<italic toggle="yes">De Novo</italic> Assembly and Phasing of Dikaryotic Genomes from Two Isolates of <italic toggle="yes">Puccinia coronata</italic> f. sp. <italic toggle="yes">avenae</italic>, the Causal Agent of Oat Crown Rust

ABSTRACT 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 i...

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Autores principales:	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
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2018
Materias:	effectors genomics oat rust fungi virulence Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/22db4e39926849009c6e1c373213226b
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spelling	oai:doaj.org-article:22db4e39926849009c6e1c373213226b2021-11-15T15:53:26Z<italic toggle="yes">De Novo</italic> Assembly and Phasing of Dikaryotic Genomes from Two Isolates of <italic toggle="yes">Puccinia coronata</italic> f. sp. <italic toggle="yes">avenae</italic>, the Causal Agent of Oat Crown Rust10.1128/mBio.01650-172150-7511https://doaj.org/article/22db4e39926849009c6e1c373213226b2018-03-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.01650-17https://doaj.org/toc/2150-7511ABSTRACT 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 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. IMPORTANCE Disease management strategies for oat crown rust are challenged by the rapid evolution of Puccinia coronata f. sp. avenae, which renders resistance genes in oat varieties ineffective. Despite the economic importance of understanding P. coronata f. 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 of P. coronata f. sp. avenae 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 P. coronata f. sp. avenae.Marisa E. MillerYing ZhangVahid OmidvarJana SperschneiderBenjamin SchwessingerCastle RaleyJonathan M. PalmerDiana GarnicaNarayana UpadhyayaJohn RathjenJennifer M. TaylorRobert F. ParkPeter N. DoddsCory D. HirschShahryar F. KianianMelania FigueroaAmerican Society for Microbiologyarticleeffectorsgenomicsoatrust fungivirulenceMicrobiologyQR1-502ENmBio, Vol 9, Iss 1 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	effectors genomics oat rust fungi virulence Microbiology QR1-502
spellingShingle	effectors genomics oat rust fungi virulence Microbiology QR1-502 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 <italic toggle="yes">De Novo</italic> Assembly and Phasing of Dikaryotic Genomes from Two Isolates of <italic toggle="yes">Puccinia coronata</italic> f. sp. <italic toggle="yes">avenae</italic>, the Causal Agent of Oat Crown Rust
description	ABSTRACT 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 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. IMPORTANCE Disease management strategies for oat crown rust are challenged by the rapid evolution of Puccinia coronata f. sp. avenae, which renders resistance genes in oat varieties ineffective. Despite the economic importance of understanding P. coronata f. 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 of P. coronata f. sp. avenae 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 P. coronata f. sp. avenae.
format	article
author	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
author_facet	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
author_sort	Marisa E. Miller
title	<italic toggle="yes">De Novo</italic> Assembly and Phasing of Dikaryotic Genomes from Two Isolates of <italic toggle="yes">Puccinia coronata</italic> f. sp. <italic toggle="yes">avenae</italic>, the Causal Agent of Oat Crown Rust
title_short	<italic toggle="yes">De Novo</italic> Assembly and Phasing of Dikaryotic Genomes from Two Isolates of <italic toggle="yes">Puccinia coronata</italic> f. sp. <italic toggle="yes">avenae</italic>, the Causal Agent of Oat Crown Rust
title_full	<italic toggle="yes">De Novo</italic> Assembly and Phasing of Dikaryotic Genomes from Two Isolates of <italic toggle="yes">Puccinia coronata</italic> f. sp. <italic toggle="yes">avenae</italic>, the Causal Agent of Oat Crown Rust
title_fullStr	<italic toggle="yes">De Novo</italic> Assembly and Phasing of Dikaryotic Genomes from Two Isolates of <italic toggle="yes">Puccinia coronata</italic> f. sp. <italic toggle="yes">avenae</italic>, the Causal Agent of Oat Crown Rust
title_full_unstemmed	<italic toggle="yes">De Novo</italic> Assembly and Phasing of Dikaryotic Genomes from Two Isolates of <italic toggle="yes">Puccinia coronata</italic> f. sp. <italic toggle="yes">avenae</italic>, the Causal Agent of Oat Crown Rust
title_sort	<italic toggle="yes">de novo</italic> assembly and phasing of dikaryotic genomes from two isolates of <italic toggle="yes">puccinia coronata</italic> f. sp. <italic toggle="yes">avenae</italic>, the causal agent of oat crown rust
publisher	American Society for Microbiology
publishDate	2018
url	https://doaj.org/article/22db4e39926849009c6e1c373213226b
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<italic toggle="yes">De Novo</italic> Assembly and Phasing of Dikaryotic Genomes from Two Isolates of <italic toggle="yes">Puccinia coronata</italic> f. sp. <italic toggle="yes">avenae</italic>, the Causal Agent of Oat Crown Rust

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