De Novo Assembly and Phasing of Dikaryotic Genomes from Two Isolates of Puccinia coronata f. sp. avenae , the Causal Agent of Oat Crown Rust
| Autor: | Cory D. Hirsch, Benjamin Schwessinger, Marisa E. Miller, Jana Sperschneider, John P. Rathjen, Jennifer M. Taylor, Castle Raley, Robert F. Park, Vahid Omidvar, Shahryar F. Kianian, Jonathan M. Palmer, Diana P. Garnica, Narayana M. Upadhyaya, Melania Figueroa, Ying Zhang, Peter N. Dodds |
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| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
Virulence Microbiology Genome Structural variation 03 medical and health sciences Puccinia coronata Virology Genotype genomics oat Genome size Gene Genetics biology Haplotype food and beverages biology.organism_classification QR1-502 virulence rust fungi 030104 developmental biology Genetic marker Research Article effectors Reference genome |
| Zdroj: | mBio, Vol 9, Iss 1 (2018) mBio mBio, Vol 9, Iss 1, p e01650-17 (2018) |
| ISSN: | 2150-7511 2161-2129 |
| DOI: | 10.1128/mbio.01650-17 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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