A Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici Reveals High Interhaplotype Diversity

MBio
Benjamin SchwessingerJohn P Rathjen

Abstract

A long-standing biological question is how evolution has shaped the genomic architecture of dikaryotic fungi. To answer this, high-quality genomic resources that enable haplotype comparisons are essential. Short-read genome assemblies for dikaryotic fungi are highly fragmented and lack haplotype-specific information due to the high heterozygosity and repeat content of these genomes. Here, we present a diploid-aware assembly of the wheat stripe rust fungus Puccinia striiformis f. sp. tritici based on long reads using the FALCON-Unzip assembler. Transcriptome sequencing data sets were used to infer high-quality gene models and identify virulence genes involved in plant infection referred to as effectors. This represents the most complete Puccinia striiformis f. sp. tritici genome assembly to date (83 Mb, 156 contigs, N50 of 1.5 Mb) and provides phased haplotype information for over 92% of the genome. Comparisons of the phase blocks revealed high interhaplotype diversity of over 6%. More than 25% of all genes lack a clear allelic counterpart. When we investigated genome features that potentially promote the rapid evolution of virulence, we found that candidate effector genes are spatially associated with conserved genes commonly f...Continue Reading

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Citations

Nov 6, 2018·BioTechniques·Alistair R McTaggartBrenda D Wingfield
Dec 18, 2018·Molecular Plant Pathology·Lamprinos FrantzeskakisRalph Panstruga
Dec 5, 2019·Phytopathology·Guus Bakkeren, Les J Szabo
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Oct 21, 2020·Microbiological Research·Rajdeep JaswalT R Sharma

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Datasets Mentioned

BETA
SRX311905
SRX311918
SRX311920
SRX311917
SRX311915
SRX3191029
SRX3191043

Methods Mentioned

BETA
RNA-seq
PCR

Software Mentioned

EvidenceModeler
numpy
GMAP
MEM
Localizer
gff
DESeq2 R
matplotlib
jupyter
BWA

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