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De Novo Assembly and Phasing of Dikaryotic Genomes from Two Isolates ofPuccinia coronataf. sp.avenae, the Causal Agent of Oat Crown Rust

  1. Author:
    Miller, Marisa E
    Zhang, Ying
    Omidvar, Vahid
    Sperschneider, Jana
    Schwessinger, Benjamin [ORCID]
    Raley, Castle
    Palmer, Jonathan M
    Garnica, Diana
    Upadhyaya, Narayana
    Rathjen, John
    Taylor, Jennifer M
    Park, Robert F
    Dodds, Peter N
    Hirsch, Cory D
    Kianian, Shahryar F
    Figueroa, Melania [ORCID]

  2. Author Address

    Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA., Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, Minnesota, USA., Centre for Environment and Life Sciences, Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Perth, WA, Australia., Research School of Biology, Australian National University, Canberra, ACT, Australia., Leidos Biomedical Research, Frederick, Maryland, USA., Center for Forest Mycology Research, Northern Research Station, USDA Forest Service, Madison, Wisconsin, USA., Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Canberra, ACT, Australia., Plant Breeding Institute, Faculty of Agriculture and Environment, School of Life and Environmental Sciences, University of Sydney, Narellan, NSW, Australia., Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA shahryar.kianian@ars.usda.gov figue031@umn.edu., USDA-ARS Cereal Disease Laboratory, St. Paul, Minnesota, USA., Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, Minnesota, USA.,
    1. Year: 2018
    2. Date: JAN-FEB
    3. Epub Date: 2018 02 20
  2. Journal: mBio
    1. 9
    2. 1
    3. Pages: pii: e01650-17
  4. Type of Article: Article
  5. Article Number: e01650-17
  6. ISSN: 2150-7511
  1. Abstract:

    Oat crown rust, caused by the fungusPucinnia coronataf. sp.avenae, is a devastating disease that impacts worldwide oat production. For much of its life cycle,P. coronataf. sp.avenaeis dikaryotic, with two separate haploid nuclei that may vary in virulence genotype, highlighting the importance of understanding haplotype diversity in this species. We generated highly contiguousde novogenome assemblies of twoP. coronataf. sp.avenaeisolates, 12SD80 and 12NC29, from long-read sequences. In total, we assembled 603 primary contigs for 12SD80, for a total assembly length of 99.16 Mbp, and 777 primary contigs for 12NC29, for a total length of 105.25 Mbp; approximately 52% of each genome was assembled into alternate haplotypes. This revealed structural variation between haplotypes in each isolate equivalent to more than 2% of the genome size, in addition to about 260,000 and 380,000 heterozygous single-nucleotide polymorphisms in 12SD80 and 12NC29, respectively. Transcript-based annotation identified 26,796 and 28,801 coding sequences for isolates 12SD80 and 12NC29, respectively, including about 7,000 allele pairs in haplotype-phased regions. Furthermore, expression profiling revealed clusters of coexpressed secreted effector candidates, and the majority of orthologous effectors between isolates showed conservation of expression patterns. However, a small subset of orthologs showed divergence in expression, which may contribute to differences in virulence between 12SD80 and 12NC29. This study provides the first haplotype-phased reference genome for a dikaryotic rust fungus as a foundation for future studies into virulence mechanisms inP. coronataf. sp.avenaeIMPORTANCEDisease management strategies for oat crown rust are challenged by the rapid evolution ofPuccinia coronataf. sp.avenae, which renders resistance genes in oat varieties ineffective. Despite the economic importance of understandingP. coronataf. sp.avenae, resources to study the molecular mechanisms underpinning pathogenicity and the emergence of new virulence traits are lacking. Such limitations are partly due to the obligate biotrophic lifestyle ofP. coronataf. sp.avenaeas well as the dikaryotic nature of the genome, features that are also shared with other important rust pathogens. This study reports the first release of a haplotype-phased genome assembly for a dikaryotic fungal species and demonstrates the amenability of using emerging technologies to investigate genetic diversity in populations ofP. coronataf. sp.avenae. Copyright © 2018 Miller et al.

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External Sources

  1. View Full Text
  2. DOI: 10.1128/mBio.01650-17
  3. PMID: 29463655
  4. View record in Web of Science®
  5. WOS: 000427006300074
  6. PII : mBio.01650-17

Library Notes

  1. Fiscal Year: FY2017-2018
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