Supplemental Material for Bensasson et al., 2018

Bensasson_etalTableS1.xlsx: a table in excel format that summarizes the results of the growth tests from \citet{kurtzman_chapter_2011-16} applied to the three oak strains (NCYC 4144, NCYC 4145, and NCYC 4146) and to the type strain (NCYC 597). Species results from \citep{lachance_chapter_2011-5} are also summarized. For each test, the following abbreviations are used: +, positive; l, delayed positive; s, slow positive; w, weakly positive; -, negative; v, variable.Bensasson_etalSupp.pdf: A pdf file with Supplemental Results, Table S2 and Figures S1 to S8. The Supplemental Results summarize our validation of methods for determining ploidy.Bensasson_etalTableS3.tsv : a table in text format with tab separated values summarizing heterozygosity analyses for every strain. This includes exact counts of high quality heterozygous base calls (highQualityHetCount); the total length of high quality sequence (highQualityLength; bases with a phred-scaled quality score over 40); the proportion of high quality heterozygous sites; the length of regions that have undergone Loss of Heterozygosity (LOHlength) assessed in 100 kb windows; heterozygosity analysis after excluding LOH regions, centromeres and annotated repeats (annotationLohFilteredHetCount, annotationLohFilteredLength, annotationLohFilteredHeterozygosity); heterozygosity analysis after excluding LOH regions, centromeres and annotated repeats, and regions with more than double the expected read depth (depthFilteredHetCount, depthFilteredLength, depthFilteredHeterozygosity); heterozygosity analysis at 948,860 nucleotide sites that are common to all strains (sitesIn950kbHetCount, sitesIn950kbLength, sitesIn950kbHeterozygosity).Supplemental data in the form of whole chromosome alignments are also available from https://github.com/bensassonlab/data (DOI: 10.5281/zenodo.1488207). Perl scripts are available at https://github.com/bensassonlab/scripts (DOI: 10.5281/zenodo.1488147). The type strain and C. albicans strains isolated from oak are available from the National Collection of Yeast Cultures in the U.K.