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

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 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) that 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.

Haplotype-phased and chromosome-level genome assembly ofPuccinia polysora, a giga-scale fungal pathogen causing southern corn rust

“…The low abundance of PCWDEs and transcription factors in P. polysora as well as other Puccinia species was in line with the above pattern (Figure 5) (Duplessis et al 2011). Despite the massive TE proliferation, P. polysora shows high gene synteny with other Puccinia species (Figure 5), as suggested by comparing BUSCO genes in another study (Henningsen et al 2022).…”

“…Compared to its close relatives, P. polysora has experienced a large genome expansion, with its genome size of 1.71 Gbp equivalent to 7–10 times of four other Puccinia species assemblies ( Pst -104E, Pgt 21-0, Pt 76, and Pca 203) (Schwessinger et al 2018; Li et al 2019; Wu et al 2021; Henningsen et al 2022). Based on a limited set of rust species, Tavares et al (2014) inferred that rusts infecting monocot Poaceae hosts have considerably smaller genomes than rusts infecting dicot Fabaceae hosts (556.6 Mbp on average).…”

“…The assembly pipeline we illustrated in Figure 1 will inform future genome assembly for other dikaryotic or non-haploid organisms. Although NuclearPhaser has been developed and successfully applied in three rust other species ( Pgt 21-0, Pt 76 and Pca 203) (Li et al 2019; Duan et al 2022; Henningsen et al 2022), whether it can handle large genome size (> 1 G) needs to be further confirmed.…”

“…The high quality of P. polysora genome provides the opportunity for comparison with other chromosome-level references, such as wheat stem rust ( Pgt 21-0), wheat left rust ( Pt 76) and oat crown rust ( Pca 203) (Li et al 2019; Duan et al 2022; Henningsen et al 2022). Syntenic gene pairs among four Puccinia species were identified using the MCSCAN toolkit (Wang et al 2012).…”

“…A recent pipeline, NuclearPhaser, was designed to phase two haplotypes from the diploid genome using Hi-C data (Duan et al 2022). Three Puccinia species, causing wheat or oat rust have been assembled to a fully-phased and chromosome level using NuclearPhaser (Li et al 2019; Duan et al 2022; Henningsen et al 2022). Unlike wheat-like rusts, which have been studied extensively, the genome information of corn rust pathogens is largely unknown.…”