Genome Assembly of the Fungus Cochliobolus miyabeanus, and Transcriptome Analysis during Early Stages of Infection on American Wildrice (Zizania palustris L.).

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PloS one, ISSN: 1932-6203, Vol: 11, Issue: 6, Page: e0154122

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10.1371/journal.pone.0154122; 10.1371/journal.pone.0154122.g002; 10.1371/journal.pone.0154122.t003; 10.1371/journal.pone.0154122.g003; 10.1371/journal.pone.0154122.t004; 10.1371/journal.pone.0154122.t005; 10.1371/journal.pone.0154122.g001; 10.1371/journal.pone.0154122.t001; 10.1371/journal.pone.0154122.t002
Claudia V. Castell-Miller; Juan J. Gutierrez-Gonzalez; Zheng Jin Tu; Kathryn E. Bushley; Matthieu Hainaut; Bernard Henrissat; Deborah A. Samac; Jae-Hyuk Yu
Public Library of Science (PLoS); Figshare
Biochemistry, Genetics and Molecular Biology; Agricultural and Biological Sciences; Microbiology; Genetics; Ecology; Plant Biology; Virology; 69999 Biological Sciences not elsewhere classified; enzyme; zizania palustris; n 50; host defenses; cochliobolus species; wildrice defense mechanisms; 31.79 mbp; fungus cochliobolus miyabeanus causes; fungus cochliobolus miyabeanus; plant defense compounds; american wildrice; pks; miyabeanus genome; transcriptome analysis; future research; north american specialty crops; effector homologs; 48 hours; ssp; reactive oxygen species; genome assembly; detoxification systems; host defense responses; polyketide synthases; leaf spot disease; cell wall; harbors 187; gene number; panicum virgatum; illumina technology; miyabeanus strain tg 12bl; oryza sativa
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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.