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

Author
item CASTELL-MILLER, CLAUDIA - University Of Minnesota
item GUTIERREZ-GONZLEZ, JUAN - University Of Minnesota
item TU, ZHENG - Mayo Clinic
item BUSHLEY, KATHYRN - University Of Minnesota
item HAINAUT, MATTHIEU - National Council For Scientific Research-Cnrs
item HENRISSAT, BERNARD - National Council For Scientific Research-Cnrs
item Samac, Deborah - Debby

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/11/2016
Publication Date: 6/2/2016
Citation: Castell-Miller, C.V., Gutierrez-Gonzlez, J.J., Tu, Z.J., Bushley, K., Hainaut, M., Henrissat, B., Samac, D.A. 2016. Genome assembly of the fungus Cochliobolus miyabeanus, and transcriptome analysis during early stages of infection on American wild rice (Zizania palustris L.). PLoS One. 11(6):e0154122. doi:10.1371/journal.pone.0154122.

Interpretive Summary: Fungal brown spot is one of the most important diseases of rice and two North American specialty crops, American wildrice and switchgrass. However, little is known about how the pathogen causes disease or interacts with host plants. To begin to gain insight into these processes, the fungal genome was sequenced and genes cataloged. The genome is 31.79 million base pairs in size and encodes 11,000 genes, of which approximately 10% are expected to encode secreted proteins. The genome is very similar to a rice-infecting strain of the fungus, although they were isolated from different continents and from different host plants. A number of the secreted proteins are similar to proteins from other fungi called effector proteins that damage plants or trigger resistance. The pathogen genome encodes enzymes for production of toxins, although no host-specific toxins have been identified in this fungus, suggesting that the enzymes play other roles in the life cycle of this organism. Approximately half of the genes in the genome were expressed during early stages of infection of wildrice. Among the most highly expressed were genes encoding cell wall degrading enzymes and proteins to protect the fungus from plant defenses. The genome sequence of the wildrice pathogen will facilitate investigation of the global diversity of the fungus while candidate effector proteins will be tools for selecting disease resistance in wildrice.

Technical Abstract: Cochliobolus miyabeanus causes a severe, yield-reducing 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 the pathogen in wildrice, little is known about mechanisms of pathogenicity or host defense responses. To bridge these gaps, the genome of isolate CmTG12bL2 from wildrice was shotgun sequenced using Illumina technology and the fungal transcriptome analyzed at 48 hours after inoculation (hai) onto wildrice. The genome assembly consists of 31.79 Mbp in 2,378 scaffolds with an N50=74,921. There are 11,000 predicted genes of which 94.5% have annotations. Approximately 10% are expected to be secreted with a total of 187 small-secreted peptides (SSPs) and some fungal effector homologs. The genome is rich in carbohydrate active enzymes. Detoxification systems were represented by a variety of enzymes that likely offer protection against plant defense compounds. The non-ribosomal peptide synthetase and polyketide synthases (PKS) present were common to other Cochliobolus species. An average of 2.4% of the transcripts identified in infected wildrice leaves were of fungal origin resulting in a total of 10,674 annotated transcripts mapped to the genome sequence. Transcripts highly expressed or enriched potentially involved in pathogenicity or response to host defenses included: hydrophobins, cutinase, cell wall degrading enzymes, enzymes related to reactive oxygen species scavenging, PKS, detoxification systems, SSPs, and a known fungal effector. The genome sequence of the wildrice pathogen will facilitate investigation of the global genetic diversity of C. miyabeanus and identification of effectors involved in pathogenicity and host-specificity.