3 files

Supplemental Material for Bensasson et al., 2018

posted on 21.11.2018 by Douda Bensasson, Jo Dicks, Christopher Bond, Adam Elliston, Ian Roberts, Stephen A. James
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.


Article title

Diverse Lineages of Candida albicans Live on Old Oaks

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