabeanus pathogen-associated molecular patterns and effectors, and in the identification of their corresponding wildrice defense mechanisms.},
doi = {10.1371/journal.pone.0154122},
journal = {PLoS ONE},
number = 6,
volume = 11,
place = {United States},
year = {Thu Jun 02 00:00:00 EDT 2016},
month = {Thu Jun 02 00:00:00 EDT 2016}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 9 works
Citation information provided by
Web of Science
Web of Science
Figures / Tables:
Table 1: Summary features of the Cochliobolus miyabeanus CmTG12bL2 isolate genome assembly and annotation.
All figures and tables
(8 total)
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Improved Prediction of Signal Peptides: SignalP 3.0
journal, July 2004
- Dyrløv Bendtsen, Jannick; Nielsen, Henrik; von Heijne, Gunnar
- Journal of Molecular Biology, Vol. 340, Issue 4, p. 783-795
Purification, Characterization, and Amino Acid Sequence of Cerato-platanin, a New Phytotoxic Protein from Ceratocystis fimbriata f. sp. platani
journal, August 1999
- Pazzagli, Luigia; Cappugi, Gianni; Manao, Giampaolo
- Journal of Biological Chemistry, Vol. 274, Issue 35
Conserved Fungal LysM Effector Ecp6 Prevents Chitin-Triggered Immunity in Plants
journal, August 2010
- de Jonge, R.; Peter van Esse, H.; Kombrink, A.
- Science, Vol. 329, Issue 5994
TopHat: discovering splice junctions with RNA-Seq
journal, March 2009
- Trapnell, Cole; Pachter, Lior; Salzberg, Steven L.
- Bioinformatics, Vol. 25, Issue 9
Activation of an AP1-Like Transcription Factor of the Maize Pathogen Cochliobolus heterostrophus in Response to Oxidative Stress and Plant Signals
journal, February 2005
- Lev, Sophie; Hadar, Ruthi; Amedeo, Paolo
- Eukaryotic Cell, Vol. 4, Issue 2
Isolation of the Carbon Catabolite Repressor ( CREA ) Gene from the Plant-pathogenic Fungus Cochliobolus carbonum
journal, January 2003
- Tonukari, Nyerhovwo J.; Scott-Craig, John S.; Walton, Jonathan D.
- DNA Sequence, Vol. 14, Issue 2
A polyketide synthase is required for fungal virulence and production of the polyketide T-toxin.
journal, November 1996
- Yang, G.; Rose, M. S.; Turgeon, B. G.
- The Plant Cell, Vol. 8, Issue 11
Cytochrome P450 enzymes in the fungal kingdom
journal, January 2011
- Črešnar, B.; Petrič, Š.
- Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1814, Issue 1
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
journal, May 2010
- Trapnell, Cole; Williams, Brian A.; Pertea, Geo
- Nature Biotechnology, Vol. 28, Issue 5
Three Extracellular Proteases from Cochliobolus carbonum: Cloning and Targeted Disruption of ALP1
journal, January 1996
- Murphy, Jenifer M.
- Molecular Plant-Microbe Interactions, Vol. 9, Issue 4
Symbol Nomenclature for Graphical Representations of Glycans
journal, November 2015
- Varki, Ajit; Cummings, Richard D.; Aebi, Markus
- Glycobiology, Vol. 25, Issue 12
Fungal enzyme sets for plant polysaccharide degradation
journal, July 2011
- van den Brink, Joost; de Vries, Ronald P.
- Applied Microbiology and Biotechnology, Vol. 91, Issue 6, p. 1477-1492
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
journal, February 2008
- Zerbino, D. R.; Birney, E.
- Genome Research, Vol. 18, Issue 5
Leaf spot on switch grass ( Panicum virgatum ), symptoms of a new disease caused by Bipolaris oryzae
journal, September 2004
- Krupinsky, J. M.; Berdahl, J. D.; Schoch, C. L.
- Canadian Journal of Plant Pathology, Vol. 26, Issue 3
Tricking the Guard: Exploiting Plant Defense for Disease Susceptibility
journal, October 2012
- Lorang, J.; Kidarsa, T.; Bradford, C. S.
- Science, Vol. 338, Issue 6107
Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi
journal, December 2012
- Ohm, Robin A.; Feau, Nicolas; Henrissat, Bernard
- PLoS Pathogens, Vol. 8, Issue 12
CYP53A15 of Cochliobolus lunatus, a Target for Natural Antifungal Compounds †
journal, June 2008
- Podobnik, Barbara; Stojan, Jure; Lah, Ljerka
- Journal of Medicinal Chemistry, Vol. 51, Issue 12
Two glucose/xylose transporter genes from the yeast Candida intermedia: first molecular characterization of a yeast xylose–H+ symporter
journal, May 2006
- Leandro, Maria José; Gonçalves, Paula; Spencer-Martins, Isabel
- Biochemical Journal, Vol. 395, Issue 3, p. 543-549
Cloning, purification and characterisation of brassinin glucosyltransferase, a phytoalexin-detoxifying enzyme from the plant pathogen Sclerotinia sclerotiorum
journal, February 2009
- Sexton, Adrienne C.; Minic, Zoran; Cozijnsen, Anton J.
- Fungal Genetics and Biology, Vol. 46, Issue 2
The novel Cladosporium fulvum lysin motif effector Ecp6 is a virulence factor with orthologues in other fungal species
journal, July 2008
- Bolton, Melvin D.; van Esse, H. Peter; Vossen, Jack H.
- Molecular Microbiology, Vol. 69, Issue 1
Phylogenomic analysis of type I polyketide synthase genes in pathogenic and saprobic ascomycetes
journal, December 2003
- Kroken, S.; Glass, N. L.; Taylor, J. W.
- Proceedings of the National Academy of Sciences, Vol. 100, Issue 26
Functional analysis and mode of action of phytotoxic Nep1-like proteins of Botrytis cinerea
journal, September 2010
- Cuesta Arenas, Yaite; Kalkman, Eric R. I. C.; Schouten, Alexander
- Physiological and Molecular Plant Pathology, Vol. 74, Issue 5-6
Simultaneous Transcriptome Analysis of Sorghum and Bipolaris sorghicola by Using RNA-seq in Combination with De Novo Transcriptome Assembly
journal, April 2013
- Yazawa, Takayuki; Kawahigashi, Hiroyuki; Matsumoto, Takashi
- PLoS ONE, Vol. 8, Issue 4
Fungal Transporters Involved in Efflux of Natural Toxic Compounds and Fungicides
journal, June 2000
- Del Sorbo, Giovanni; Schoonbeek, Henk-jan; De Waard, Maarten A.
- Fungal Genetics and Biology, Vol. 30, Issue 1
Impact of fungal drug transporters on fungicide sensitivity, multidrug resistance and virulence
journal, January 2006
- de Waard, Maarten A.; Andrade, Alan C.; Hayashi, Keisuke
- Pest Management Science, Vol. 62, Issue 3
NPS6 , Encoding a Nonribosomal Peptide Synthetase Involved in Siderophore-Mediated Iron Metabolism, Is a Conserved Virulence Determinant of Plant Pathogenic Ascomycetes
journal, October 2006
- Oide, Shinichi; Moeder, Wolfgang; Krasnoff, Stuart
- The Plant Cell, Vol. 18, Issue 10
The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics
journal, January 2009
- Cantarel, B. L.; Coutinho, P. M.; Rancurel, C.
- Nucleic Acids Research, Vol. 37, Issue Database
Histone deacetylases in fungi: novel members, new facts
journal, July 2003
- Trojer, P.
- Nucleic Acids Research, Vol. 31, Issue 14
Molecular Cloning and Characterization of cel2 from the Fungus Cochlibolus carbonum
journal, January 2001
- Ahn, Joong-Hoon; Sposato, Paola; Kim, Su-Il
- Bioscience, Biotechnology, and Biochemistry, Vol. 65, Issue 6, p. 1406-1411
Genetic and Genomic Dissection of the Cochliobolus heterostrophus Tox1 Locus Controlling Biosynthesis of the Polyketide Virulence Factor T‐toxin
book, January 2007
- Turgeon, B. Gillian; Baker, Scott E.
- Advances in Genetics, Vol. 57
β-Glucan biosynthesis inhibitors isolated from fungi as hyphal malformation inducer
journal, June 1993
- Fukushima, Yoshito; Sakagami, Youji; Marumo, Shingo
- Bioorganic & Medicinal Chemistry Letters, Vol. 3, Issue 6
Gene Expression Modulation of Two Biosynthesis Pathways via Signal Transduction in Cochliobolus heterostrophus
journal, January 2014
- Degani, Ofir
- Advances in Bioscience and Biotechnology, Vol. 05, Issue 04
Molecular Characterization and Functional Analysis of MgNLP , the Sole NPP1 Domain–Containing Protein, from the Fungal Wheat Leaf Pathogen Mycosphaerella graminicola
journal, July 2009
- Motteram, Juliet; Küfner, Isabell; Deller, Siân
- Molecular Plant-Microbe Interactions®, Vol. 22, Issue 7
Disruption of phacA , an Aspergillus nidulans Gene Encoding a Novel Cytochrome P450 Monooxygenase Catalyzing Phenylacetate 2-Hydroxylation, Results in Penicillin Overproduction
journal, May 1999
- Mingot, José Manuel; Peñalva, Miguel Angel; Fernández-Cañón, José Manuel
- Journal of Biological Chemistry, Vol. 274, Issue 21
Creating and screening Cochliobolus heterostrophus non-ribosomal peptide synthetase mutants
journal, February 2008
- Gillian Turgeon, B.; Oide, Shinichi; Bushley, Kathryn
- Mycological Research, Vol. 112, Issue 2
Wild Rice Domestication, Fungal Brown Spot Disease, and the Future of Commercial Production in Minnesota
journal, January 1992
- Johnson, David R.
- Plant Disease, Vol. 76, Issue 12
Transcription of the yeast TNA1
gene is not only regulated by nicotinate but also by p
-aminobenzoate
journal, September 2000
- Klebl, F.; Zillig, M.; Sauer, N.
- FEBS Letters, Vol. 481, Issue 1
Two Polyketide Synthase-Encoding Genes Are Required for Biosynthesis of the Polyketide Virulence Factor, T-toxin, by Cochliobolus heterostrophus
journal, February 2006
- Baker, Scott E.; Kroken, Scott; Inderbitzin, Patrik
- Molecular Plant-Microbe Interactions, Vol. 19, Issue 2
Cochliobolus Heterostrophus. Cause of Southern Corn Leaf Blight
book, January 1988
- Yoder, O. C.
- Genetics of Plant Pathogenic Fungi
(1,3;1,4)-β-D-Glucans in Cell Walls of the Poaceae, Lower Plants, and Fungi: A Tale of Two Linkages
journal, September 2009
- Burton, Rachel A.; Fincher, Geoffrey B.
- Molecular Plant, Vol. 2, Issue 5
Phylogeny and biogeography of the eastern Asian–North American disjunct wild-rice genus (Zizania L., Poaceae)
journal, June 2010
- Xu, Xinwei; Walters, Christina; Antolin, Michael F.
- Molecular Phylogenetics and Evolution, Vol. 55, Issue 3
(1,3;1,4)-β-D-Glucans in Cell Walls of the Poaceae, Lower Plants, and Fungi: A Tale of Two Linkages
journal, September 2009
- Burton, Rachel A.; Fincher, Geoffrey B.
- Molecular Plant, Vol. 2, Issue 5
Development of Fungal Brown Spot and Spot Blotch on Cultivated Wild Rice in Minnesota
journal, October 1999
- Nyvall, R. F.; Percich, J. A.
- Plant Disease, Vol. 83, Issue 10
Fungal LysM effectors: extinguishers of host immunity?
journal, April 2009
- de Jonge, Ronnie; Thomma, Bart P. H. J.
- Trends in Microbiology, Vol. 17, Issue 4
Chitinases of filamentous fungi: a large group of diverse proteins with multiple physiological functions
journal, February 2008
- Seidl, Verena
- Fungal Biology Reviews, Vol. 22, Issue 1
CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes
journal, March 2007
- Parra, G.; Bradnam, K.; Korf, I.
- Bioinformatics, Vol. 23, Issue 9
A Gene Related to Yeast HOS2 Histone Deacetylase Affects Extracellular Depolymerase Expression and Virulence in a Plant Pathogenic Fungus
journal, July 2001
- Baidyaroy, Dipnath; Brosch, Gerald; Ahn, Joong-hoon
- The Plant Cell, Vol. 13, Issue 7
Phytotoxins Produced by Germinating Spores of Bipolaris oryzae
journal, January 1991
- Xiao, J. Z.
- Phytopathology, Vol. 81, Issue 1
The Cochliobolus carbonum SNF1 Gene Is Required for Cell Wall–Degrading Enzyme Expression and Virulence on Maize
journal, February 2000
- Tonukari, Nyerhovwo J.; Scott-Craig, John S.; Waltonb, Jonathan D.
- The Plant Cell, Vol. 12, Issue 2
The carbohydrate-active enzymes database (CAZy) in 2013
journal, November 2013
- Lombard, Vincent; Golaconda Ramulu, Hemalatha; Drula, Elodie
- Nucleic Acids Research, Vol. 42, Issue D1
Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training
journal, October 2008
- Ter-Hovhannisyan, V.; Lomsadze, A.; Chernoff, Y. O.
- Genome Research, Vol. 18, Issue 12
Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes
journal, January 2013
- Levasseur, Anthony; Drula, Elodie; Lombard, Vincent
- Biotechnology for Biofuels, Vol. 6, Issue 1, Article No. 41
A Eukaryotic Alanine Racemase Gene Involved in Cyclic Peptide Biosynthesis
journal, February 2000
- Cheng, Yi-Qiang; Walton, Jonathan D.
- Journal of Biological Chemistry, Vol. 275, Issue 7
A MAP kinase gene, BMK1, is required for conidiation and pathogenicity in the rice leaf spot pathogen Bipolaris oryzae
journal, April 2007
- Moriwaki, Akihiro; Kihara, Junichi; Mori, Chie
- Microbiological Research, Vol. 162, Issue 2
An eight-cysteine-containing CFEM domain unique to a group of fungal membrane proteins
journal, March 2003
- Kulkarni, Resham D.; Kelkar, Hemant S.; Dean, Ralph A.
- Trends in Biochemical Sciences, Vol. 28, Issue 3
Glucose uptake and growth of glucose-limited chemostat cultures of Aspergillus niger and a disruptant lacking MstA, a high-affinity glucose transporter
journal, June 2007
- Jorgensen, T. R.; vanKuyk, P. A.; Poulsen, B. R.
- Microbiology, Vol. 153, Issue 6
Structure of victorin C, the major host-selective toxin fromCochliobolus victoriae
journal, December 1985
- Wolpert, T. J.; Macko, V.; Acklin, W.
- Experientia, Vol. 41, Issue 12
Endopolygalacturonase is not required for pathogenicity of Cochliobolus carbonum on maize.
journal, December 1990
- Scott-Craig, J. S.; Panaccione, D. G.; Cervone, F.
- The Plant Cell, Vol. 2, Issue 12
A putative cyclic peptide efflux pump encoded by the TOXA gene of the plant-pathogenic fungus Cochliobolus carbonum
journal, June 1996
- Pitkin, J. W.; Panaccione, D. G.; Walton, J. D.
- Microbiology, Vol. 142, Issue 6
Cloning, purification and characterisation of brassinin glucosyltransferase, a phytoalexin-detoxifying enzyme from the plant pathogen Sclerotinia sclerotiorum
journal, February 2009
- Sexton, Adrienne C.; Minic, Zoran; Cozijnsen, Anton J.
- Fungal Genetics and Biology, Vol. 46, Issue 2
Cloning, disruption, and expression of two endo-beta 1, 4-xylanase genes, XYL2 and XYL3, from Cochliobolus carbonum
journal, November 1996
- Apel-Birkhold, P. C.; Walton, J. D.
- Applied and Environmental Microbiology, Vol. 62, Issue 11
Analysis and annotation of the hexaploid oat seed transcriptome
journal, January 2013
- Gutierrez-Gonzalez, Juan J.; Tu, Zheng; Garvin, David F.
- BMC Genomics, Vol. 14, Issue 1
Hydrophobins—Unique Fungal Proteins
journal, May 2012
- Bayry, Jagadeesh; Aimanianda, Vishukumar; Guijarro, J. Iñaki
- PLoS Pathogens, Vol. 8, Issue 5
NPS6 , Encoding a Nonribosomal Peptide Synthetase Involved in Siderophore-Mediated Iron Metabolism, Is a Conserved Virulence Determinant of Plant Pathogenic Ascomycetes
journal, October 2006
- Oide, Shinichi; Moeder, Wolfgang; Krasnoff, Stuart
- The Plant Cell, Vol. 18, Issue 10
Creating and screening Cochliobolus heterostrophus non-ribosomal peptide synthetase mutants
journal, February 2008
- Gillian Turgeon, B.; Oide, Shinichi; Bushley, Kathryn
- Mycological Research, Vol. 112, Issue 2
Endopolygalacturonase Is Not Required for Pathogenicity of Cochliobolus carbonum on Maize
journal, December 1990
- Scott-Craig, John S.; Panaccione, Daniel G.; Cervone, Felice
- The Plant Cell, Vol. 2, Issue 12
Systematic and searchable classification of cytochrome P450 proteins encoded by fungal and oomycete genomes
journal, January 2012
- Moktali, Venkatesh; Park, Jongsun; Fedorova-Abrams, Natalie D.
- BMC Genomics, Vol. 13, Issue 1
Intracellular Siderophores Are Essential for Ascomycete Sexual Development in Heterothallic Cochliobolus heterostrophus and Homothallic Gibberella zeae
journal, June 2007
- Oide, Shinichi; Krasnoff, Stuart B.; Gibson, Donna M.
- Eukaryotic Cell, Vol. 6, Issue 8
AP1-mediated Multidrug Resistance in Saccharomyces cerevisiae Requires FLR1 Encoding a Transporter of the Major Facilitator Superfamily
journal, August 1997
- Alarco, Anne-Marie; Balan, Inga; Talibi, Driss
- Journal of Biological Chemistry, Vol. 272, Issue 31
Efflux in Fungi: La Pièce de Résistance
journal, June 2009
- Coleman, Jeffrey J.; Mylonakis, Eleftherios
- PLoS Pathogens, Vol. 5, Issue 6
FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes
journal, January 2004
- Al-Shahrour, F.; Diaz-Uriarte, R.; Dopazo, J.
- Bioinformatics, Vol. 20, Issue 4
Nonribosomal peptides: from genes to products
journal, January 2003
- Schwarzer, Dirk; Finking, Robert; Marahiel, Mohamed A.
- Natural Product Reports, Vol. 20, Issue 3
Gepard: a rapid and sensitive tool for creating dotplots on genome scale
journal, February 2007
- Krumsiek, J.; Arnold, R.; Rattei, T.
- Bioinformatics, Vol. 23, Issue 8
Cloning and characterization of the PDA6-1 gene encoding a fungal cytochrome P-450 which detoxifies the phytoalexin pisatin from garden pea
journal, September 1994
- Reimmann, Cornelia; VanEtten, Hans D.
- Gene, Vol. 146, Issue 2
Helminthosporium oryzae toxin suppresses phenol metabolism in rice plants and aids pathogen colonization
journal, November 1992
- Vidhyasekaran, P.; Borromeo, E. S.; Mew, T. W.
- Physiological and Molecular Plant Pathology, Vol. 41, Issue 5
Functional analysis of the Alternaria brassicicola non-ribosomal peptide synthetase gene AbNPS2 reveals a role in conidial cell wall construction
journal, January 2007
- Kim, Kwang-Hyung; Cho, Yangrae; La Rota, Mauricio
- Molecular Plant Pathology, Vol. 8, Issue 1
Correction: Sequential Delivery of Host-Induced Virulence Effectors by Appressoria and Intracellular Hyphae of the Phytopathogen Colletotrichum higginsianum
journal, August 2012
- Kleemann, Jochen; Rincon-Rivera, Linda J.; Takahara, Hiroyuki
- PLoS Pathogens, Vol. 8, Issue 8
Transcriptional regulation of the Saccharomyces cerevisiae DAL5 gene family and identification of the high affinity nicotinic acid permease TNA1 ( YGR260w )
journal, June 2000
- Llorente, Bertrand; Dujon, Bernard
- FEBS Letters, Vol. 475, Issue 3
Glycosyltransferases and their products: cryptococcal variations on fungal themes
journal, June 2006
- Klutts, James Stacey; Yoneda, Aki; Reilly, Morgann C.
- FEMS Yeast Research, Vol. 6, Issue 4
Phylogenomics reveals subfamilies of fungal nonribosomal peptide synthetases and their evolutionary relationships
journal, January 2010
- Bushley, Kathryn E.; Turgeon, B. Gillian
- BMC Evolutionary Biology, Vol. 10, Issue 1
Improved Prediction of Signal Peptides: SignalP 3.0
journal, July 2004
- Dyrløv Bendtsen, Jannick; Nielsen, Henrik; von Heijne, Gunnar
- Journal of Molecular Biology, Vol. 340, Issue 4, p. 783-795
Purification, Characterization, and Amino Acid Sequence of Cerato-platanin, a New Phytotoxic Protein from Ceratocystis fimbriata f. sp. platani
journal, August 1999
- Pazzagli, Luigia; Cappugi, Gianni; Manao, Giampaolo
- Journal of Biological Chemistry, Vol. 274, Issue 35
Conserved Fungal LysM Effector Ecp6 Prevents Chitin-Triggered Immunity in Plants
journal, August 2010
- de Jonge, R.; Peter van Esse, H.; Kombrink, A.
- Science, Vol. 329, Issue 5994
Disruption of phacA , an Aspergillus nidulans Gene Encoding a Novel Cytochrome P450 Monooxygenase Catalyzing Phenylacetate 2-Hydroxylation, Results in Penicillin Overproduction
journal, May 1999
- Mingot, José Manuel; Peñalva, Miguel Angel; Fernández-Cañón, José Manuel
- Journal of Biological Chemistry, Vol. 274, Issue 21
Isolation of the Carbon Catabolite Repressor ( CREA ) Gene from the Plant-pathogenic Fungus Cochliobolus carbonum
journal, January 2003
- Tonukari, Nyerhovwo J.; Scott-Craig, John S.; Walton, Jonathan D.
- DNA Sequence, Vol. 14, Issue 2
Analysis of Two in Planta Expressed LysM Effector Homologs from the Fungus Mycosphaerella graminicola Reveals Novel Functional Properties and Varying Contributions to Virulence on Wheat
journal, April 2011
- Marshall, Rosalind; Kombrink, Anja; Motteram, Juliet
- Plant Physiology, Vol. 156, Issue 2
Cytochrome P450 enzymes in the fungal kingdom
journal, January 2011
- Črešnar, B.; Petrič, Š.
- Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1814, Issue 1
CYP53A15 of Cochliobolus lunatus, a Target for Natural Antifungal Compounds †
journal, June 2008
- Podobnik, Barbara; Stojan, Jure; Lah, Ljerka
- Journal of Medicinal Chemistry, Vol. 51, Issue 12
Proteomics of rice and Cochliobolus miyabeanus fungal interaction: Insight into proteins at intracellular and extracellular spaces
journal, August 2014
- Kim, Jin Yeong; Wu, Jingni; Kwon, Soon Jae
- PROTEOMICS, Vol. 14, Issue 20
Gene Expression Modulation of Two Biosynthesis Pathways via Signal Transduction in Cochliobolus heterostrophus
journal, January 2014
- Degani, Ofir
- Advances in Bioscience and Biotechnology, Vol. 05, Issue 04
A Decarboxylase Encoded at the Cochliobolus heterostrophus Translocation-Associated Tox1B Locus Is Required for Polyketide (T-toxin) Biosynthesis and High Virulence on T-cytoplasm Maize
journal, September 2002
- Rose, Mark S.; Yun, Sung-Hwan; Asvarak, Thipa
- Molecular Plant-Microbe Interactions®, Vol. 15, Issue 9
Cloning and characterization of the PDA6-1 gene encoding a fungal cytochrome P-450 which detoxifies the phytoalexin pisatin from garden pea
journal, September 1994
- Reimmann, Cornelia; VanEtten, Hans D.
- Gene, Vol. 146, Issue 2
Wild Rice Yield Losses Associated with Growth-Stage-Specific Fungal Brown Spot Epidemics
journal, January 1987
- Kohls, C. L.
- Plant Disease, Vol. 71, Issue 5
The biology of ophiobolins
journal, July 2000
- Au, T. K.; Chick, Wallace S. H.; Leung, P. C.
- Life Sciences, Vol. 67, Issue 7
TopHat: discovering splice junctions with RNA-Seq
journal, March 2009
- Trapnell, Cole; Pachter, Lior; Salzberg, Steven L.
- Bioinformatics, Vol. 25, Issue 9
Cerato-platanin protein is located in the cell walls of ascospores, conidia and hyphae of Ceratocystis fimbriata f. sp. platani
journal, April 2004
- Boddi, Silvia; Comparini, Cecilia; Calamassi, Roberto
- FEMS Microbiology Letters, Vol. 233, Issue 2
Mapping and quantifying mammalian transcriptomes by RNA-Seq
journal, May 2008
- Mortazavi, Ali; Williams, Brian A.; McCue, Kenneth
- Nature Methods, Vol. 5, Issue 7, p. 621-628
EST mining identifies proteins putatively secreted by the anthracnose pathogen Colletotrichum truncatum
journal, June 2011
- Bhadauria, Vijai; Banniza, Sabine; Vandenberg, Albert
- BMC Genomics, Vol. 12, Issue 1
Phylogenomic analysis of type I polyketide synthase genes in pathogenic and saprobic ascomycetes
journal, December 2003
- Kroken, S.; Glass, N. L.; Taylor, J. W.
- Proceedings of the National Academy of Sciences, Vol. 100, Issue 26
Plant cells recognize chitin fragments for defense signaling through a plasma membrane receptor
journal, July 2006
- Kaku, H.; Nishizawa, Y.; Ishii-Minami, N.
- Proceedings of the National Academy of Sciences, Vol. 103, Issue 29
Analysis and annotation of the hexaploid oat seed transcriptome
journal, January 2013
- Gutierrez-Gonzalez, Juan J.; Tu, Zheng; Garvin, David F.
- BMC Genomics, Vol. 14, Issue 1
A putative cyclic peptide efflux pump encoded by the TOXA gene of the plant-pathogenic fungus Cochliobolus carbonum
journal, June 1996
- Pitkin, J. W.; Panaccione, D. G.; Walton, J. D.
- Microbiology, Vol. 142, Issue 6
Cerato-platanins: Elicitors and effectors
journal, November 2014
- Pazzagli, Luigia; Seidl-Seiboth, Verena; Barsottini, Mario
- Plant Science, Vol. 228
Effect of Calcium Silicate on Blast and Brown Spot Intensities and Yields of Rice
journal, January 1991
- Datnoff, L. E.
- Plant Disease, Vol. 75, Issue 7
Nonribosomal peptides: from genes to products
journal, January 2003
- Schwarzer, Dirk; Finking, Robert; Marahiel, Mohamed A.
- Natural Product Reports, Vol. 20, Issue 3
Tomato Cf resistance proteins mediate recognition of cognate homologous effectors from fungi pathogenic on dicots and monocots
journal, April 2010
- Stergiopoulos, I.; van den Burg, H. A.; Okmen, B.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 16
A novel class of gene controlling virulence in plant pathogenic ascomycete fungi
journal, May 2003
- Lu, S. -W.; Kroken, S.; Lee, B. -N.
- Proceedings of the National Academy of Sciences, Vol. 100, Issue 10
LysM receptors recognize friend and foe
journal, July 2006
- Knogge, Wolfgang; Scheel, Dierk
- Proceedings of the National Academy of Sciences, Vol. 103, Issue 29
Symbol Nomenclature for Graphical Representations of Glycans
journal, November 2015
- Varki, Ajit; Cummings, Richard D.; Aebi, Markus
- Glycobiology, Vol. 25, Issue 12
Rapid preparation of DNA from filamentous fungi
journal, January 1985
- Raeder, U.; Broda, P.
- Letters in Applied Microbiology, Vol. 1, Issue 1
Fungal chitinases: diversity, mechanistic properties and biotechnological potential
journal, December 2011
- Hartl, Lukas; Zach, Simone; Seidl-Seiboth, Verena
- Applied Microbiology and Biotechnology, Vol. 93, Issue 2
A polyketide synthase is required for fungal virulence and production of the polyketide T-toxin.
journal, November 1996
- Yang, G.; Rose, M. S.; Turgeon, B. G.
- The Plant Cell, Vol. 8, Issue 11
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
journal, February 2008
- Zerbino, D. R.; Birney, E.
- Genome Research, Vol. 18, Issue 5
Using the Velvet de novo Assembler for Short‐Read Sequencing Technologies
journal, September 2010
- Zerbino, Daniel R.
- Current Protocols in Bioinformatics, Vol. 31, Issue 1
Fungal enzyme sets for plant polysaccharide degradation
journal, July 2011
- van den Brink, Joost; de Vries, Ronald P.
- Applied Microbiology and Biotechnology, Vol. 91, Issue 6, p. 1477-1492
Targeted Mutants of Cochliobolus carbonum Lacking the Two Major Extracellular Polygalacturonases
journal, April 1998
- Scott-Craig, John S.; Cheng, Yi-Qiang; Cervone, Felice
- Applied and Environmental Microbiology, Vol. 64, Issue 4
Phylogenomics reveals subfamilies of fungal nonribosomal peptide synthetases and their evolutionary relationships
journal, January 2010
- Bushley, Kathryn E.; Turgeon, B. Gillian
- BMC Evolutionary Biology, Vol. 10, Issue 1
A MAP kinase gene, BMK1, is required for conidiation and pathogenicity in the rice leaf spot pathogen Bipolaris oryzae
journal, April 2007
- Moriwaki, Akihiro; Kihara, Junichi; Mori, Chie
- Microbiological Research, Vol. 162, Issue 2
Glycosyltransferases and their products: cryptococcal variations on fungal themes
journal, June 2006
- Klutts, James Stacey; Yoneda, Aki; Reilly, Morgann C.
- FEMS Yeast Research, Vol. 6, Issue 4
Fungal LysM effectors: extinguishers of host immunity?
journal, April 2009
- de Jonge, Ronnie; Thomma, Bart P. H. J.
- Trends in Microbiology, Vol. 17, Issue 4
The carbohydrate-active enzymes database (CAZy) in 2013
journal, November 2013
- Lombard, Vincent; Golaconda Ramulu, Hemalatha; Drula, Elodie
- Nucleic Acids Research, Vol. 42, Issue D1
G-Protein β Subunit of Cochliobolus heterostrophus Involved in Virulence, Asexual and Sexual Reproductive Ability, and Morphogenesis
journal, December 2004
- Ganem, Sherif; Lu, Shun-Wen; Lee, Bee-Na
- Eukaryotic Cell, Vol. 3, Issue 6
Novel phacB-Encoded Cytochrome P450 Monooxygenase from Aspergillus nidulans with 3-Hydroxyphenylacetate 6-Hydroxylase and 3,4-Dihydroxyphenylacetate 6-Hydroxylase Activities
journal, December 2006
- Ferrer-Sevillano, Francisco; Fernández-Cañón, José M.
- Eukaryotic Cell, Vol. 6, Issue 3
Carbohydrate-binding modules: fine-tuning polysaccharide recognition
journal, September 2004
- Boraston, Alisdair B.; Bolam, David N.; Gilbert, Harry J.
- Biochemical Journal, Vol. 382, Issue 3
Gepard: a rapid and sensitive tool for creating dotplots on genome scale
journal, February 2007
- Krumsiek, J.; Arnold, R.; Rattei, T.
- Bioinformatics, Vol. 23, Issue 8
A putative branched-chain-amino-acid transaminase gene required for HC-toxin biosynthesis and pathogenicity in Cochliobolus carbonum The GenBank accession number for the nucleotide sequence reported in this paper is AF157629.
journal, December 1999
- Cheng, Yi-Qiang; Ahn, Joong-Hoon; Walton, Jonathan D.
- Microbiology, Vol. 145, Issue 12
Two LysM receptor molecules, CEBiP and OsCERK1, cooperatively regulate chitin elicitor signaling in rice: LysM receptors for rice chitin signaling
journal, September 2010
- Shimizu, Takeo; Nakano, Takuto; Takamizawa, Daisuke
- The Plant Journal, Vol. 64, Issue 2
CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes
journal, March 2007
- Parra, G.; Bradnam, K.; Korf, I.
- Bioinformatics, Vol. 23, Issue 9
Functional analysis of the Alternaria brassicicola non-ribosomal peptide synthetase gene AbNPS2 reveals a role in conidial cell wall construction
journal, January 2007
- Kim, Kwang-Hyung; Cho, Yangrae; La Rota, Mauricio
- Molecular Plant Pathology, Vol. 8, Issue 1
The novel Cladosporium fulvum lysin motif effector Ecp6 is a virulence factor with orthologues in other fungal species
journal, July 2008
- Bolton, Melvin D.; van Esse, H. Peter; Vossen, Jack H.
- Molecular Microbiology, Vol. 69, Issue 1
The Cochliobolus Carbonum SNF1 Gene Is Required for Cell Wall-Degrading Enzyme Expression and Virulence on Maize
journal, February 2000
- Tonukari, Nyerhovwo J.; Scott-Craig, John S.; Walton, Jonathan D.
- The Plant Cell, Vol. 12, Issue 2
Histone deacetylases in fungi: novel members, new facts
journal, July 2003
- Trojer, P.
- Nucleic Acids Research, Vol. 31, Issue 14
FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes
journal, January 2004
- Al-Shahrour, F.; Diaz-Uriarte, R.; Dopazo, J.
- Bioinformatics, Vol. 20, Issue 4
A novel class of gene controlling virulence in plant pathogenic ascomycete fungi
journal, May 2003
- Lu, S. -W.; Kroken, S.; Lee, B. -N.
- Proceedings of the National Academy of Sciences, Vol. 100, Issue 10
Expression of a Phytophthora sojae necrosis-inducing protein occurs during transition from biotrophy to necrotrophy
journal, November 2002
- Qutob, Dinah; Kamoun, Sophien; Gijzen, Mark
- The Plant Journal, Vol. 32, Issue 3
Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi
journal, December 2012
- Ohm, Robin A.; Feau, Nicolas; Henrissat, Bernard
- PLoS Pathogens, Vol. 8, Issue 12
Impact of fungal drug transporters on fungicide sensitivity, multidrug resistance and virulence
journal, January 2006
- de Waard, Maarten A.; Andrade, Alan C.; Hayashi, Keisuke
- Pest Management Science, Vol. 62, Issue 3
The In Planta-Produced Extracellular Proteins ECP1 and ECP2 of Cladosporium fulvum Are Virulence Factors
journal, August 1997
- Laugé, Richard; Joosten, Matthieu H. A. J.; Van den Ackerveken, Guido F. J. M.
- Molecular Plant-Microbe Interactions®, Vol. 10, Issue 6
Glucose uptake and growth of glucose-limited chemostat cultures of Aspergillus niger and a disruptant lacking MstA, a high-affinity glucose transporter
journal, June 2007
- Jorgensen, T. R.; vanKuyk, P. A.; Poulsen, B. R.
- Microbiology, Vol. 153, Issue 6
Molecular Cloning and Characterization of cel2 from the Fungus Cochlibolus carbonum
journal, January 2001
- Ahn, Joong-Hoon; Sposato, Paola; Kim, Su-Il
- Bioscience, Biotechnology, and Biochemistry, Vol. 65, Issue 6, p. 1406-1411
Fungal chitinases: diversity, mechanistic properties and biotechnological potential
journal, December 2011
- Hartl, Lukas; Zach, Simone; Seidl-Seiboth, Verena
- Applied Microbiology and Biotechnology, Vol. 93, Issue 2
Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training
journal, October 2008
- Ter-Hovhannisyan, V.; Lomsadze, A.; Chernoff, Y. O.
- Genome Research, Vol. 18, Issue 12
A Gene Related to Yeast HOS2 Histone Deacetylase Affects Extracellular Depolymerase Expression and Virulence in a Plant Pathogenic Fungus
journal, July 2001
- Baidyaroy, D.
- THE PLANT CELL ONLINE, Vol. 13, Issue 7
The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics
journal, January 2009
- Cantarel, B. L.; Coutinho, P. M.; Rancurel, C.
- Nucleic Acids Research, Vol. 37, Issue Database
Fungal Transporters Involved in Efflux of Natural Toxic Compounds and Fungicides
journal, June 2000
- Del Sorbo, Giovanni; Schoonbeek, Henk-jan; De Waard, Maarten A.
- Fungal Genetics and Biology, Vol. 30, Issue 1
CCL5 derived from tumor-associated macrophages promotes prostate cancer stem cells and metastasis via activating β-catenin/STAT3 signaling
journal, April 2020
- Huang, Renlun; Wang, Shengqi; Wang, Neng
- Cell Death & Disease, Vol. 11, Issue 4
Phylogeny and biogeography of the eastern Asian–North American disjunct wild-rice genus (Zizania L., Poaceae)
journal, June 2010
- Xu, Xinwei; Walters, Christina; Antolin, Michael F.
- Molecular Phylogenetics and Evolution, Vol. 55, Issue 3
Cerato-platanins: Elicitors and effectors
journal, November 2014
- Pazzagli, Luigia; Seidl-Seiboth, Verena; Barsottini, Mario
- Plant Science, Vol. 228
A Eukaryotic Alanine Racemase Gene Involved in Cyclic Peptide Biosynthesis
journal, February 2000
- Cheng, Yi-Qiang; Walton, Jonathan D.
- Journal of Biological Chemistry, Vol. 275, Issue 7
Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes
journal, January 2013
- Levasseur, Anthony; Drula, Elodie; Lombard, Vincent
- Biotechnology for Biofuels, Vol. 6, Issue 1, Article No. 41
Analysis of Two in Planta Expressed LysM Effector Homologs from the Fungus Mycosphaerella graminicola Reveals Novel Functional Properties and Varying Contributions to Virulence on Wheat
journal, April 2011
- Marshall, Rosalind; Kombrink, Anja; Motteram, Juliet
- Plant Physiology, Vol. 156, Issue 2
Functional Analysis of All Nonribosomal Peptide Synthetases in Cochliobolus heterostrophus Reveals a Factor, NPS6, Involved in Virulence and Resistance to Oxidative Stress
journal, March 2005
- Lee, Bee-Na; Kroken, Scott; Chou, David Y. T.
- Eukaryotic Cell, Vol. 4, Issue 3
The cyclic peptide synthetase catalyzing HC-toxin production in the filamentous fungus Cochliobolus carbonum is encoded by a 15.7-kilobase open reading frame.
journal, December 1992
- Scott-Craig, J. S.; Panaccione, D. G.; Pocard, J. A.
- Journal of Biological Chemistry, Vol. 267, Issue 36
Works referencing / citing this record:
Genome sequence and spore germination-associated transcriptome analysis of Corynespora cassiicola from cucumber
journal, July 2020
- Gao, Shigang; Zeng, Rong; Xu, Lihui
- BMC Microbiology, Vol. 20, Issue 1
Figures / Tables found in this record:
Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.