Pangenomes evolve in prokaryotes as a result of promiscuous horizontal transfer of genetic material and other rapid evolutionary processes. Although eukaryotes are generally under more restrictive evolutionary constraints than prokaryotes (e.g. lower levels of HGT), pangenomic structure has also been identified in plant, algal and fungal species. A number of methodologies for pangenome analysis have been published in recent years, but these methodologies are generally specifically-intended or optimized for prokaryotes. We have developed a software pipeline based around the previously-published PanOCT method of pangenome construction with additional pre- and post-processing methodologies tailored for eukaryote pangenome analysis. We have previously used this pipeline to analyze the pangenomes of model fungal species such as Saccharomyces cerevisiae, and we are currently testing our pipeline by constructing and analyzing the pangenome of the industrially-relevant yeast species Yarrowia lipolytica. Analysis of fungal pangenomes shows that core and accessory eukaryotic species genomes encompass a variety of phenotypes and suggest that gene duplication events play a larger role in eukaryote pangenome evolution than HGT.

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