Skip to Main Content
De novo assembly and phasing of dikaryotic genomes from two isolates of Puccini coronata f. sp. avenae, the causal agent of oat crown rustAuthor(s): Marisa E. Miller; Ying Zhang; Vahid Omidvar; Jana Sperschneider; Benjamin Schwessinger; Castle Raley; Jonathan M. Palmer; Diana Garnica; Narayana Upadhyaya; John Rathjen; Jennifer M. Taylor; Robert F. Park; Peter N. Dodds; Cory D. Hirsch; Shahryar F. Kianian; Melania Figueroa
Source: mBio. 9(1): e01650-17. 21 p.
Publication Series: Scientific Journal (JRNL)
Station: Northern Research Station
View PDF (2.0 MB)
DescriptionOat crown rust, caused by the fungus Pucinnia coronata f. sp. avenae, is a devastating disease that impacts worldwide oat production. For much of its life cycle, P. coronata f. sp. avenae is 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 contiguous de novo genome assemblies of two P. coronata f. sp. avenae isolates, 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 in P. coronata f. sp. avenae.
- Check the Northern Research Station web site to request a printed copy of this publication.
- Our on-line publications are scanned and captured using Adobe Acrobat.
- During the capture process some typographical errors may occur.
- Please contact Sharon Hobrla, firstname.lastname@example.org if you notice any errors which make this publication unusable.
- We recommend that you also print this page and attach it to the printout of the article, to retain the full citation information.
- This article was written and prepared by U.S. Government employees on official time, and is therefore in the public domain.
CitationMiller, Marisa E.; Zhang, Ying; Omidvar, Vahid; Sperschneider, Jana; Schwessinger, Benjamin; 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. 2018. De novo assembly and phasing of dikaryotic genomes from two isolates of Puccini coronata f. sp. avenae, the causal agent of oat crown rust. mBio. 9(1): e01650-17. 21 p.
Keywordseffectors, genomics, oat, rust fungi, virulence
- Effect on Grass and Cereal Seedlings of Hydrogen Cyanide Produced by Mycelium and Sporophores of Marasmius oreades
- Panel Discussion: Application of Living Mulch for Spring-Sown Loblolly Pine
- Rapid 2,2'-bicinchoninic-based xylanase assay compatible with high throughput screening
XML: View XML