SUPPLEMENTARY INFORMATION                                                                                         doi:10.1...
doi:10.1038/nature09984                                                                                                   ...
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Supplementary information 1 & 2


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Supplementary information 1 & 2

  1. 1. SUPPLEMENTARY INFORMATION doi:10.1038/nature09984 a Basidiomycota b Ascomycota Glomeromycota Zygomycota Basidiomycota Olpidium Blastocladiomycota Chytridiomycota Neocallimastigomycota Microsporidia Ascomycota Rozella Classic fungi that grow with a chitin-rich cell wall. Glomeromycota Zygomycota Olpidium Blastocladiomycota Chytridiomycota Neocallimastigomycota Microsporidia Highly diverse novel basal group identified in this study. Cryptomycota: organisms that branch with the Key fungi but putatively Branching relationship grow and weakly supported develop without Rozella synthesizing Branching relationship a chitin-rich cell wall strongly supported Opisthokont outgroup and therefore appear Group forms flagellated to lack this classically zoospores defining fungal feature.Supplementary Figure 1. Summary of the main findings of the paper. a, Standard working model of the fungal tree of life.b, Identification of a very large uncultured basal clade in the kingdom Fungi, marked in red and, with Rozella, named here ascryptomycota. This study therefore demonstrates that current models of fungal evolution and biodiversity, which are based oncultured microbes, have missed a huge fraction of the kingdom (perhaps even approaching one half). Furthermore, this group ofmicrobes appears to grow without the defining fungal characteristics a chitin-rich cell wall (although this characteristic is also absentduring the flagellated zoospore stage of many other chytrid fungi). Therefore these data challenge existing ideas of fungal biodiversityand current concepts regarding the adaptive features that drove the evolutionary diversification and ecological success of the fungalkingdom. W W W. N A T U R E . C O M / N A T U R E | 1
  2. 2. doi:10.1038/nature09984 RESEARCH SUPPLEMENTARY INFORMATION a Batrachochytrium dendrobatidis Rhizophydium sphaerotheca Entophlyctis helioformis Rhizophydium brooksianum Rhizoclosmatium sp. Chytriomyces hyalinus Rhizophlyctis rosea Catenomyces sp. Powellomyces sp. Triparticalcar arcticum ‘Chytrids’ Polychytrium aggregatum Karlingiomyces sp. Cladochytrium replicatum Nowakowskiella sp. Endochytrium sp. Oedogoniomyces sp. Monoblepharella sp. Hyaloraphidium curvatum Cyllamyces aberensis Piptocephalis corymbifera Smittium culisetae Zygomycota Basidiobolus ranarum Allomyces arbuscula Blastocladiella emersonii Blastocladiomycota Physoderma maydis Fungi Neurospora crassa Magnaporthe grisea Hypocrea jecorina Monilinia fructicola Monascus purpureus Ascomycota 0.93/44/-- Dothidea sambuci Disciotis venosa Candida glabrata Debaryomyces hansenii Schizosaccharomyces pombe Ustilago maydis Tilletiaria anomala Platygloea disciformis Basidiomycota 1/95/99 Coprinopsis cinerea Calocera cornea Filobasidiella neoformans Phycomyces blakesleeanus Zygomycota Rhizopus oryzae Glomus mosseae Paraglomus occultum Glomeromycota 1/100/100 Lily Stem/Washington Singer CM2 Washington Singer CM1 Cryptomycota 1/96/96 Rozella sp. Rozella Rozella allomycis Nuclearia simplex Suberites ficus Aurelia sp. Outgroup Amoebidium parasiticum Capsaspora owczarzaki 0.9/80/80 0.6/50/50 0.07 subs/site b Basidiobolus ranarum ‘Chytrids’ Piptocephalis corymbifera Zygomycota Smittium culisetae Blastocladiomycota Lily Stem/Washington Singer CM2 Washington Singer CM1 Cryptomycota Rozella sp. JEL347 Rozella Rozella allomycis Ascomycota Glomeromycota Encephalitozoon cuniculi Heterosporis anguillarum microsporidia Brachiola algerae Antonospora locustae Filobasidiella neoformans Platygloea disciformis Coprinopsis cinerea Basidiomycota Calocera cornea Ustilago maydis Tilletiaria anomala Zygomycota Oedogoniomyces sp. CR84 ‘Chytrids’ Monoblepharella sp. M15 Nuclearia simplex Outgroup c 0.9/80/80 0.6/50/50 0.02 subs/site 21/71 Ascomycota Glomeromycota Basidiomycota Antonospora locustae Brachiola algerae microsporidia Heterosporis anguillarum 63/75 Encephalitozoon cuniculi Rhizopus oryzae Zygomycota Phycomyces blakesleeanus Washington Singer CM1 Lily Stem/Washington Singer CM2 Cryptomycota Rozella allomycis Rozella sp. JEL347 Rozella Chytridiomycota Smittium culisetae Zygomycota Piptocephalis corymbifera Batrachochytrium dendrobatidis Chytriomyces hyalinus ‘Chytrids’ Rhizoclosmatium sp. JEL347 Basidiobolus ranarum Zygomycota Monoblepharella sp. M15 Oedogoniomyces sp. CR84 ‘Chytrids’ Hyaloraphidium curvatum Blastocladiomycota Nuclearia simplex Outgroup 80/80 50/50 0.09 subs/siteSupplementary Figure 2. Phylogenetic analysis of the SSU-5.8S-LSU alignment demonstrating the branching position of thecryptomycota. a, The phylogeny was calculated from an alignment of 54 sequences and 1,877 nucleotide alignment charactersand demonstrates strong support for the placement of the novel clade as a sister group to Rozella. Node support values are labelledusing the same convention as Fig. 1. b, Bayesian phylogeny based on SSU-LSU alignment with four microsporidia sequences added(58 sequences and 1,072 DNA characters – character number is reduced from a because of alignment of divergent microsporidiasequences). c, PhyML (fast Maximum Likelihood) tree topology with 1000 bootstrap values using PhyML and Log-Det distance methodscalculated from the same alignments as b. These phylogenetic analyses followed the same procedure as described for the analysesshown in a and described in the methods section. Key topology support values are shown, however all other bootstrap values are notatedwith symbols: nodes supported by 0.9 posterior probability or greater and 80% bootstrap support or greater by both methods are markedwith a black dot; nodes supported by 0.6 posterior probability or greater and 50% bootstrap support or greater by both methods are markedwith a ringed circle.