10.5061/DRYAD.7QV72
Spribille, Toby
Nawi Graz
Tuovinen, Veera
Uppsala University
Resl, Philipp
Nawi Graz
Vanderpool, Dan
University of Montana
Wolinski, Heimo
BioTechMed-Graz
Aime, M. Catherine
Purdue University
Schneider, Kevin
Nawi Graz
Stabentheiner, Edith
Nawi Graz
Toome-Heller, Merje
Purdue University
Thor, Göran
Swedish University of Agricultural Sciences
Mayrhofer, Helmut
Nawi Graz
Johannesson, Hanna
Uppsala University
McCutcheon, John P.
University of Montana
Data from: Basidiomycete yeasts in the cortex of ascomycete macrolichens
Dryad
dataset
2016
Ascomycota
Lecanoromycetes
Bryoria
Microbiology
Basidiomycota
Cystobasidiomycetes
Symbiosis
Cyphobasidiales
lichens
fluorescent imaging
Parmeliaceae
Holocene
Letharia
2016-08-02T18:34:37Z
2016-08-02T18:34:37Z
en
https://doi.org/10.1126/science.aaf8287
22083250 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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_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.
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