Distinct Life Histories Impact Dikaryotic Genome Evolution in the Rust Fungus Puccinia striiformis Causing Stripe Rust in Wheat

Abstract

Stripe rust of wheat, caused by the obligate biotrophic fungus Puccinia striiformis f.sp. tritici, is a major threat to wheat production worldwide with an estimated yearly loss of US $1 billion. The recent advances in long-read sequencing technologies and tailored-assembly algorithms enabled us to disentangle the two haploid genomes of Pst. This provides us with haplotype-specific information at a whole-genome level. Exploiting this novel information, we perform whole-genome comparative genomics of two P. striiformis f.sp. tritici isolates with contrasting life histories. We compare one isolate of the old European lineage (PstS0), which has been asexual for over 50 years, and a Warrior isolate (PstS7 lineage) from a novel incursion into Europe in 2011 from a sexual population in the Himalayan region. This comparison provides evidence that long-term asexual evolution leads to genome expansion, accumulation of transposable elements, and increased heterozygosity at the single nucleotide, structural, and allele levels. At the whole-genome level, candidate effectors are not compartmentalized and do not exhibit reduced levels of synteny. Yet we were able to identify two subsets of candidate effector populations. About 70% of candidate effectors are invariant between the two isolates, whereas 30% are hypervariable. The latter might be involved in host adaptation on wheat and explain the different phenotypes of the two isolates. Overall, this detailed comparative analysis of two haplotype-aware assemblies of P. striiformis f.sp. tritici is the first step in understanding the evolution of dikaryotic rust fungi at a whole-genome level.

Austropuccinia psidii, causing myrtle rust, has a gigabase-sized genome shaped by transposable elements

“…Three primary scaffolds; APSI_P012 (37 965 047 bp), APSI_P025 (8 512 731 bp), APSI_P027 (3 316 254 bp), have telomeric regions at both the start and end indicating potential complete chromosomes. The final hexamer repeat numbers and lengths (Table 2) indicate extraordinarily long telomeres, over 1000 bp in length for 24 of the scaffolds, when compared to other fungi which have telomeres in the size range of 100-300 bp (Lucía et al 2010; Pérez et al 2009; Schwessinger et al 2020; Sperschneider et al 2020). Telomerase related transcripts were expressed, including telomerase reverse transcriptase (RNA-dependent DNA polymerase) and telomerase ribonucleoprotein complex -RNA binding domains (PF12009 and PF00078 protein ID: APSI_P017.12297.t3 and APSI_H002.12793.t2).…”

“…Detailed description of the repeat annotation and analysis can be found in the associated github repository https://github.com/Team-Schwessinger/TE_myrtle_rust. Most of the RIP index analysis, GC-content and CG:GC depletion analysis of TEs was inspired by previous publications (Schwessinger et al 2020). We identified AT-rich regions using OcculterCut (Testa et al 2016).…”

A haplotype-phased genome of wheat stripe rust pathogen Puccinia striiformis f. sp. tritici, race PST-130 from the Western USA

“…4B) and PST-104E ( Fig. 4C) based on MUMmer / Assemblytics recalculated from the published primary contigs and haplotigs [17,18]. PST-DK0911 (Fig.…”

“…With the use of PacBio long reads and new assemblers [16], it became possible to generate separate contigs for maternal and paternal alleles, or in the case of the dikaryotic Pst, the two haploid genomes (phasing). Two additional Pst races, PST-104E [17] and DK0911 [18], have been sequenced using these new tools and have their genomes phased. PST-104E is the Australian founder pathotype of Pst collected in 1982 (before the appearance of the new virulent races), and belongs to the European clonal lineage PstS0.…”

“…Its genome has been assembled into a primary assembly of 83 Mb (156 contigs) and a secondary or 'haplotig' assembly of 73 Mb (475 secondary haplotype contigs or haplotigs). PST-DK0911 was collected in Denmark in 2011 and belongs to the new more virulent Pst race group (also known as "Warrior"), which is different from previous European races and similar to isolates from the near-Himalayan region [18]. The genome of this race was assembled into a primary assembly of 74.4 Mb (94 contigs) and a more fragmented 'haplotig' assembly of 52 Mb (1,176 haplotigs).…”