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.
readme_scripts
File describing the scripts included in this Dryad accession
01_count_SNPs_extended_version
python script for counting SNPs
001_get_longest_transcript
Python script for identifying longest transcripts
002_get_orfs_from_longest_seqs
Python script for retrieving open reading frames from longest Trinity transcripts per component
02_merge_SNP_counts_w_lens
Python script for performing merge of counts and lengths files
03_collapse_to_longest
Python script for collapsing a set of transcripts to only the longest single splicing isoforms
003_get_best_evalues
Python script for identifying the best blast e-values from a set of multiple blast results for a single transcript
004_add_taxa_to_abundance_table
Python script to link taxon lineage information with an eXpress gene abundance output
04_add_taxon_to_SNPs
Python script to annotate a transcript SNP table with taxon information from a blast result
05_collapse_to_best_evalue
Python 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_targets
Python script to strip out pre-identified targets from a variant call format file
all_master_work_wSNPs
An 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 paper
edgeR_mar2016
R script used to identify differentially expressed genes between samples coded as Bryoria tortuosa and those coded as B. fremontii
39Dikary.349loci.CONCAT
Protein fasta file for 349 loci used in phylogenomic analysis; see readme_align file
39Dikary.58loci.CONCAT
Phylip file used for dating the phylogenomic tree of fungi
A_ITS_all_red_mafft_replaced_cut
see readme_align.txt
A_ITS_all_red_mafft_replaced
see readme_align.txt
B_SSU_all_red_mafft_replaced_cut
see readme_align.txt
B_SSU_all_red_mafft_replaced
see readme_align.txt
C_LSU_all_red_mafft_replaced_cut
see readme_align.txt
C_LSU_all_red_mafft_replaced
see readme_align.txt
concat_cut
see readme_align.txt
Fig2A_FigS3A_Dikary39.NOcal_lnrootP_sample.chronogram
Tree file underlying Fig2A. See readme_align.txt
Fig2B_Fig3B_RAxML_bipartitions.cystos_130316_correct_names
Tree file underlying Fig. 2B. See readme_align.txt
FigS4_Dikary39.1calConcat_lnrootP_sample.chronogram
Tree file underlying Fig. S4. See readme_align.txt
FigS5_Dikary39.4cal_lnrootP_sample.chronogram
Tree file underlying Fig. S5. See readme_align.txt
FigS12_RAxML_bipartitions.cystosITS_120316_correct_names.test
Tree file underlying Fig. S12. See readme_align.txt
FigS13_RAxML_bipartitions.cystosLSU_120316_correct_names.test
Tree file underlying Fig. S13. See readme_align.txt
FigS14_RAxML_bipartitions.cystosSSU_120316_correct_names.test
Tree file underlying Fig. S14. See readme_align.txt
MLSuperMatrix.wIC.75BTSP.CONSENSE
Alignment used for internode uncertainty analysis
SuperTREE_IC.MRE.39tax.58loci.CON75percent
Tree file underlying internode certainty analysis
readme_align
ReadMe file for all alignments and tree files associated with this submission.