2020
DOI: 10.1093/gbe/evaa071
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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. stri… Show more

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Cited by 35 publications
(42 citation statements)
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“…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).…”
Section: Resultsmentioning
confidence: 94%
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“…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).…”
Section: Resultsmentioning
confidence: 94%
“…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).…”
Section: Methodsmentioning
confidence: 99%
“…4B) and PST-104E ( Fig. 4C) based on MUMmer / Assemblytics recalculated from the published primary contigs and haplotigs [17,18]. PST-DK0911 (Fig.…”
Section: Comparisons Between the Two Pst-130 Genomesmentioning
confidence: 99%
“…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.…”
Section: Introductionmentioning
confidence: 99%
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