A chromosome-level, fully phased genome assembly of the oat crown rust fungus Puccinia coronata f. sp. avenae: a resource to enable comparative genomics in the cereal rusts

被引:13
作者
Henningsen, Eva C. [1 ,2 ,6 ]
Hewitt, Tim [2 ]
Dugyala, Sheshanka [1 ]
Nazareno, Eric S. [1 ]
Gilbert, Erin [3 ]
Li, Feng [4 ]
Kianian, Shahryar F. [1 ,5 ]
Steffenson, Brian J. [1 ]
Dodds, Peter N. [2 ]
Sperschneider, Jana [2 ]
Figueroa, Melania [2 ]
机构
[1] Univ Minnesota, Dept Plant Pathol, St Paul, MN 55108 USA
[2] CSIRO, Agr & Food, GPO Box 1700, Canberra, ACT 2601, Australia
[3] Bayer CropSci, Creve Coeur, MO 63141 USA
[4] eGenesis Inc, Cambridge, MA 02139 USA
[5] USDA ARS, Cereal Dis Lab, St Paul, MN 55108 USA
[6] Australian Natl Univ, Res Sch Biol, Canberra, ACT 2601, Australia
基金
澳大利亚研究理事会;
关键词
oat; rust; virulence; genome; chromosome; isolate Pca203; HI-C; VICTORIN; RESISTANCE; VIRULENCE; ALIGNMENT; PROTEIN; FORMAT; TOXIN;
D O I
10.1093/g3journal/jkac149
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
Advances in sequencing technologies as well as development of algorithms and workflows have made it possible to generate fully phased genome references for organisms with nonhaploid genomes such as dikaryotic rust fungi. To enable discovery of pathogen effectors and further our understanding of virulence evolution, we generated a chromosome-scale assembly for each of the 2 nuclear genomes of the oat crown rust pathogen, Puccinia coronata f. sp. avenae (Pca). This resource complements 2 previously released partially phased genome references of Pca, which display virulence traits absent in the isolate of historic race 203 (isolate Pca203) which was selected for this genome project. A fully phased, chromosome-level reference for Pca203 was generated using PacBio reads and Hi-C data and a recently developed pipeline named NuclearPhaser for phase assignment of contigs and phase switch correction. With 18 chromosomes in each haplotype and a total size of 208.10 Mbp, Pca203 has the same number of chromosomes as other cereal rust fungi such as Puccinia graminis f. sp. tritici and Puccinia triticina, the causal agents of wheat stem rust and wheat leaf rust, respectively. The Pca203 reference marks the third fully phased chromosome-level assembly of a cereal rust to date. Here, we demonstrate that the chromosomes of these 3 Puccinia species are syntenous and that chromosomal size variations are primarily due to differences in repeat element content.
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页数:10
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