DOI: 10.5061/dryad.7qv72
title: Data from: Basidiomycete yeasts in the cortex of ascomycete macrolichens

description: For over 140 years, lichens have been regarded as a symbiosis between a
 single fungus, usually an ascomycete, and a photosynthesizing partner.
 Other fungi have long been known to occur as occasional parasites or
 endophytes, but the one lichen–one fungus paradigm has seldom been
 questioned. Here we show that many common lichens are composed of the
 known ascomycete, the photosynthesizing partner, and, unexpectedly,
 specific basidiomycete yeasts. These yeasts are embedded in the cortex,
 and their abundance correlates with previously unexplained variations in
 phenotype. Basidiomycete lineages maintain close associations with
 specific lichen species over large geographical distances and have been
 found on six continents. The structurally important lichen cortex, long
 treated as a zone of differentiated ascomycete cells, appears to
 consistently contain two unrelated fungi.
description: readme_scriptsFile describing the scripts included in this Dryad accession01_count_SNPs_extended_versionpython script for counting SNPs001_get_longest_transcriptPython script for identifying longest transcripts002_get_orfs_from_longest_seqsPython script for retrieving open reading frames from longest Trinity transcripts per component02_merge_SNP_counts_w_lensPython script for performing merge of counts and lengths files03_collapse_to_longestPython script for collapsing a set of transcripts to only the longest single splicing isoforms003_get_best_evaluesPython script for identifying the best blast e-values from a set of multiple blast results for a single transcript004_add_taxa_to_abundance_tablePython script to link taxon lineage information with an eXpress gene abundance output04_add_taxon_to_SNPsPython script to annotate a transcript SNP table with taxon information from a blast result05_collapse_to_best_evaluePython script to identify the blast result with the highest e-value from a set of multiple blast results on a single contig (different input data formats)06_filter_vcf_for_targetsPython script to strip out pre-identified targets from a variant call format fileall_master_work_wSNPsAn Excel spreadsheet showing all blast-annotated non-redundant transcripts with eXpress abundance data for each transcriptome and a final column showing which of these transcripts contain passing SNPs based on analyses described in the paperedgeR_mar2016R script used to identify differentially expressed genes between samples coded as Bryoria tortuosa and those coded as B. fremontii39Dikary.349loci.CONCATProtein fasta file for 349 loci used in phylogenomic analysis; see readme_align file39Dikary.58loci.CONCATPhylip file used for dating the phylogenomic tree of fungiA_ITS_all_red_mafft_replaced_cutsee readme_align.txtA_ITS_all_red_mafft_replacedsee readme_align.txtB_SSU_all_red_mafft_replaced_cutsee readme_align.txtB_SSU_all_red_mafft_replacedsee readme_align.txtC_LSU_all_red_mafft_replaced_cutsee readme_align.txtC_LSU_all_red_mafft_replacedsee readme_align.txtconcat_cutsee readme_align.txtFig2A_FigS3A_Dikary39.NOcal_lnrootP_sample.chronogramTree file underlying Fig2A. See readme_align.txtFig2B_Fig3B_RAxML_bipartitions.cystos_130316_correct_namesTree file underlying Fig. 2B. See readme_align.txtFigS4_Dikary39.1calConcat_lnrootP_sample.chronogramTree file underlying Fig. S4. See readme_align.txtFigS5_Dikary39.4cal_lnrootP_sample.chronogramTree file underlying Fig. S5. See readme_align.txtFigS12_RAxML_bipartitions.cystosITS_120316_correct_names.testTree file underlying Fig. S12. See readme_align.txtFigS13_RAxML_bipartitions.cystosLSU_120316_correct_names.testTree file underlying Fig. S13. See readme_align.txtFigS14_RAxML_bipartitions.cystosSSU_120316_correct_names.testTree file underlying Fig. S14. See readme_align.txtMLSuperMatrix.wIC.75BTSP.CONSENSEAlignment used for internode uncertainty analysisSuperTREE_IC.MRE.39tax.58loci.CON75percentTree file underlying internode certainty analysisreadme_alignReadMe file for all alignments and tree files associated with this submission.