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

Miller, Marisa E; Zhang, Ying; Omidvar, Vahid; Sperschneider, Jana; Schwessinger, Benjamin; Raley, Castle; Palmer, Jonathan M; garnica, Diana; Upadhyaya, Narayana M; Rathjen, John; Taylor, Jennifer; Park, Robert; Dodds, Peter N; Hirsch, Corey; Kianian, Shahryar

Description

Oat 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...[Show more]

dc.contributor.authorMiller, Marisa E
dc.contributor.authorZhang, Ying
dc.contributor.authorOmidvar, Vahid
dc.contributor.authorSperschneider, Jana
dc.contributor.authorSchwessinger, Benjamin
dc.contributor.authorRaley, Castle
dc.contributor.authorPalmer, Jonathan M
dc.contributor.authorgarnica, Diana
dc.contributor.authorUpadhyaya, Narayana M
dc.contributor.authorRathjen, John
dc.contributor.authorTaylor, Jennifer
dc.contributor.authorPark, Robert
dc.contributor.authorDodds, Peter N
dc.contributor.authorHirsch, Corey
dc.contributor.authorKianian, Shahryar
dc.date.accessioned2021-10-26T01:49:04Z
dc.date.available2021-10-26T01:49:04Z
dc.identifier.issn2161-2129
dc.identifier.urihttp://hdl.handle.net/1885/251177
dc.description.abstractOat 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.
dc.description.sponsorshipThis work was funded by the USDA-ARS and the University of Minnesota Standard Cooperative Agreement (grant 3002-11031-00053115 shared by S.F.K. and M.F.), the University of Minnesota Experimental Station USDA-NIFA Hatch/Figueroa project MIN22-058, and an Organization for Economic Cooperation and Development Fellowship to M.F. M.E.M. was partially supported by a USDA-NIFA Postdoctoral Fellowship Award (2017-67012-26117). J.S. was supported by an OCE Postdoctoral Fellowship. R.F.P. receives funding from the Australian Grains Research Development Corporation (grant US00067). J.M.P. was supported by the Northern Research Station of the USDA Forest Service.
dc.format.mimetypeapplication/pdf
dc.language.isoen_AU
dc.publisherAmerican Society for Microbiology
dc.rights© 2018 Miller et al.
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.sourcemBio
dc.subjecteffectors
dc.subjectgenomics
dc.subjectoat
dc.subjectrust fungi
dc.subjectvirulence
dc.titleDe novo assembly and phasing of dikaryotic genomes from two isolates of puccinia coronata f. Sp. avenae, the causal agent of oat crown rust
dc.typeJournal article
local.description.notesImported from ARIES
local.identifier.citationvolume9
dc.date.issued2018
local.identifier.absfor060408 - Genomics
local.identifier.absfor060704 - Plant Pathology
local.identifier.ariespublicationa383154xPUB9549
local.publisher.urlhttp://mbio.asm.org/
local.type.statusPublished Version
local.contributor.affiliationMiller, Marisa E, University of Minnesota
local.contributor.affiliationZhang , Ying , University of Minnesota
local.contributor.affiliationOmidvar, Vahid, University of Minnesota
local.contributor.affiliationSperschneider, Jana , Commonwealth Scientific and Industrial Research Organization
local.contributor.affiliationSchwessinger, Benjamin, College of Science, ANU
local.contributor.affiliationRaley, Castle, Leidos Biomedical Research
local.contributor.affiliationPalmer, Jonathan M , Center for Forest Mycology Research
local.contributor.affiliationgarnica, Diana , Agriculture and Food, Commonwealth Scientific and Industrial Research Organization
local.contributor.affiliationUpadhyaya, Narayana M, CSIRO Plant Industry
local.contributor.affiliationRathjen, John, College of Science, ANU
local.contributor.affiliationTaylor, Jennifer, CSIRO
local.contributor.affiliationPark, Robert, University of Sydney
local.contributor.affiliationDodds, Peter N, CSIRO
local.contributor.affiliationHirsch, Corey, University of Minnesota
local.contributor.affiliationKianian, Shahryar, University of Minnesota
local.bibliographicCitation.issue1
local.bibliographicCitation.startpage1
local.bibliographicCitation.lastpage21
local.identifier.doi10.1128/mBio.01650-17
local.identifier.absseo820506 - Oats
dc.date.updated2020-11-23T11:38:05Z
local.identifier.scopusID2-s2.0-85043503432
dcterms.accessRightsOpen Access
dc.provenanceThis is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
dc.rights.licenseCreative Commons License (Attribution 4.0 International)
CollectionsANU Research Publications

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