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

2017 ◽  
Author(s):  
Marisa E. Miller ◽  
Ying Zhang ◽  
Vahid Omidvar ◽  
Jana Sperschneider ◽  
Benjamin Schwessinger ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
De Novo ◽  
Rust Fungus ◽  
Expression Patterns ◽  
Haplotype Diversity ◽  
Crown Rust ◽  
Puccinia Coronata ◽  
Small Subset ◽  
Nucleotide Polymorphisms ◽  
Oat Crown Rust

AbstractOat 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 genotype, highlighting 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. 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, and 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 co-expressed 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 Pca.ImportanceDisease management strategies for oat crown rust are challenged by the rapid evolution of Puccinia coronata f. sp. avenae (Pca), which renders resistance genes in oat varieties ineffective. Despite 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 due to 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.

scholarly journals 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 ◽  
2018 ◽  
Vol 9 (1) ◽  
Author(s):  
Marisa E. Miller ◽  
Ying Zhang ◽  
Vahid Omidvar ◽  
Jana Sperschneider ◽  
Benjamin Schwessinger ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
De Novo ◽  
Rust Fungus ◽  
Expression Patterns ◽  
Haplotype Diversity ◽  
Crown Rust ◽  
Puccinia Coronata ◽  
Small Subset ◽  
Nucleotide Polymorphisms ◽  
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 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.

scholarly journals Virulence of Oat Crown Rust in Brazil and Uruguay

Plant Disease ◽  
2005 ◽  
Vol 89 (8) ◽  
pp. 802-808 ◽  
Author(s):  
K. J. Leonard ◽  
J. A. Martinelli
Keyword(s):  
Avena Sativa ◽  
Western Siberia ◽  
Specific Resistance ◽  
The United States ◽  
Crown Rust ◽  
Puccinia Coronata ◽  
South American ◽  
Oat Crown Rust ◽  
High Virulence ◽  
Important Disease

Race-specific resistance to crown rust, the most important disease of oat (Avena sativa) in Bra-zil, often fails within a few years of use in Brazilian cultivars. Virulence of 144 isolates of Puccinia coronata from cultivated oat in Brazil in 1997 to 1999 and 36 isolates from Uruguay in 1994-95 and 1998 was tested on a set of 27 oat crown rust differentials lines, each with a different Pc gene for race-specific resistance. Frequencies of virulence and mean virulence complexity were compared among these five collections from Brazil and Uruguay as well as with mean virulence complexity for a collection of 17 isolates from cultivated oat in western Siberia in Russia. Virulence-avirulence for each of the 27 Pc genes was polymorphic in both Brazil and Uruguay. Virulence frequencies were similar for collections from Brazil in 1998 and 1999 and for the collection from Uruguay from 1998, but there were large differences between the 1997 collection and the 1998 and 1999 collections from Brazil. Mean virulence complexity in both Brazil and Uruguay was greater than reported in the United States and much greater than in the Russian collection of P. coronata. A large number of races of P. coronata were found, with no more than five isolates of any race found in a single year in Brazil or Uruguay. The high virulence complexity and great diversity of virulence polymorphisms in Brazil and Uruguay make it unlikely that race-specific resistance can be effective there even though the South American populations of P. coronata are apparently entirely asexual.

scholarly journals Transcriptome Analysis of Ramie (Boehmeria niveaL. Gaud.) in Response to Ramie Moth (Cocytodes coeruleaGuenée) Infestation

2016 ◽  
Vol 2016 ◽  
pp. 1-10 ◽  
Author(s):  
Liangbin Zeng ◽  
Airong Shen ◽  
Jia Chen ◽  
Zhun Yan ◽  
Touming Liu ◽  
...  
Keyword(s):  
Protein Function ◽  
Molecular Mechanisms ◽  
Defense Mechanism ◽  
Natural Fiber ◽  
De Novo ◽  
Average Length ◽  
Expression Patterns ◽  
Transcriptome Profiling ◽  
Cdna Libraries ◽  
Pcr Analysis

The ramie mothCocytodes coeruleaGuenée (RM) is an economically important pest that seriously impairs the yield of ramie, an important natural fiber crop. The molecular mechanisms that underlie the ramie-pest interactions are unclear up to date. Therefore, a transcriptome profiling analysis would aid in understanding the ramie defense mechanisms against RM. In this study, we first constructed two cDNA libraries derived from RM-challenged (CH) and unchallenged (CK) ramie leaves. The subsequent sequencing of the CH and CK libraries yielded 40.2 and 62.8 million reads, respectively. Furthermore,de novoassembling of these reads generated 26,759 and 29,988 unigenes, respectively. An integrated assembly of data from these two libraries resulted in 46,533 unigenes, with an average length of 845 bp per unigene. Among these genes, 24,327 (52.28%) were functionally annotated by predicted protein function. A comparative analysis of the CK and CH transcriptome profiles revealed 1,980 differentially expressed genes (DEGs), of which 750 were upregulated and 1,230 were downregulated. A quantitative real-time PCR (qRT-PCR) analysis of 13 random selected genes confirmed the gene expression patterns that were determined by Illumina sequencing. Among the DEGs, the expression patterns of transcription factors, protease inhibitors, and antioxidant enzymes were studied. Overall, these results provide useful insights into the defense mechanism of ramie against RM.

Assessment of virulence patterns in crown rust populations

1968 ◽  
Vol 46 (5) ◽  
pp. 613-617 ◽  
Author(s):  
George Fleischmann
Keyword(s):  
Crown Rust ◽  
Puccinia Coronata ◽  
Western Canada ◽  
Differential Host ◽  
Oat Crown Rust ◽  
Virulence Pattern ◽  
Continued Use ◽  
Race Identification

Two methods of determining the virulence pattern of oat crown rust, Puccinia coronata f. sp. avenae, populations collected in 1965, 1966, and 1967, in Eastern and Western Canada were compared. The results with a single-pustule isolate from each of 50 field collections were as accurate as those obtained with two single-pustule isolates from 100 or more field collections. The continued use of Bond and Ukraine as differential host varieties is of little value except for purposes of race identification, because they are attacked by most of the isolates.

scholarly journals Identification of the germination self-inhibitor from uredospores of the oat crown rust fungus.

1984 ◽  
Vol 48 (8) ◽  
pp. 2147-2148 ◽  
Author(s):  
Tetsu TSURUSHIMA ◽  
Tamio UENO ◽  
Hiroshi FUKAMI ◽  
Shigeyuki MAYAMA ◽  
Toshikazu TANI
Keyword(s):  
Rust Fungus ◽  
Crown Rust ◽  
Oat Crown Rust

scholarly journals Crown rust pathotypes determined on oats in the Czech Republic from 2004 to 2006 and reaction to oat cultivars

2008 ◽  
Vol 44 (No. 2) ◽  
pp. 60-65 ◽  
Author(s):  
H. Jiráková ◽  
A. Hanzalová
Keyword(s):  
Czech Republic ◽  
Resistance Genes ◽  
Virulence Genes ◽  
Resistance Breeding ◽  
Crown Rust ◽  
Puccinia Coronata ◽  
The Czech Republic ◽  
Oat Crown Rust ◽  
Oat Cultivars ◽  
High Diversity

The incidence of oat crown rust (Puccinia coronata var. avenae Fraser et Ledingham) pathotypes was recorded in the Czech Republic in 2004–2006. The virulence of collected 79 monopustule oat crown rust isolates was assessed on 23 differentials. High diversity was observed; the isolates possessed from 0 to 8 virulence genes. More than 80% of pathotypes were recorded only once. Pathotypes BLBG and BLBC were the most frequent. None of the tested isolates was virulent to resistance genes Pc39, Pc50, Pc52, Pc59, Pc62 and Pc68. Registered cultivars Avenuda, Dalimil, Auron, Isak were susceptible to the majority of pathotypes, cvs. Abel, Ardo, Atego, Azur, Neklan, Radius and Saul to all used pathotypes. Only the Czech cultivar Vok was resistant to all but four used pathotypes. Acquired data are useful for resistance breeding.

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