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 found in basidiomycetes. Yet, candidate effectors that lack an allelic counterpart are more distant from conserved genes than allelic candidate effectors and are less likely to be evolutionarily conserved within the P. striiformis species complex and Pucciniales. In summary, this haplotype-phased assembly enabled us to discover novel genome features of a dikaryotic plant-pathogenic fungus previously hidden in collapsed and fragmented genome assemblies. IMPORTANCE Current representations of eukaryotic microbial genomes are haploid, hiding the genomic diversity intrinsic to diploid and polyploid life forms. This hidden diversity contributes to the organism’s evolutionary potential and ability to adapt to stress conditions. Yet, it is challenging to provide haplotype-specific information at a whole-genome level. Here, we take advantage of long-read DNA sequencing technology and a tailored-assembly algorithm to disentangle the two haploid genomes of a dikaryotic pathogenic wheat rust fungus. The two genomes display high levels of nucleotide and structural variations, which lead to allelic variation and the presence of genes lacking allelic counterparts. Nonallelic candidate effector genes, which likely encode important pathogenicity factors, display distinct genome localization patterns and are less likely to be evolutionary conserved than those which are pres- ent as allelic pairs. This genomic diversity may promote rapid host adaptation and/or be related to the age of the sequenced isolate since last meiosis.
Bibliographical noteFunding Information:
We thank the following colleagues for technical advice: Ying Zhang, Sylvain Forêt, Marcin Adamski, Adam Taranto, and Megan McDonald. We thank Ashlea Grewar for technical assistance with rust multiplication. We thank the following colleagues for feedback on the manuscript: Adam Taranto, Megan McDonald, Sajid Ali, Annemarie Fejér Justesen, and Sambasivam Periyannan. We thank Teresa Neeman from the statistical consulting unit at ANU. We acknowledge support by the Genome Discovery Unit (GDU), which provided computing facilities. We thank Ashlea Grewar for technical assistance with rust multiplication.
The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under contract number DE-AC02-05CH11231. This research project was undertaken with the assistance of resources and services from the National Computational Infrastructure (NCI), which is supported by the Australian Government. B.S. was supported by a Human Frontiers Science Program long-term postdoctoral fellowship (LT000674/2012) and a Discovery Early Career research award (DE150101897). B.S. and J.P.R. were supported by a sequencing voucher from Bioplatforms Australia. J.S. is supported by a CSIRO OCE postdoctoral fellowship. R.F.P. acknowledges the generous support of Judith and David Coffey and family. R.F.P. and W.S.C. acknowledge the outstanding support of the Australian Grains Research and Development Corporation. M.F. is supported by the University of Minnesota Experimental Station USDA-NIFA Hatch/Figueroa project MIN-22-058, and M.E.M. is supported by a USDA-NIFA postdoctoral fellowship award (2017-67012-26117).
© 2018 Schwessinger et al.
- Plant pathogens