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Title: Genome assembly of the fungus Cochliobolus miyabeanus, and transcriptome analysis during early stages of infection on American wildrice ( Zizania palustris L.)

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 N 50 = 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 responsemore » 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.« less
 [1] ;  [2] ;  [3] ;  [4] ;  [5] ;  [6] ;  [7]
  1. Univ. of Minnesota, St. Paul, MN (United States). Dept. of Plant Pathology
  2. 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)
  3. Mayo Clinic, Div. of Biomedical Statistics and Informatics, Rochester, MN (United States)
  4. Univ. of Minnesota, St. Paul, MN (United States). Dept. of Plant Biology
  5. Aix-Marseille Univ., Marseille (France). CNRS UMR 7257
  6. Aix-Marseille Univ., Marseille (France). CNRS UMR 7257; King Abdulaziz Univ., Jeddah (Saudi Arabia). Dept. of Biological Sciences
  7. Univ. of Minnesota, St. Paul, MN (United States). Dept. of Plant Pathology; USDA-ARS-Plant Science Research Unit, St. Paul, MN (United States)
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Accepted Manuscript
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Additional Journal Information:
Journal Volume: 11; Journal Issue: 6; Journal ID: ISSN 1932-6203
Public Library of Science
Research Org:
Univ. of Minnesota, St. Paul, MN (United States)
Sponsoring Org:
USDOE Office of Science (SC)
Country of Publication:
United States
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
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