RT Journal Article
SR Electronic
T1 A chromosome-level, fully phased genome assembly of the oat crown rust fungus <em>Puccinia coronata</em> f. sp. <em>avenae</em>: a resource to enable comparative genomics in the cereal rusts
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2022.01.26.477636
DO 10.1101/2022.01.26.477636
A1 Eva C. Henningsen
A1 Tim Hewitt
A1 Sheshanka Dugyala
A1 Eric S. Nazareno
A1 Erin Gilbert
A1 Feng Li
A1 Shahryar F. Kianian
A1 Brian J. Steffenson
A1 Peter N. Dodds
A1 Jana Sperschneider
A1 Melania Figueroa
YR 2022
UL http://biorxiv.org/content/early/2022/01/28/2022.01.26.477636.abstract
AB 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 non-haploid 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 two nuclear genomes of the oat crown rust pathogen, Puccinia coronata f. sp. avenae (Pca). This resource complements two previous 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 three Puccinia species are syntenous and that chromosomal size variations are primarily due to differences in repeat element content.Competing Interest StatementThe authors have declared no competing interest.