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.

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  • Name: Schwessinger, Benjamin, Type: Corresponding Author,
  • Name: Chen, Yan-Jun, Type: Corresponding Author,
  • Name: Tien, Richard, Type: Corresponding Author,
  • Name: Vogt, Josef Korbinian, Type: Corresponding Author,
  • Name: Sperschneider, Jana, Type: Corresponding Author,
  • Name: Nagar, Ramawatar, Type: Corresponding Author,
  • Name: McMullan, Mark, Type: Corresponding Author,
  • Name: Sicheritz-Ponten, Thomas, Type: Corresponding Author,
  • Name: Sørensen, Chris K, Type: Corresponding Author,
  • Name: Hovmøller, Mogens Støvring, Type: Corresponding Author,
  • Name: Rathjen, John P, Type: Corresponding Author,
  • Name: Justesen, Annemarie Fejer, Type: Corresponding Author,
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Article Is Open Access true
Article License Type cc-by
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Citation Report https://scite.ai/reports/10.1093/gbe/evaa071
DFW Organisation EI
DFW Work Package 2
DOI 10.1093/gbe/evaa071
Date Last Updated 2021-09-10T12:22:01.392789
Evidence oa journal (via doaj)
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Journal Is Open Access true
Open Access Status gold
PDF URL https://academic.oup.com/gbe/article-pdf/12/5/597/33302188/evaa071.pdf
Publisher URL https://doi.org/10.1093/gbe/evaa071