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

Claudia V. Castell-Miller, Juan J. Gutierrez-Gonzalez, Zheng Jin Tu, Kathryn E. Bushley, Matthieu Hainaut, Bernard Henrissat, Deborah A. Samac

Research output: Contribution to journalArticlepeer-review

6 Scopus citations

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 diseasecausing 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. This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

Original languageEnglish (US)
Article numbere0154122
JournalPloS one
Volume11
Issue number6
DOIs
StatePublished - Jun 1 2016

Bibliographical note

Funding Information:
We would like to thank Bruce Elckloff from the Mayo Clinic, Rochester, MN for sequencing the C. miyabeanus isolate, and Dr. B. Gillian Turgeon and Bradford Condon for NRPS sequence data from the C. miyabeanus WK-1C and C. heterostrophus C4 and C5 strains, and other ascomycetes used in the analyses, and to Dr. B. Gillian Turgeon and the U.S. Department of Energy Joint Genome Institute ( http://genome.jgi.doe.gov ) for sharing the C. miyabeanus WK-1C DNA sequences and proteins. The genome and transcriptome of C. miyabeanus work were sequenced and annotated by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.

Publisher Copyright:
© 2016, Public Library of Science. All rights reserved. This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

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