Graduate Thesis Or Dissertation

Genome Organization in the Ectomycorrhizal Truffle Rhizopogon vesiculosus

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  • Rhizopogon vesiculosus is a common ectomycorrhizal (EM) symbiont of Pseudotusga menziesii (Douglas-fir) in the coast range of the Pacific Northwest. The species has been studied for its systematics, genet size, population structure, and competitive ability in several field and experimental studies. This thesis seeks to provide a more thorough characterization of the genome of R. vesiculosus using bioinformatic analyses with the objective of improving our understanding of its genomic architecture and to obtain a more robust reference for future studies on Rhizopogon. The analysis was facilitated by Chromatin conformation capture assay (Hi-C) sequencing which enabled the assembly of our previous draft genome into 10 chromosome level linkage groups. Kingdom wide comparative genomic studies in fungi suggest that there are particular signatures in ectomycorrhizal genomes including an increase of transposable elements (TE) and lineage specific small secreted proteins (SSPs). This observation was true for R. vesiculosus as we mined the genome for TEs and SSPs. We sought to classify the TEs, but found that a large proportion of them had no hits to curated TE databases. The abundance of SSPs fit the profile of other EM fungi with approximately 200 SSPs and half of them being species specific. We identified species specific genes (SSG) and orthologous clusters shared with the sister genus Suillus, along with clusters unique to genus Rhizopogon and R. subgenus Villosuli, as well as the mating loci and centromeric regions. The long-range contiguity allowed us to map all these elements together with single nucleotide polymorphisms (SNPs). We hypothesized that the SSPs, TE, and lineage specific genes would cluster more around the ends of our linkage groups where recombination rate tends to be elevated, and that the centromeres would be highly enriched for TEs, but the pattern turned out to be more complex. Centromeres were regional in nature, comprising an average length of 40,000 bp and a gene density similar to the remainder of the genome. Most chromosomes contained regions that were enriched for species specific genes, but these regions were not clustered towards the ends of linkage groups. However genome mapping revealed higher SNP densities in TEs and species specific genes, in contrast to reduced levels in the orthologs shared with Suillus, suggestive of a “two-speed-genome” with heterogeneous rates of evolution. Moreover, the transition/transversion ratio was found to be significantly higher in TEs, which we interpreted as a possible signature of genome defense mechanisms, highlighting the many opposing evolutionary forces that a genome must balance. This work represents a significant step forward in the genomics of Rhizopogon, and we have demonstrated the utility of Hi-C sequencing for improving assemblies of dikaryotic fungi. A number of bioinformatics pipelines were developed or refined, and these may serve to streamline future Hi-C analysis of other genomes.
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