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Mycological Progress

, Volume 17, Issue 3, pp 333–341 | Cite as

Phylogenomics of Bartheletia paradoxa reveals its basal position in Agaricomycotina and that the early evolutionary history of basidiomycetes was rapid and probably not strictly bifurcating

  • Bagdevi Mishra
  • Young-Joon Choi
  • Marco Thines
Original Article

Abstract

The higher level phylogeny of fungi has been addressed in previous studies, but for those analyses, either taxon sampling or gene sampling was low, or some basal lineages important for the inference of basidiomycete phylogeny were lacking. Here, a phylogenomic analysis based on highly conserved genes and including the enigmatic species Bartheletia paradoxa from Ginkgo biloba is presented. While phylogenetic analyses including also less conserved parts of core eukaryotic genes yielded a basal position for the extremophile genus Wallemia with low support, an exclusion of highly variable parts of these genes suggested Bartheletia paradoxa as the most basal member of the Agaricomycotina, but again with low support. Network analyses suggest a network-like evolution at the base of the Basidiomycota, supported by phylogenies based on single genes and gene clusters with shared topology. When further removing noise by removing poorly resolving genes, strong but not maximum support was obtained for Bartheletia paradoxa being the sister lineage to all other Agaricomycotina. We speculate that the lack of support for the early splits in Agaricomycotina and Basidiomycota can probably be explained by rapid radiation, linked to major evolutionary developments, such as, in the case of Basidiomycota, the advent of basidia in the last common ancestor.

Keywords

ABBA/BABA testing Basidiomycota Core eukaryotic genes Fungi Genomes Phylogenetic network Phylogeny 

Notes

Acknowledgements

Funding support by the LOEWE excellence initiative of the federal state of Hessen in the framework of the cluster for Integrative Fungal Research (IPF) is gratefully acknowledged. The authors are indebted to Rahul Sharma for providing gene orthologs based on the unpublished genome of Bartheletia paradoxa and to Franz Oberwinkler for contributing discussions and for input on the manuscript. This manuscript is dedicated to the memory of Robert Bauer, who initiated the study but did not live to see its conclusion.

Supplementary material

11557_2017_1349_MOESM1_ESM.pptx (4.9 mb)
ESM 1 Figure S1. Maximum likelihood tree of 67 highly conserved orthologous loci from 51 fungal species. Support values from 1000 bootstrap replicates are given as branch labels. Figure S2. Minimum evolution tree of 67 highly conserved orthologous loci from 51 fungal species. Support values based on the Shimodaira–Hasegawa (SH) test are given as branch labels. Figure S3. Bayesian inference-based tree of 67 highly conserved orthologous loci from 51 fungal species. Posterior probability values are given as branch labels. Figure S4. Bayesian species densi-tree inferred from 67 highly conserved orthologous loci from 51 fungal species. Figure S5. Maximum likelihood-based tree of eight orthologous loci from 51 fungal species. These eight loci each group Ustilaginomycotina and Pucciniomycotina together. Support values from 1000 bootstrap replicates are given as branch labels. Figure S6. Maximum likelihood-based tree of two orthologous loci from 51 fungal species. These two loci each group all species from Agaricomycotina together with Pucciniomycotina. Support values from 1000 bootstrap replicates are given as branch labels. Figure S7. Maximum likelihood-based tree of five orthologous loci from 51 fungal species. These five loci each group all species from Agaricomycotina together with Ustilaginomycotina. Support values from 1000 bootstrap replicates are given as branch labels. Figure S8. Maximum likelihood-based tree of three orthologous loci from 51 fungal species. These three loci each group Bartheletia paradoxa together with Tremellomycetes. Support values from 1000 bootstrap replicates are given as branch labels. Figure S9. Maximum likelihood-based tree of seven orthologous loci from 51 fungal species. These seven loci each group Bartheletia paradoxa together with Wallemiomycetes. Support values from 1000 bootstrap replicates are given as branch labels. Figure S10. Maximum likelihood-based tree of three orthologous loci from 51 fungal species. These three loci each group Bartheletia paradoxa as basal to all other species in Agaricomycotina. Support values from 1000 bootstrap replicates are given as branch labels. Figure S11. Maximum likelihood-based tree of four orthologous loci from 51 fungal species. These four loci each group Bartheletia paradoxa together with Agaricomycetes and Dacrymycetes. Support values from 1000 bootstrap replicates are given as branch labels. (PPTX 5024 kb)
11557_2017_1349_MOESM2_ESM.pdf (166 kb)
Table S1 Genomes included in the current study. (PDF 166 kb)
11557_2017_1349_MOESM3_ESM.pdf (23 kb)
Table S2 Number of genes supporting particular higher level splits in maximum likelihood analyses. (PDF 23 kb)
11557_2017_1349_MOESM4_ESM.docx (15 kb)
Table S3 Results of the ABBA BABA test for all loci. (DOCX 15 kb)
11557_2017_1349_MOESM5_ESM.docx (16 kb)
Table S4 Results of the ABBA BABA test for the 26 highly resolving loci. (DOCX 15 kb)

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Copyright information

© German Mycological Society and Springer-Verlag GmbH Germany 2017

Authors and Affiliations

  • Bagdevi Mishra
    • 1
    • 2
    • 3
  • Young-Joon Choi
    • 1
    • 2
    • 4
  • Marco Thines
    • 1
    • 2
    • 3
    • 5
  1. 1.Biodiversity and Climate Research Centre (BiK-F)Frankfurt (Main)Germany
  2. 2.Department for Biological Sciences, Institute of Ecology, Evolution and DiversityGoethe UniversityFrankfurt (Main)Germany
  3. 3.Senckenberg Gesellschaft für NaturforschungFrankfurt (Main)Germany
  4. 4.Department of Biology, College of Natural SciencesKunsan National UniversityGunsanSouth Korea
  5. 5.Cluster for Integrative Fungal Research (IPF)Frankfurt (Main)Germany

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