De novo assembly and phasing of dikaryotic genomes from two isolates of Puccinia coronata f. sp. avenae, the causal agent of oat crown rust

Authors: MILLER, MARISA - University Of Minnesota; ZHANG, YING - University Of Minnesota; OMIDVAR, VAHID - University Of Minnesota; SPERSCHNEIDER, JANA - Commonwealth Scientific And Industrial Research Organisation (CSIRO); SCHWESSINGER, BENJAMIN - The Australian National University; RALEY, CASTLE - Leidos; PALMER, JONATHAN - Forest Service (FS); GARNICA, DIANA - Commonwealth Scientific And Industrial Research Organisation (CSIRO); UPADHYAYA, NARAYANA - University Of Sydney; RATHJEN, JOHN - The Australian National University; TAYLER, JENNIFER - Commonwealth Scientific And Industrial Research Organisation (CSIRO); PARK, ROBERT - University Of Sydney; DODDS, PETER - The Australian National University; HIRSCH, CORY - University Of Minnesota; Kianian, Shahryar; FIGUEROA, MELANIA - University Of Minnesota

Submitted to: mBio
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/9/2018
Publication Date: 2/20/2018
Citation: Miller, M.E., Zhang, Y., Omidvar, V., Sperschneider, J., Schwessinger, B., Raley, C., Palmer, J.M., Garnica, D., Upadhyaya, N., Rathjen, J., Tayler, J., Park, R.F., Dodds, P.N., Hirsch, C., Kianian, S., Figueroa, M. 2018. De novo assembly and phasing of dikaryotic genomes from two isolates of Puccinia coronata f. sp. avenae, the causal agent of oat crown rust. mBio. 9(1):1-21. https://doi: 10.1128/mBio.01650-17.
DOI: https://doi.org/10.1128/mBio.01650-17

Interpretive Summary: Disease management strategies to manage oat crown rust are challenged by the rapid evolution of Puccinia coronata f. sp. avenae (Pca), which renders resistance genes in oat varieties ineffective. In spite of the economic importance of understanding Pca, resources to study the molecular mechanisms underpinning pathogenicity and emergence of new virulence traits are lacking. Such limitations are partly driven by the obligate biotrophic lifestyle of Pca as 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 of Pca.

Technical Abstract: Oat crown rust, caused by the fungus Puccinia coronata f. sp. avenae (Pca), is a devastating disease that impacts worldwide oat production. For much of its life cycle Pca is dikaryotic with two separate haploid nuclei that may vary in virulence genotypes, which highlights the importance of understanding haplotype diversity in this species. We generated highly contiguous de novo genome assemblies of two Pca isolates, 12SD80 and 12NC29, from long-read sequences using the FALCON assembler. In total, we assembled 603 primary contigs for a total assembly length of 99.16 Mbp for 12SD80 and 777 primary contigs with a total length of 105.25 Mbp for 12NC29. Overall, 53% of the Pca genomes were composed of interspersed repeats. To evaluate genetic variation between haplotypes, FALCON-Unzip was used to phase haplotype sequences and approximately 52% of each genome could be assembled into alternate haplotypes. This revealed large-scale 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 and about 4,500 genes unique to one or other haplotype. Analysis of orthologous genes between the isolates indicated that orthologs could not be detected for approximately 45% of genes when accounting for synteny. Furthermore, expression profiling revealed clusters of co-expressed secreted effector candidates.