Honors College Thesis
 

Hi-C genome assembly of the ectomycorrhizal fungus Rhizopogon salebrosus

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https://ir.library.oregonstate.edu/concern/honors_college_theses/2r36v672h

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  • Rhizopogon salebrosus is an abundant ectomycorrhizal fungus common throughout Western North America that forms mutualistic partnerships with Pinus species. Studied for its systematics, use in sapling nurseries, post-fire seedling establishment, and unique evolutionary history, R. salebrosus holds many secrets within its genome. This thesis aims to characterize the mating system, genomic architecture, and functional capabilities of this dikaryotic fungus. Consistent with the life cycles of the Basidiomycota, fluorescence microscopy revealed that R. salebrosus is a dikaryon with two nuclei per hyphal compartment. By iteratively improving the genome using Nanopore, Illumina, and Hi-C sequencing, we were able to achieve a highly contiguous assembly of eleven chromosome-level linkage groups. Hi-C interaction maps reveal that seven (1, 2, 3, 5, 6, 8, and 10) of the linkage groups have comparable interactions. However, linkage group 4 displayed significantly diminished Hi-C interactions with linkage groups 7, 9, and 11. We identified MAT-A and MAT-B on separate linkage groups, LGs 2 and 1, respectively, thus resolving the mating system of R. salebrosus to be bifactorial/tetrapolar. Phasing the genome using Nanopore sequences resulted in putative haplotypes of MAT-A and MAT-B. Using Hi-C data, we propose a heterokaryon model of the dikaryon with universal and variably present chromosomes.
  • Keywords: Ectomycorrhizal, fungi, Hi-C, Reference genome, phasing, Mating
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