title: Genome Assembly of the Fungus Cochliobolus miyabeanus, and Transcriptome Analysis during Early Stages of Infection on American Wildrice (Zizania palustris L.).
abstract: 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 virgatum). 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.
authors.affiliation: Department of Plant Pathology, University of Minnesota, Saint Paul, Minnesota, United States of America.
authors.forename: Claudia V
authors.initials: CV
authors.lastname: Castell-Miller
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, Minnesota, United States of America.|USDA-ARS-Plant Science Research Unit, Saint Paul, Minnesota, United States of America.
authors.forename: Juan J
authors.initials: JJ
authors.lastname: Gutierrez-Gonzalez
authors.affiliation: Mayo Clinic, Division of Biomedical Statistics and Informatics, Rochester, Minnesota, United States of America.
authors.forename: Zheng Jin
authors.initials: ZJ
authors.lastname: Tu
authors.affiliation: Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota, United States of America.
authors.forename: Kathryn E
authors.initials: KE
authors.lastname: Bushley
authors.affiliation: CNRS UMR 7257, Aix-Marseille University, Marseille, France.|INRA, USC 1408 AFMB, Marseille, France.
authors.forename: Matthieu
authors.initials: M
authors.lastname: Hainaut
authors.affiliation: CNRS UMR 7257, Aix-Marseille University, Marseille, France.|INRA, USC 1408 AFMB, Marseille, France.|Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
authors.forename: Bernard
authors.initials: B
authors.lastname: Henrissat
authors.affiliation: Department of Plant Pathology, University of Minnesota, Saint Paul, Minnesota, United States of America.|USDA-ARS-Plant Science Research Unit, Saint Paul, Minnesota, United States of America.
authors.forename: Deborah A
authors.initials: DA
authors.lastname: Samac
mesh_terms: D001203:Ascomycota / Q000235:genetics* / Q000472:pathogenicity; D020869:Gene Expression Profiling; D016681:Genome, Fungal / Q000235:genetics*; D012275:Oryza / Q000382:microbiology; D008897:Panicum / Q000382:microbiology; D000069452:Pathogen-Associated Molecular Pattern Molecules; D010453:Peptide Synthases / Q000235:genetics; D010935:Plant Diseases / Q000235:genetics* / Q000382:microbiology; D018515:Plant Leaves / Q000382:microbiology; D048630:Polyketide Synthases / Q000235:genetics; D059467:Transcriptome / Q000235:genetics*; D014481:United States
chemical_list: D000069452:Pathogen-Associated Molecular Pattern Molecules; D048630:Polyketide Synthases; D010453:Peptide Synthases