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

Eva C Henningsen, Tim Hewitt, Sheshanka Dugyala, Eric S Nazareno, Erin Gilbert, Feng Li, Shahryar F. Kianian, Brian J. Steffenson, Peter N. Dodds, Jana Sperschneider, Melania Figueroa

Research output: Contribution to journalArticlepeer-review

10 Scopus citations

Abstract

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.

Original languageEnglish (US)
Article numberjkac149
JournalG3: Genes, Genomes, Genetics
Volume12
Issue number8
DOIs
StatePublished - Aug 2022

Bibliographical note

Funding Information:
This work was supported by PepsiCo Inc. and the USDA-ARS/The University of Minnesota Standard Cooperative Agreement (3002-11031-00053115). ECH was partially supported by a scholarship from the College of Food, Agriculture, and Natural Resource Science at the University of Minnesota. TH was supported by a CSIRO Research Office Postdoctoral Fellowship. JS was supported by an ARC Discovery Early Career Researcher Award (DE190100066) Fellowship.

Publisher Copyright:
© 2022 Genetics Society of America. All rights reserved.

Keywords

  • chromosome
  • genome
  • isolate Pca203
  • oat
  • rust
  • virulence

PubMed: MeSH publication types

  • Journal Article
  • Research Support, Non-U.S. Gov't

Fingerprint

Dive into the research topics of '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'. Together they form a unique fingerprint.

Cite this