A Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus <italic toggle="yes">Puccinia striiformis</italic> f. sp. <italic toggle="yes">tritici</italic> Reveals High Interhaplotype Diversity
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 hapl...
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American Society for Microbiology
2018
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oai:doaj.org-article:e211b4aa07a740498d5f344358f41b322021-11-15T15:53:26ZA Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus <italic toggle="yes">Puccinia striiformis</italic> f. sp. <italic toggle="yes">tritici</italic> Reveals High Interhaplotype Diversity10.1128/mBio.02275-172150-7511https://doaj.org/article/e211b4aa07a740498d5f344358f41b322018-03-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.02275-17https://doaj.org/toc/2150-7511ABSTRACT 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 present 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.Benjamin SchwessingerJana SperschneiderWilliam S. CuddyDiana P. GarnicaMarisa E. MillerJennifer M. TaylorPeter N. DoddsMelania FigueroaRobert F. ParkJohn P. RathjenAmerican Society for MicrobiologyarticleDikaryonbasidiomycetesgenomicsplant pathogensMicrobiologyQR1-502ENmBio, Vol 9, Iss 1 (2018) |
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DOAJ |
| collection |
DOAJ |
| language |
EN |
| topic |
Dikaryon basidiomycetes genomics plant pathogens Microbiology QR1-502 |
| spellingShingle |
Dikaryon basidiomycetes genomics plant pathogens Microbiology QR1-502 Benjamin Schwessinger Jana Sperschneider William S. Cuddy Diana P. Garnica Marisa E. Miller Jennifer M. Taylor Peter N. Dodds Melania Figueroa Robert F. Park John P. Rathjen A Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus <italic toggle="yes">Puccinia striiformis</italic> f. sp. <italic toggle="yes">tritici</italic> Reveals High Interhaplotype Diversity |
| description |
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 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 present 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. |
| format |
article |
| author |
Benjamin Schwessinger Jana Sperschneider William S. Cuddy Diana P. Garnica Marisa E. Miller Jennifer M. Taylor Peter N. Dodds Melania Figueroa Robert F. Park John P. Rathjen |
| author_facet |
Benjamin Schwessinger Jana Sperschneider William S. Cuddy Diana P. Garnica Marisa E. Miller Jennifer M. Taylor Peter N. Dodds Melania Figueroa Robert F. Park John P. Rathjen |
| author_sort |
Benjamin Schwessinger |
| title |
A Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus <italic toggle="yes">Puccinia striiformis</italic> f. sp. <italic toggle="yes">tritici</italic> Reveals High Interhaplotype Diversity |
| title_short |
A Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus <italic toggle="yes">Puccinia striiformis</italic> f. sp. <italic toggle="yes">tritici</italic> Reveals High Interhaplotype Diversity |
| title_full |
A Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus <italic toggle="yes">Puccinia striiformis</italic> f. sp. <italic toggle="yes">tritici</italic> Reveals High Interhaplotype Diversity |
| title_fullStr |
A Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus <italic toggle="yes">Puccinia striiformis</italic> f. sp. <italic toggle="yes">tritici</italic> Reveals High Interhaplotype Diversity |
| title_full_unstemmed |
A Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus <italic toggle="yes">Puccinia striiformis</italic> f. sp. <italic toggle="yes">tritici</italic> Reveals High Interhaplotype Diversity |
| title_sort |
near-complete haplotype-phased genome of the dikaryotic wheat stripe rust fungus <italic toggle="yes">puccinia striiformis</italic> f. sp. <italic toggle="yes">tritici</italic> reveals high interhaplotype diversity |
| publisher |
American Society for Microbiology |
| publishDate |
2018 |
| url |
https://doaj.org/article/e211b4aa07a740498d5f344358f41b32 |
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