Figure S1. Representative plant-symbiotic Mucoromycotina detected in this study. Gene tree of the fungal translation elongation factor 1 alpha showing the placement of representative plant-symbiotic fungi detected, including multiple independently cloned DNA sequences.

Figure S2. Six-gene highest likelihood tree of representatives of major fungal lineages. Bootstrap support values are shown above the branches.

Figure S3. Maximum clade credibility tree inferred using a Bayesian relaxed molecular clock. Node bars are 95% highest posterior density intervals of node heights, expressed in average number of substitutions per site. Posterior probabilities are shown above branches.

Table S1. The plants and fungi sampled and the DNA sequence data generated.

Collection / Sample / Organism / Fungi / Location / fungal 5' SSU / fungal SSU / fungal TEF / fungal ITS+LSU
Basal liverworts (Haplomitriopsida)
M2 / 8448 / Haplomitrium blumei / Mucoromycotina / Genting Highlands, Malaysia / Y
N1 / 8352.2 / Haplomitrium gibbsiae / Mucoromycotina / Bridal Veil Track, S. New Zealand / Y / Y
N71 / 8357.1 / Haplomitrium gibbsiae / Mucoromycotina / Rahu Saddle, S. New Zealand / Y
N71 / 8357.2 / Haplomitrium gibbsiae / Mucoromycotina / Rahu Saddle, S. New Zealand / Y
N79 / 8360.1 / Haplomitrium gibbsiae / Mucoromycotina / Mt. Arthur, S. New Zealand / Y
JD15 / 8447 / Haplomitrium hookeri / Mucoromycotina / Ben Lawers, Scotland / Y / Y
N77 / 8359 / Haplomitrium ovalifolium / Mucoromycotina / Mt. Arthur, S. New Zealand / Y
N2 / 8353.1 / Treubia lacunosa / Mucoromycotina / Kelly Creek, S. New Zealand / Y / Y / Y
N2 / 8353.2 / Treubia lacunosa / Mucoromycotina / Kelly Creek, S. New Zealand / Y
N34 / 8354.1 / Treubia lacunosa / Mucoromycotina / Ross, S. New Zealand / Y / Y
N34 / 8354.2 / Treubia lacunosa / Mucoromycotina / Ross, S. New Zealand / Y / Y / Y
N60 / 8355.1 / Treubia lacunosa / Mucoromycotina / Cobb, S. New Zealand / Y / Y / Y
N60 / 8355.2 / Treubia lacunosa / Mucoromycotina / Cobb, S. New Zealand / Y
NN96 / 8363.3 / Treubia lacunosa / Mucoromycotina / Piha, N. New Zealand / Y / Y / Y
NN100 / 8364.1 / Treubia lacunosa / Mucoromycotina / Piha, N. New Zealand / Y / Y
NN100 / 8364.2 / Treubia lacunosa / Mucoromycotina / Piha, N. New Zealand / Y / Y
NN105 / 8365.1 / Treubia lacunosa / Mucoromycotina / Wainau, N. New Zealand / Y / Y
NN105 / 8365.2 / Treubia lacunosa / Mucoromycotina / Wainau, N. New Zealand / Y
N69 / 8356.1 / Treubia pygmaea / Mucoromycotina / Rahu Saddle, S. New Zealand / Y
N69 / 8356.2 / Treubia pygmaea / Mucoromycotina / Rahu Saddle, S. New Zealand / Y
N74 / 8358.1 / Treubia pygmaea / Mucoromycotina / Mt. Arthur, S. New Zealand / Y / Y
N74 / 8358.2 / Treubia pygmaea / Mucoromycotina / Mt. Arthur, S. New Zealand / Y / Y
N93 / 8362.1 / Treubia pygmaea / Mucoromycotina / Punchbowl Falls, S. New Zealand / Y / Y
N93 / 8362.2 / Treubia pygmaea / Mucoromycotina / Punchbowl Falls, S. New Zealand / Y / Y
T1 / 8349.1 / Treubia tasmanica / Mucoromycotina / Mt. Wellington, Tasmania / Y / Y
T1 / 8349.2 / Treubia tasmanica / Mucoromycotina / Mt. Wellington, Tasmania / Y
T13 / 8350 / Treubia tasmanica / Mucoromycotina / Arve Valley, Tasmania / Y
T20 / 8351.1 / Treubia tasmanica / Mucoromycotina / Tahune Airwalk, Tasmania / Y / Y
T20 / 8351.2 / Treubia tasmanica / Mucoromycotina / Tahune Airwalk, Tasmania / Y / Y
Simple thalloid liverworts
N3 / 8372.1 / Allisonia cockaynii / Mucoromycotina / Kelly Creek, S. New Zealand / Y / Y
N3 / 8372.2 / Allisonia cockaynii / Mucoromycotina / Kelly Creek, S. New Zealand / Y
N80 / 8388 / Allisonia cockaynii / Mucoromycotina / Mt. Arthur, S. New Zealand / Y
N54 / 8384 / Austrofossombronia australis / Glomerales / Denniston, S. New Zealand / Y
N24 / 8381 / Jensenia connivens / Glomerales / Fox Glacier, S. New Zealand / Y
NN109 / 8393.1 / Podomitrium phyllanthus / Glomerales / Spraggs Bush, N. New Zealand / Y
N7 / 8375 / Symphyogyna prolifera / Glomerales / Kelly Creek, S. New Zealand / Y
T3 / 8366 / Symphyogyna hymenophyton / Glomerales, Diversisporales / Mt. Wellington, Tasmania / Y
T23 / 8371 / Symphyogyna podophylla / Archaeosporales / Tahune Airwalk, Tasmania / Y
N23 / 8379 / Symphyogyna subsimplex / Glomerales / Fox Glacier, S. New Zealand / Y
NN104 / 8392 / Symphyogyna subsimplex / Glomerales / Spraggs Bush, N. New Zealand / Y
Complex thalloid liverworts
N63 / 8386 / Asterella tenera / Glomerales / Lyell Valley, S. New Zealand / Y
N8 / 8376 / Marchantia foliacea / Glomerales / Bridal Veil Track, S. New Zealand / Y
N72 / 8387 / Neohodgsonia mirabilis / Mucoromycotina / Flora Hut, Mt. Arthur, S. New Zealand / Y
8472 / 8472 / Conocephalum conicum / Glomerales / Kew Gardens, England / Y
Hornworts
N66 / 8443 / Anthoceros laminiferus / Glomerales, Diversisporales / Greymouth, S. New Zealand / Y
JD152 / JD152.1 / Anthoceros husnotti / Archaeosporales / Dunoon, Scotland / Y
DC1220 / 8478 / Paraphymatoceros sp. / Mucoromycotina / W. Australia / Y
N37 / 8439 / Paraphymatoceros coriaceus / Mucoromycotina / Ross, S. New Zealand / Y
N55 / 8441 / Phaeoceros carolineanus / Glomerales, Diversisporales / Denniston, S. New Zealand / Y
NN101 / 8446 / Phaeoceros carolineanus / Glomerales, Diversisporales / Spraggs Bush, N. New Zealand / Y
N56 / 8442 / Phaeoceros carolineanus / Archaeosporales / Greymouth, S. New Zealand / Y
JD78 / JD78.1 / Phaeoceros laevis / Archaeosporales / Dartington, England / Y
Ferns
JD92 / JD92.1 / Anogramma leptophylla / Mucoromycotina / Cannes, France / Y
T21 / 8369 / Tmesipteris billardieri / Glomerales / Tahune Airwalk, Tasmania / Y
T22 / 8370 / Tmesipteris billardieri / Glomerales / Tahune Airwalk, Tasmania / Y
N36 / 8383 / Tmesipteris tannensis / Glomerales / Ross, S. New Zealand / Y
NN103 / 8391 / Tmesipteris elongata / Glomerales / Spraggs Bush, N. New Zealand / Y
Fungi
OSC130580 / T18078 / Endogone aggregata / Mucoromycotina / Alpine National Park, Australia / Y
OSC111442 / T30685 / Endogone flammicorona / Mucoromycotina / Benton, Oregon / Y
T33845 / Endogone flammicorona / Mucoromycotina / Jalisco, Mexico / Y / Y
T33851 / Endogone flammicorona / Mucoromycotina / Jalisco, Mexico / Y
T32530 / Endogone lactiflua / Mucoromycotina / Talxcala, Mexico / Y
T32544 / Endogone lactiflua / Mucoromycotina / Tlaxcala, Mexico / Y
T32674 / Endogone lactiflua / Mucoromycotina / Tamaulipas, Mexico / Y / Y
T33849 / Endogone lactiflua / Mucoromycotina / Jalisco, Mexico / Y / Y
OSC130614 / T32321 / Endogone oregonensis / Mucoromycotina / Polk, Oregon / Y
OSC80931 / T28028 / Endogone pisiformis / Mucoromycotina / Benton, Oregon / Y
T13431 / Endogone sp. nov. / Mucoromycotina / Davies Creek, Australia / Y
T26631 / Endogone sp. nov. / Mucoromycotina / Bournda National Park, Australia / Y / Y
T32417 / Endogone sp. nov. / Mucoromycotina / Veracruz, Mexico / Y
T32492 / Endogone sp. nov. / Mucoromycotina / Tlaxcala, Mexico / Y / Y

Table S2. Diameter (µm) of fungal structures within representative plants.

Plant / Vesicle / Swelling / Trunk
hypha / Fine hypha or arbuscule / Spore / Fungi
Complex thalloid liverworts
Asterella tenera / 25-35 / - / 3-6 / 0.8-1.5 / - / Glomeromycota
Marchantia foliacea / 25-35 / - / 3-6 / 0.8-1.5 / - / Glomeromycota
Simple thalloid liverworts
Alisonia cockaynii / - / 8-12 / - / 0.8-1.5 / - / Mucoromycotina
Jensenia connivens / 20-30 / - / 3-6 / 0.8-1.5 / - / Glomeromycota
Symphyogyna hymenophton / 20-30 / - / 3-6 / 0.8-1.5 / - / Glomeromycota
Symphyogyna subsimplex / 20-30 / - / 3-6 / 0.8-1.5 / - / Glomeromycota
Basal liverworts (Haplomitriopsida)
Haplomitrium gibbsiae / - / 8-12 / - / 0.8-1.5 / 5-6 / Mucoromycotina
Haplomitrium hookeri / - / 8-12 / - / 0.8-1.5 / 5-6 / Mucoromycotina
Haplomitrium ovalifolium / - / 8-12 / - / 0.8-1.5 / 5-6 / Mucoromycotina
Treubia lacunosa / - / 8-12 / - / 0.8-1.5 / 5-6 / Mucoromycotina
Treubia pygmaea / - / 8-12 / - / 0.8-1.5 / 5-6 / Mucoromycotina

Table S3. Taxon sampling and Genbank accessions used for the phylogenetic inference of Mucoromycotina and Glomeromycota.

Ascomycota / 18S rDNA / 28S rDNA / 5.8S rDNA / PRB1 / PRB2 / TEF
Schizosaccharomyces pombe / X54866 / Z19136 / Z19578 / X56564 / D13337 / U42189
Caloscypha fulgens / DQ247807 / DQ247799 / DQ491483 / DQ471126 / DQ247787 / DQ471054
Aspergillus nidulans / ENU77377 / AF454167 / AY373888 / XM_653321 / XM_677297 / XM_656730
Pleospora herbarum / DQ247812 / DQ247804 / DQ491516 / DQ471163 / DQ247794 / DQ471090
Trapelia placodioides / AF119500 / AF274103 / AF274081 / DQ366259 / DQ366260 / DQ366258
Orbilia vinosa / DQ471000 / DQ470952 / DQ491511 / DQ471145 / --- / DQ471071
Ashbya gossypii / AF113137 / AF113137 / AF113137 / NM_209535 / NM_211306 / NM_209079
Simonyella variegata / AY584669 / AY584645 / DQ782835 / DQ782819 / DQ782861 / DQ782891
Xylaria acuta / AY544719 / AY544676 / DQ491493 / DQ471118 / DQ247797 / DQ471048
Chlorociboria aeruginosa / AY544713 / AY544669 / DQ491501 / DQ471125 / DQ470886 / DQ471053
Basidiomycota
Coprinus comatus / AY665772 / AY635772 / AY854066 / AY857983 / AY780934 / AY881026
Collybia tuberosa / AY771606 / AY639884 / AY854072 / AY857982 / AY787219 / AY881025
Fomitopsis pinicola / AY705967 / AY684164 / AY854083 / AY864874 / AY786056 / AY885152
Echinodontium tinctorium / AF026578 / AF393056 / AY854088 / AY864882 / AY218482 / AY885157
Ramaria rubella / AY707095 / AY645057 / AY854078 / AY864866 / AY786064 / AY883435
Coltricia perennis / AF026583 / AF287854 / --- / AY864867 / AY218526 / AY885147
Dacryopinax spathularia / AY771603 / AY701525 / AY854070 / AY857981 / AY786054 / AY881020
Ustilago maydis / X62396 / AF453938 / AY854090 / XM401478 / AY485636 / AY885160
Colacogloea peniophorae / DQ234564 / AY629313 / DQ202270 / DQ234569 / DQ234550 / DQ234566
Agaricostilbum hyphaenes / AY665775 / AY634278 / AY789077 / AY788845 / AY780933 / AY879114
Glomeromycota
Scutellospora heterogama / AY635832 / DQ273792 / AY997088 / DQ294604 / DQ302780 / DQ282612
Glomus mosseae / AY635833 / DQ273793 / AY997053 / DQ294592 / DQ302781 / DQ282613
Glomus intraradices / DQ322630 / DQ273828 / AY997054 / DQ294603 / DQ302794 / DQ282611
Glomus proliferum
Geosiphon pyriformis / AM183923 / AM183920 / --- / AM183921 / --- / AM183922
AF157262 / AF157262 / AF157262 / AF157262 / AF157262 / AF157262 / AF157262
Mucoromycotina
Mortierella verticillata / AF157145 / DQ273794 / AY997063 / DQ294595 / DQ302784 / AF157262
Umbelopsis ramanniana / DQ322627 / DQ273797 / AY997097 / DQ294598 / DQ302787 / AF157258
Phycomyces blakesleeanus / AY635837 / DQ273800 / AY997071 / DQ294607 / DQ302789 / DQ282620
Rhizopus oryzae / AF113440 / AY213626 / AB097334 / a / a / a
Endogone pisiformis / DQ322628 / DQ273811 / AY997046 / DQ294601 / DQ302776 / DQ282618
Endogone lactiflua / DQ536471 / DQ273811 / AY997045 / XXX / --- / ---
Mucor hiemalis / AF113428 / AJ876782 / AJ876489 / EF014381 / EF014398 / AF157265
Dissophora decumbens / AF157133 / AF157187 / --- / --- / --- / AF157247
Rhizomucor miehei / AF205941 / AF205941 / AF205941 / --- / --- / AF157282
Basal fungi
Dimargaris bacillispora / AB016020 / DQ273791 / AY997043 / DQ294588 / DQ302775 / DQ282609
Coemansia reversa / AF007533 / AY546689 / AY997039 / DQ294594 / DQ302783 / DQ282615
Orphella aff. Haysii / DQ322626 / DQ273830 / AY997068 / DQ294606 / --- / ---
Smittium culisetae / AF007540 / DQ273773 / AY997089 / DQ294593 / DQ302782 / AB077104
Spiromyces aspiralis / AF007543 / DQ273801 / AY997090 / DQ294599 / DQ302790 / DQ282621
Rhopalomyces elegans / AY635834 / DQ273795 / --- / DQ294596 / DQ302785 / DQ282616
Piptocephalis corymbifera / AB016023 / AY546690 / AY997073 / DQ294610 / DQ302788 / DQ282619
Basidiobolus ranarum / AY635841 / DQ273807 / AY997030 / DQ294589 / DQ302777 / DQ282610
Olpidium brassicae / DQ322624 / DQ273818 / AY997067 / DQ294609 / --- / --
Entomophthora muscae / AY635820 / DQ273772 / AY997047 / DQ294590 / DQ302778 / ---
Conidiobolus coronatus / AF113418 / AY546691 / AY997041 / DQ294591 / DQ302779 / ---
Physoderma maydis / AY601708 / DQ273767 / AY997072 / DQ294580 / DQ302767 / DQ282600
Coelomomyces stegomyiae / AF322406 / DQ273767 / AY997038 / DQ294579 / DQ302766 / ---
Allomyces arbusculus / AY552524 / AY552525 / AY997028 / DQ294578 / DQ302765 / ---
Outgroups
Rhizophydium macroporosum / DQ322622 / DQ273823 / AY997084 / DQ294600 / DQ302793 / DQ282603
Hyaloraphidium curvatum / Y17504 / DQ273771 / AY997055 / DQ294585 / DQ302772 / DQ282606
Polychytrium aggregatum / AY601711 / AY546686 / AY997074 / DQ294584 / DQ302770 / DQ282604

a: Rhizopus oryzae genomes were accessed through the Genbank submissions from the Fungal Genome Initiative at the Broad Institute (

XXX = to be submitted.