Chromosomal assembly and analyses of genome-wide recombination rates in the forest pathogenic fungus Armillaria ostoyae

Recombination shapes the evolutionary trajectory of populations and plays an important role in the faithful transmission of chromosomes during meiosis. Levels of sexual reproduction and recombination are important properties of host-pathogen interactions because the speed of antagonistic co-evolutio...

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Bibliographic Details
Published in:Heredity 2020-06, Vol.124 (6), p.699-713
Main Authors: Heinzelmann, Renate, Rigling, Daniel, Sipos, György, Münsterkötter, Martin, Croll, Daniel
Format: Article
Language:English
Subjects:
Armillaria ostoyae
Chromosomes
Conifers
Deoxyribonucleic acid
DNA
DNA sequencing
Fungi
Genetic crosses
Genetic diversity
Genomes
Meiosis
Nucleotides
Pathogens
Pectin
Polymorphism
Population studies
Progeny
Recombination
Recombination hot spots
Reproduction (biology)
Sexual reproduction
Single-nucleotide polymorphism
Telomeres
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Summary:Recombination shapes the evolutionary trajectory of populations and plays an important role in the faithful transmission of chromosomes during meiosis. Levels of sexual reproduction and recombination are important properties of host-pathogen interactions because the speed of antagonistic co-evolution depends on the ability of hosts and pathogens to generate genetic variation. However, our understanding of the importance of recombination is limited because large taxonomic groups remain poorly investigated. Here, we analyze recombination rate variation in the basidiomycete fungus Armillaria ostoyae, which is an aggressive pathogen on a broad range of conifers and other trees. We analyzed a previously constructed, dense genetic map based on 198 single basidiospore progeny from a cross. Progeny were genotyped at a genome-wide set of single-nucleotide polymorphism (SNP) markers using double digest restriction site associated DNA sequencing. Based on a linkage map of on 11,700 SNPs spanning 1007.5 cM, we assembled genomic scaffolds into 11 putative chromosomes of a total genome size of 56.6 Mb. We identified 1984 crossover events among all progeny and found that recombination rates were highly variable along chromosomes. Recombination hotspots tended to be in regions close to the telomeres and were more gene-poor than the genomic background. Genes in proximity to recombination hotspots were encoding on average shorter proteins and were enriched for pectin degrading enzymes. Our analyses enable more powerful population and genome-scale studies of a major tree pathogen.
ISSN:0018-067X
1365-2540
DOI:10.1038/s41437-020-0306-z