phylogenomics of the zygomycetes - fungal genetics 2015

Fungal Genetics 2015

Phylogenomics of the Zygomycete lineages: Exploring phylogeny and genome evolution Jason Stajich

@hyphaltip @zygolife @stajichlab

Gaining Momentum

Goals • Facilitate the sequencing of fungal genomes across the

Kingdom Fungi • Produce a genome-‐scale phylogeny for Kingdom Fungi • Create genome reference data sets for Kingdom Fungi • Pan-‐fungal genome, Models to non-‐models

Joey Spatafora Igor Grigoriev

0.4

Ogataea_parapolymorpha_DL_1

Meliniomyces_variabilis_F

Debaryomyces_hansenii_CBS_767

Choiromyces_venosus_120613_1

Rhizoctonia_solani_AG_1_IA

Enterocytozoon_bieneusi_H348

Agaricus_bisporus_var_bisporus_H97

Moniliophthora_perniciosa_FA553

Trichosporon_oleaginosus_IBC0246

Zygosaccharomyces_rouxii_CBS_732

Hydnomerulius_pinastri

Exophiala_dermatitidis_NIH_UT8656

Wilcoxina_mikolae_CBS_423_85

Kluyveromyces_lactis_NRRL_Y_1140

Oidiodendron_maius_Zn

Apiospora_montagnei_NRRL_25634

Suillus_brevipes

Pleurotus_ostreatus_PC15

Clavicorona_pyxidata_HHB10654

Exidia_glandulosa_HHB12029

Sordaria_macrospora_k_hell

Lichtheimia_hyalospora_FSU_10163

Amanita_thiersii_Skay4041

Gymnopus_luxurians

Ajellomyces_capsulatus_NAm1

Meyerozyma_guilliermondii_ATCC_6260

Jaapia_argillacea_MUCL_33604

Sporisorium_reilianum_SRZ2

Auriscalpium_vulgare_FP105234_Sp

Mucor_circinelloides_CBS277_49

Phanerochaete_chrysosporium_2

Cortinarius_glaucopus_AT_2004_276

Cryphonectria_parasitica_EP155

Uncinocarpus_reesii_1704

Chaetomium_globosum_CBS_148_51

Ganoderma_sp_10597_SS1

Lodderomyces_elongisporus_NRRL_YB_4239

Aspergillus_niger_ATCC_1015

Plicaturopsis_crispa_CBS_459_81

Ophiostoma_piceae_UAMH_11346

Spathaspora_passalidarum_NRRL_Y_27907

Paxillus_involutus_ATCC_200175

Orpinomyces_sp_C1A

Hysterium_pulicare_CBS_123377

Piedraia_hortae_CBS_480_64_1

Candida_albicans_SC5314

Sporobolomyces_roseus_CBS_119925

Capronia_coronata_CBS_617_96

Arthroderma_benhamiae_CBS_112371

Wallemia_sebi_CBS_633_66

Phaeoacremonium_aleophilum_UCRPA7

Melampsora_laricis_populina_98AG31

Sphaerulina_musiva_SO2202

Tritirachium_sp_CBS_265_96

Beauveria_bassiana_ARSEF_2860

Catenaria_anguillulae_PL171

Pleomassaria_siparia_CBS_279_74

Aulographum_hederae_CBS_113979

Karstenula_rhodostoma_CBS_690_94

Grosmannia_clavigera_kw1407

Piromyces_sp_E2

Botrytis_cinerea_B05_10

Lepidopterella_palustris

Fibulorhizoctonia_sp_CBS_109695

Neolentinus_lepideus_HHB14362_ss_1

Dothistroma_septosporum_NZE10

Encephalitozoon_romaleae_SJ_2008

Amanita_muscaria_Koide

Ashbya_gossypii_FDAG1

Millerozyma_farinosa_CBS_7064

Polychaeton_citri_CBS_116435

Cyberlindnera_jadinii_NRRL_Y_1542

Phycomyces_blakesleeanus_NRRL_1555

Trichosporon_asahii_var_asahii_CBS_8904

Tremella_mesenterica_Fries

Encephalitozoon_hellem_ATCC_50504

Metarhizium_anisopliae_ARSEF_23

Paracoccidioides_brasiliensis_Pb18

Thelebolus_stercoreus

Rhizophagus_irregularis_DAOM_181602

Monascus_ruber_NRRL_1597

Coniochaeta_ligniaria

Xanthoria_parietina_46_1

Pisolithus_tinctorius_Marx_270

Tricholoma_matsutake_945

Leucogyrophana_mollusca_KUC20120723A_06

Fusarium_graminearum_PH_1

Postia_placenta_MAD_698_R

Amorphotheca_resinae_ATCC_22711

Fistulina_hepatica_ATCC_64428

Sporormia_fimetaria

Phaeosphaeria_nodorum_SN15

Schizopora_paradoxa_KUC8140

Magnaporthe_oryzae_70_15

Leptosphaeria_maculans_JN3

Cenococcum_geophilum_1_58

Suillus_luteus_UH_Slu_Lm8_n1

Rhodotorula_minuta_MCA_4210

Meliniomyces_bicolor_E

Conidiobolus_coronatus_NRRL_28638

Verticillium_dahliae_JR2

Batrachochytrium_dendrobatidis_JAM81

Botryobasidium_botryosum_FD_172_SS1

Coccidioides_immitis_RS

Lichtheimia_corymbifera_FSU_9682

Rhizopus_delemar_RA_99_880

Sebacina_vermifera_MAFF_305830

Saccharomyces_cerevisiae_S288C

Cucurbitaria_berberidis_CBS_394_84

Sporobolomyces_linderae_CBS_7893

Fomitopsis_pinicola_FP_58527_SS1

Phlebia_brevispora_HHB_7030_SS6

Cochliobolus_heterostrophus_C5Pyrenophora_tritici_repentis

Schizophyllum_commune_H4_8

Dendrothele_bispora_CBS_962_96

Exobasidium_vaccinii_MPITM

Thermoascus_aurantiacus_ATCC26904

Patellaria_atrata_CBS_101060

Baudoinia_compniacensis_UAMH_10762

Blumeria_graminis_fsp_hordei_DH14

Hypholoma_sublateritium

Chalara_longipes_BDJ

Fibroporia_radiculosa_TFFH_294

Melanomma_pulvis_pyrius_CBS_109_77

Lophiostoma_macrostomum_CBS_122681

Punctularia_strigosozonata_HHB_11173_SS5

Torulaspora_delbrueckii_CBS_1146

Schizosaccharomyces_octosporus_yFS286

Didymella_exigua_CBS_183_55

Naiadella_fluitans_ATCC_64713

Symbiotaphrina_kochii_250_77

Serpula_lacrymans_S7_3

Gymnascella_citrina_NRRL_5970_1Trichophyton_rubrum_CBS_118892

Arthrobotrys_oligospora_ATCC_24927

Antonospora_locustae_HM_2013

Calocera_cornea_HHB12733

Hortaea_werneckii_v2_M0

Myriangium_duriaei_CBS_260_36

Pneumocystis_jirovecii_SE8

Cordyceps_militaris_CM01

Kazachstania_africana_CBS_2517

Trematosphaeria_pertusa_CBS_122368

Mortierella_elongata

Phlebiopsis_gigantea_11061_1_CR5_6

Ascobolus_immersus_RN42

Encephalitozoon_intestinalis_ATCC_50506

Laccaria_amethystina_LaAM_08_1

Dacryopinax_sp_DJM_731_SS1

Myceliophthora_thermophila_ATCC_42464

Aplosporella_prunicola_CBS_121_167

Zopfia_rhizophila_CBS_207_26

Togninia_minima_UCRPA7

Wallemia_ichthyophaga_EXF_994

Coprinopsis_cinerea_okayama7_130

Neurospora_crassa_OR74A

Glarea_lozoyensis_74030

Acidomyces_richmondensis_BFW_Aciri1_iso

Trametes_versicolor_FP_101664_SS1

Chaetosphaeria_innumera

Wolfiporia_cocos_MD_104_SS10

Clavulina_sp_PMI_390

Marssonina_brunnea_fsp_multigermtubi_MB_m1

Mortierella_verticillata_NRRL_6337

Laccaria_bicolor_S238N_H82

Boletus_edulis_BED1

Aspergillus_fumigatus_Af293

Tilletiaria_anomala_UBC_951

Volvariella_volvacea_V23

Lentithecium_fluviatile_CBS_122367

Umbelopsis_ramanniana_NRRL_5844

Colletotrichum_graminicola_M1_001

Yarrowia_lipolytica_CLIB122

Nematocida_parisii_ERTm1

Macrolepiota_fuliginosa

Rhytidhysteron_rufulum_CBS_306_38

Xylona_heveae_TC161

Mycosphaerella_graminicola_IPO323

Penicillium_chrysogenum_Wisconsin_54_1255

Rhodosporidium_toruloides_NP11

Taphrina_deformans

Coemansia_reversa_NRRL_1564

Sistotremastrum_suecicum_HHB10207_ss_3

Daldinia_eschscholzii_EC12

Rhodotorula_graminis_WP1_1

Microbotryum_violaceum_p1A1_Lamole

Komagataella_pastoris_GS115

Eutypa_lata_UCREL1

Talaromyces_stipitatus_ATCC_10500

Botryosphaeria_dothidea_CBS_115476

Cadophora_sp_DSE1049

Sclerotinia_sclerotiorum_1980_UF_70

Clavispora_lusitaniae_ATCC_42720

Cryptococcus_neoformans_var_neoformans_JEC21

Auricularia_subglabra_TFB10046_SS_5

Ophiostoma_piliferum

Dichomitus_squalens_LYAD_421_SS1

Rozella_allomycis_CSF55

Cylindrobasidium_torrendii_FP15055_ss_10

Heterobasidion_annosum_TC_32_1

Malassezia_globosa

Coniophora_puteana_RWD_64_598_SS2

Fusarium_fujikuroi_IMI58289

Armillaria_mellea_DSM_3731

Claviceps_purpurea_20_1

Scleroderma_citrinum_Foug_A

Mixia_osmundae_IAM_14324

Nosema_ceranae_BRL01

Trypethelium_eluteriae

Trichoderma_atroviride_IMI_206040

Calosphaeria_pulchella

Sphaerobolus_stellatus_SS14

Saccharata_proteae_CBS_121410

Pseudogymnoascus_destructans_20631_21

Pichia_stipitis_CBS_6054

Puccinia_graminis_fsp_tritici_CRL_75_36_700_3

Pseudozyma_antarctica_T_34

Stereum_hirsutum_FP_91666_SS1

Hebeloma_cylindrosporum_h7

Melanconium_sp_NRRL_54901

Cyphellophora_europaea_CBS_101466

Zasmidium_cellare_ATCC_36951

Glomerella_cingulata_23

Atractiellales_sp_PMI_95

Tetrapisispora_phaffii_CBS_4417

Dekkera_bruxellensis_CBS_2499

Protomyces_inouyei

Gonapodya_prolifera_JEL478

Encephalitozoon_cuniculi_GB_M1

Anthostoma_avocetta_NRRL_3190

Talaromyces_marneffei_ATCC_18224

Galerina_marginata_CBS_339_88

Nectria_haematococca_FGSC_9596

Ramaria_rubella_UT_36052_T

Ascocoryne_sarcoides_NRRL_50072

Bjerkandera_adusta

Mycosphaerella_fijiensis

Aureobasidium_pullulans_var_pullulans_EXF_150

Monascus_purpureus_NRRL_1596

Backusella_circina_FSU_941

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99Basidiomycota

Ascomycota

Early Diverging Fungi

1000 Fungal Genomes Program -‐ Project Status

Num

ber

0

75

150

225

300

Status

107

13

28

16

119

awaiLng materialssequencinganalysisannotaLoncomplete

RAxML Tree 241 taxa 180 proteins

Stajich, Spatafora

ZygomycetesDiverse, early branching lineages that could contain transition states for zoosporic to Dikarya and multicellular states

“Conundrum of the fungi” because the placement of the groups has varied

Date

Mucormycotina

Date

Spinellus fusiger on Mycena capillaripesDarvin DeShazer

Date

Phycomyces zygospore

Date

Endogene

Date

Entomophthora muscae on house flyGryganskyi et al 2013; DOI: 10.1371/journal.pone.0071168

Syncephalis!•  ~60 described species

•  Obligate mycoparasites

•  Penetrate host hyphae with haustoria, grow intracellularly

•  Common in soil and dung

•  Global distribution (probably)

•  May be grown in dual culture with their host

host hyphae

parasite hyphae

S. dispora!

rhizoids

merosporangium

sporangiophore

Katy Lazarus

(Gehrig et al 1996, Jensen et al 1998), the Ascomycota+ Basidiomycota (Helgason et al 2003) or theirrelationships were unresolved (Bruns et al 1992,Tanabe et al 2000). Phylogenetic relationships ofthe Mucorales also were unresolved in a BayesianSSU+LSU two-locus phylogeny (Lutzoni et al 2004).Similarly phylogenies inferred from amino acidsequence data from one or two loci have failed toresolve evolutionary relationships of the Mucorales(Keeling et al 2000, Keeling 2003, Helgason et al2003), except for a possible sister group relationshipwith the Mortierellales (Tanabe et al 2004, Tanabe etal 2005) or the Entomophthorales (Keeling 2003).Sequences of the Endogonales however were

noticeably absent from all of the amino acid-basedphylogenies. Phylogeny reconstructions based onb-tubulin weakly supported a Mucorales + Ento-mophthorales sister group relationship but did notinclude sequences of the Mortierellales (Keeling2003).

The genera currently classified within the mono-phyletic Mucorales (Lutzoni et al 2004) have beenclassified in up to 16 families, based primarily ondifferences in sexual and asexual reproductive mor-phology (Benny et al 2001). However our studysupports the results of another based on three genesthat indicated large scale polyphyly at the family level(O’Donnell et al 2001); in that study four of seven

FIG. 2. Scanning electron micrographs of Zygomycetes illustrating morphological diversity of sexual and asexualreproductive structures. A–E. Mucorales. Zygospores of A. Cokeromyces recurvatus, B. Cunninghamella homothallicus, C.Radiomyces spectabilis and D. Absidia spinosa. E. Hesseltinella vesiculosa sporangia. F–G. Mortierellales. F. Mortierella(Gamsiella) multidivaricata chlamydospore. G. Lobosporangium transversalis sporangia borne on arachnoid mycelium. H–J.Zoopagales. H. Piptocephalis cormbifera immature sporangia. I. Syncephalis cornu sporophore bearing senescent sporangia withuniseriate sporangiospores. J. Rhopalomyces elegans fertile vesicle with monosporous sporangia. K. Basidiobolus ranarummonosporous sporangium. L. Dimargaritales. Dispira cornuta two-spored sporangia. M–O. Kickxellales. Monosporoussporangia of M. Spiromyces minutus, N. Linderina pennispora and O. Kickxella alabastrina. Bars: A–F, I–O 5 10 mm; G, H 520 mm.

876 MYCOLOGIA

A–E. Mucorales. Zygospores of A. Cokeromyces recurvatus, B. Cunninghamella homothallicus, C. Radiomyces spectabilis and D. Absidia spinosa. E. Hesseltinella vesiculosa sporangia. F–G. Mortierellales. F. Mortierella (Gamsiella) multidivaricata chlamydospore. G. Lobosporangium transversalis sporangia borne on arachnoid mycelium. H–J. Zoopagales. H. Piptocephalis cormbifera immature sporangia. I. Syncephalis cornu sporophore bearing senescent sporangia with uniseriate sporangiospores.

SEM of zygomycete sexual and asexual reproductive structures

White et al 2006

ARTICLES

Reconstructing the early evolution of Fungiusing a six-gene phylogenyTimothy Y. James1, Frank Kauff1, Conrad L. Schoch2*, P. Brandon Matheny3*, Valerie Hofstetter1*, Cymon J. Cox1{,Gail Celio4, Cecile Gueidan1, Emily Fraker1, Jolanta Miadlikowska1, H. Thorsten Lumbsch5, Alexandra Rauhut6,Valerie Reeb1, A. Elizabeth Arnold1{, Anja Amtoft7, Jason E. Stajich8, Kentaro Hosaka2{, Gi-Ho Sung2,Desiree Johnson2, Ben O’Rourke2, Michael Crockett2, Manfred Binder3, Judd M. Curtis3, Jason C. Slot3,Zheng Wang3{, Andrew W. Wilson3, Arthur Schußler9, Joyce E. Longcore10, Kerry O’Donnell11,Sharon Mozley-Standridge12, David Porter12, Peter M. Letcher13, Martha J. Powell13, John W. Taylor14,Merlin M. White15, Gareth W. Griffith16, David R. Davies17, Richard A. Humber18, Joseph B. Morton19,Junta Sugiyama20, Amy Y. Rossman21, Jack D. Rogers22, Don H. Pfister23, David Hewitt23, Karen Hansen23,Sarah Hambleton24, Robert A. Shoemaker24, Jan Kohlmeyer25, Brigitte Volkmann-Kohlmeyer25, Robert A. Spotts26,Maryna Serdani26, Pedro W. Crous27, Karen W. Hughes28, Kenji Matsuura29, Ewald Langer30, Gitta Langer30,Wendy A. Untereiner31, Robert Lucking5, Burkhard Budel6, David M. Geiser32, Andre Aptroot33, Paul Diederich34,Imke Schmitt5{, Matthias Schultz35, Rebecca Yahr1{, David S. Hibbett3, Francois Lutzoni1, David J. McLaughlin4,Joseph W. Spatafora2 & Rytas Vilgalys1

The ancestors of fungi are believed to be simple aquatic forms with flagellated spores, similar to members of the extantphylum Chytridiomycota (chytrids). Current classifications assume that chytrids form an early-diverging clade within thekingdom Fungi and imply a single loss of the spore flagellum, leading to the diversification of terrestrial fungi. Here wedevelop phylogenetic hypotheses for Fungi using data from six gene regions and nearly 200 species. Our results indicate thatthere may have been at least four independent losses of the flagellum in the kingdom Fungi. These losses of swimming sporescoincided with the evolution of new mechanisms of spore dispersal, such as aerial dispersal in mycelial groups and polar tubeeversion in the microsporidia (unicellular forms that lack mitochondria). The enigmatic microsporidia seem to be derivedfrom an endoparasitic chytrid ancestor similar to Rozella allomycis, on the earliest diverging branch of the fungalphylogenetic tree.

Fungi, Viridiplantae and Animalia are all large clades descended fromunicellular, flagellated, aquatic forms that radiated extensively onland. For both plants and animals, biologists have developed unifiedhypotheses regarding the evolution of morphology and ecology fromancestral to highly derived traits. For example, among green plants,morphologically simple photosynthetic forms, such as unicellular

green algae, gave rise to multicellular forms such as bryophytes,and were followed by a radiation of complex flowering forms withhighly derived sexual mechanisms at the tips of the plant phylo-geny1,2. Similarly, animals seem to have evolved increasingly complextissue systems and development from a simple, flagellated, protist-like ancestor similar to extant Choanoflagellida3.

*These authors contributed equally to this work.

1Department of Biology, Duke University, Durham, North Carolina 27708-0338, USA. 2Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331-2902, USA. 3Department of Biology, Clark University, Worcester, Massachusetts 01610, USA. 4Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108,USA. 5Field Museum of Natural History, Chicago, Illinois 60605-2496, USA. 6Fachbereich Biologie, Abteilung Pflanzenokologie und Systematik, 67653 Kaiserslautern, Germany.7Institute of Systematic Botany, New York Botanical Garden, Bronx, New York 10458-6126, USA. 8University Program in Genetics and Genomics, Duke University, Durham, NorthCarolina 27708-0338, USA. 9Institute of Botany, Darmstadt University of Technology, D-64287 Darmstadt, Germany. 10Department of Biological Sciences, University of Maine,Orono, Maine 04469, USA. 11National Center for Agricultural Utilization Research, USDA Agricultural Research Service, Peoria, Illinois 61604, USA. 12Department of Plant Biology,University of Georgia, Athens, Georgia 30605, USA. 13Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama 35487, USA. 14Department of Plant andMicrobial Biology, University of California, Berkeley, California 94720, USA. 15Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045-7534,USA. 16Institute of Biological Sciences, University of Wales, Aberystwyth, Ceredigion SY23 3DA, UK. 17Institute of Grassland and Environmental Research, Plas Gogerddan,Aberystwyth, Ceredigion SY23 3EB, UK. 18United States Plant, Soil and Nutrition Laboratory, USDA-ARS Plant Protection Research Unit, Ithaca, New York 14853-2901, USA. 19Divisionof Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia 26506-6057, USA. 20TechnoSuruga, Chiyoda-ku, Tokyo 101-0052, Japan. 21Systematic Botany andMycology Laboratory, USDA Agricultural Research Service, Beltsville, Maryland 20705, USA. 22Department of Plant Pathology, Washington State University, Pullman, Washington99164, USA. 23Harvard University Herbaria, Cambridge, Massachusetts 02138, USA. 24Biodiversity (Mycology and Botany), Agriculture and Agri-Food Canada, Ottawa, Ontario K1A0C6, Canada. 25Institute of Marine Sciences, University of North Carolina at Chapel Hill, Morehead City, North Carolina 28557, USA. 26Mid-Columbia Agricultural Research andExtension Center, Oregon State University, Hood River, Oregon 97031, USA. 27Centraalbureau voor Schimmelcultures, Fungal Biodiversity Centre, 3508 AD Utrecht, The Netherlands.28Botany Department, University of Tennessee, Knoxville, Tennessee 37996, USA. 29Faculty of Agriculture, Okayama University, Okayama 700-8530, Japan. 30Institut fur Biologie,Universitat Kassel, D-34132 Kassel, Germany. 31Department of Botany, Brandon University, Brandon, Manitoba R7A 6A9, Canada. 32Department of Plant Pathology, Penn StateUniversity, University Park, Pennsylvania 16802, USA. 33Adviesbureau voor Bryologie en Lichenologie, NL-3762 XK Soest, The Netherlands. 34Musee national d’histoire naturelle,L-2160 Luxembourg. 35Biozentrum Klein Flottbek und Botanischer Garten, Universitat Hamburg, Systematik der Pflanzen, D-22609 Hamburg, Germany. {Present addresses: Biometryand Molecular Research, Department of Zoology, Natural History Museum, London SW7 5BD, UK (C.J.C.); Department of Plant Sciences, University of Arizona, Tucson, Arizona85721, USA (A.E.A.); Department of Botany, The Field Museum, Chicago, Illinois 60605-2496, USA (K.H.); Department of Biological Sciences, Roy J. Carver Center for ComparativeGenomics, University of Iowa, Iowa City, Iowa 52242, USA (Z.W.); Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoll-Institute, D-07745 Jena, Germany(I.S.); Royal Botanic Garden Edinburgh, Edinburgh EH3 5LA, UK (R.Y.).

Vol 443 | 19 October 2006 | doi:10.1038/nature05110

818Nature Publishing Group ©2006

‘Chytridiomycota’:euchytrids

‘Zygomycota’

microsporidia

1087 Coprinopsis cinerea480 Lycoperdon pyriforme626 Coprinus comatus

563 Clavaria zollingeri673 Amanita brunnescens

625 Pluteus romellii285 Cortinarius iodes564 Pleurotus ostreatus449 Armillaria mellea558 Flammulina velutipes

556 Marasmius alliaceus542 Ampulloclitocybe clavipes

557 Collybia tuberosa468 Henningsomyces candidus

729 Hygrocybe aff. conica439 Calostoma cinnabarinum

713 Boletellus projectellus714 Hygrophoropsis aurantiaca717 Suillus pictus

576 Fibulorhizoctonia sp.455 Echinodontium tinctorium682 Lactarius deceptivus

452 Bondarzewia montana492 Stereum hirsutum

447 Coltricia perennis688 Fomitiporia mediterranea

484 Phlebia radiata767 Climacodon septentrionalis776 Phanerochaete chrysosporium562 Grifola sordulenta701 Grifola frondosa770 Fomitopsis pinicola

518 Hyphoderma praetermissum700 Cotylidia sp.

466 Gautieria otthii724 Ramaria rubella471 Hydnum albomagnum

438 Calocera cornea454 Dacryopinax spathularia

867 Cintractia sorghi vulgaris870 Tilletiopsis sp.

865 Tilletiaria anomala675 Agaricostilbum hyphaenes

674 Rhodotorula hordea456 Endocronartium harknessii

1459 Puccinia graminis

138 Scutellospora heterogama139 Glomus mosseae

845 Glomus intraradices574 Geosiphon pyriformis

141 Mortierella verticillata144 Umbelopsis ramanniana

184 Phycomyces blakesleeanus1241 Rhizopus oryzae

136 Dimargaris bacillispora140 Coemansia reversa

1062 Orphella aff. haysii29 Smittium culisetae

185 Spiromyces aspiralis142 Rhopalomyces elegans145 Piptocephalis corymbifera

28 Entomophthora muscae

19 Physoderma maydis18 Coelomomyces stegomyiae

24 Polychytrium aggregatum27 Cladochytrium replicatum

21 Batrachochytrium dendrobatidis689 Rhizophydium macroporosum

43 Rhizophlyctis rosea182 Spizellomyces punctatus

635 Synchytrium macrosporum25 Monoblepharella sp.26 Hyaloraphidium curvatum

1068 Encephalitozoon cuniculi1089 Antonospora locustae

Ciona intestinalisHomo sapiens

Populus trichocarpaOryza sativa

Chlamydomonas reinhardtii

0.05 substitutions per site

to Ascomycota

709 Colacogloea peniophorae

‘Zygomycota’:Mucormycotina

Dikarya

Fungi

Y

Y

Y

Y

Y

Cyanidioschyzon merolaeArabidopsis thaliana

Phytophthora sojaeThalassiosira pseudonana

Monosiga brevicollis

Cryptosporidium parvumToxoplasma gondii

Dictyostelium discoideum

Drosophila melanogaster

Caenorhabditis elegans297 Rozella allomycis Y

300 Allomyces arbusculus20 Rhizoclosmatium sp.

638 Neocallimastix sp.

137 Conidiobolus coronatus‘Zygomycota’:

Entomophthorales

301 Basidiobolus ranarum633 Olpidium brassicae

844 Paraglomus occultum

539 Endogone pisiformis

710 Platygloea disciformis

1088 Cryptococcus neoformans505 Ustilago maydis

1078 Neurospora crassa216 Sordaria fimicola

1085 Podospora anserina217 Chaetomium globosum

1081 Magnaporthe grisea935 Diaporthe eres

952 Gnomonia gnomon51 Xylaria hypoxylon63 Xylaria acuta1082 Fusarium graminearum

161 Fusarium aff. solani186 Hydropisphaera erubescens

52 Hypocrea citrina914 Microascus trigonosporus

413 Lindra thalassiae424 Lulworthia grandispora

1 Leotia lubrica147 Coccomyces dentatus

744 Potebniamyces pyri151 Chlorociboria aeruginosa76 Mollisia cinerea

279 Monilinia fructicola59 Botryotinia fuckeliana

941 Dermea acerina166 Cudoniella clavus

49 Lachnum virgineum56 Geoglossum nigritum64 Trichoglossum hirsutum1004 Pleopsidium chlorophanum1005 Acarospora schleicheri1007 Acarospora laqueata

106 Echinoplaca strigulacea958 Diploschistes ocellatus

78 Acarosporina microspora398 Stictis radiata

296 Orceolina kerguelensis962 Trapelia placodioides224 Pertusaria dactylina

358 Dibaeis baeomyces645 Umbilicaria mammulata

687 Hypocenomyce scalaris134 Peltigera degenii

196 Mycoblastus sanguinarius639 Lecanora hybocarpa

6 Canoparmelia caroliniana3 Cladonia caroliniana

642 Bacidia schweinitzii84 Physcia aipolia1079 Aspergillus fumigatus

1080 Aspergillus nidulans426 Monascus purpureus

1083 Histoplasma capsulatum1084 Coccidioides immitis

430 Spiromastix warcupii657 Capronia pilosella668 Exophiala dermatitidis659 Ramichloridium anceps

669 Exophiala pisciphila684 Agonimia sp.91 Dermatocarpon miniatum661 Endocarpon pallidulum

697 Staurothele frustulenta342 Pyrgillus javanicus387 Pyrenula pseudobufonia

891 Peltula umbilicata892 Peltula auriculata896 Lichinella iodopulchra

101 Anisomeridium polypori1036 Trematosphaeria heterospora

1037 Westerdykella cylindrica283 Pyrenophora phaeocomes54 Cochliobolus heterostrophus940 Pleospora herbarum110 Trypethelium sp.

274 Dothidea sambuci921 Dothidea insculpta

939 Capnodium coffeae355 Dendrographa minor

126 Roccella fuciformis80 Simonyella variegata

148 Cheilymenia stercorea62 Scutellinia scutellata

65 Aleuria aurantia949 Pyronema domesticum50 Sarcoscypha coccinea

152 Caloscypha fulgens176 Gyromitra californica179 Disciotis sp.60 Morchella aff. esculenta66 Helvella compressa181 Ascobolus crenulatus507 Peziza vesiculosa71 Peziza proteana

905 Orbilia vinosa906 Orbilia auricolor

1069 Saccharomyces cerevisiae1070 Saccharomyces castellii1073 Candida glabrata

1071 Kluyveromyces waltii1072 Ashbya gossypii1075 Kluyveromyces lactis

1074 Candida albicans1269 Candida tropicalis

1270 Candida guilliermondii1077 Debaryomyces hansenii1268 Candida lusitaniae

1076 Yarrowia lipolytica1199 Schizosaccharomyces pombe

265 Taphrina wiesneri266 Protomyces inouyei

1192 Pneumocystis carinii

Pezizomycotina

Y

PhagotrophPhototrophLichenizedMycorrhizalPlant pathogenAnimal pathogenMycoparasiteInsect commensalSaprobeUncertain

GenomesequencedMotile cell stagepresent

SaprobeUncertain

PathogenMutualistPhototrophPhagotroph

Viridiplantae

Metazoa

Glomeromycota

Basidiomycota:Pucciniomycotina

Basidiomycota:Ustilaginomycotina

Basidiomycota:Agaricomycotina

100/100

100/92

100/73

100/71

--/85

‘Chytridiomycota’:Blastocladiales

...

...

RhodophytaStramenopiles

ApicomplexaMycetozoa

Choanoflagellida

‘Chytridiomycota’

‘Chytridiomycota’

100/80

100/100

100/81

100/94

100/93

100/98

100/94

Ascomycota:Lichinomycetes

Ascomycota:

Eurotiomycetes

Ascomycota:Lecanoromycetes

Ascomycota:Leotiomycetes

Ascomycota: Sordariom

ycetes

HOLMPA

IS?

SS

S

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S

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A

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AA

I

II

HH

?

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?

OO

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A

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H

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S A

PS A

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PA

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PP

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PP

A

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A

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L

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LLL

LL

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LL

LL

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LL

LL

LL

LL

L

LL

L

S

S

S

H

Ascomycota:Taphrinomycotina

Ascomycota:Saccharomycotina

Ascomycota: Orbiliomycetes

Ascomycota:Pezizomycetes

Ascomycota:Arthoniomycetes

Ascomycota:Dothideomycetes

Figure 1 | Phylogeny of the kingdom Fungi using bayesian analysis of thecombined, six-gene data set. Each fungal species begins with a unique‘Assembling the Fungal Tree of Life’ identifier, followed by genus andspecies. Indicated for each terminal taxon are: nutritional mode, whetherthey produce flagellated cells and if there is a genome sequence for the taxoncompleted or underway. Thickened branches indicate those that aresupported both by heterogeneous bayesian analysis (BPP $95%) and byMLBS ($70%). Almost every branch was supported by BPP and thus valuesare not shown. Where indicated, support values (percentage of trees in

agreement out of 58,611 trees) indicate BPP followed by MLBS. Branches areshaded according to reconstruction of nutritional mode. Microsporidiabranches have been shortened three times (double black break) to increasereadability. Red vertical ticks on branches indicate alternative placements ofmicrosporidia that might be significantly rejected (P , 0.05) and green ticksindicate placements that cannot be rejected. Quotation marks indicate non-monophyly of the taxon. The name ‘Mucormycotina’ will be validated in amanuscript that is in preparation.

ARTICLES NATURE | Vol 443 | 19 October 2006

820Nature Publishing Group ©2006

Assembling Fungal Tree Of Life - AFTOL (2006)

Molecular-based phylogeny resolving major relationships of Fungi.

Rozella and Microsporidia as earliest lineages of Fungi

FIG. 1. Phylogeny of Zygomycota based on rRNA operon (18S+28S+5.8S genes). Shown is a majority-rule consensusphylogram computed from the set of 36 000 credible trees with branch lengths averaged over trees. Numbers above branchesindicate nodes that were supported by $ 95% Bayesian posterior probability. Branches supported by parsimony bootstrap $70% are indicated by thickened lines. Hashed lines indicate long branches divided by 8 to improve visibility of branch lengths.

WHITE ET AL: PHYLOGENY OF THE ZYGOMYCOTA 875

Phylogeny of the Zygomycota based on nuclear ribosomal sequence data

Merlin M. White1,2

Department of Ecology & Evolutionary Biology,University of Kansas, Lawrence, Kansas 66045-7534

Timothy Y. JamesDepartment of Biology, Duke University, Durham,North Carolina 27708

Kerry O’DonnellNCAUR, ARS, USDA, Peoria, Illinois 61604

Matıas J. CafaroDepartment of Biology, University of Puerto Rico atMayaguez, Mayaguez, Puerto Rico 00681

Yuuhiko TanabeLaboratory of Intellectual Fundamentals forEnvironmental Studies, National Institute forEnvironmental Studies, Ibaraki 305-8506, Japan

Junta SugiyamaTokyo Office, TechnoSuruga Co. Ltd., 1-8-3, KandaOgawamachi, Chiyoda-ku, Tokyo 101-0052, Japan

Abstract: The Zygomycota is an ecologically heter-ogenous assemblage of nonzoosporic fungi compris-ing two classes, Zygomycetes and Trichomycetes.Phylogenetic analyses have suggested that the phylumis polyphyletic; two of four orders of Trichomycetesare related to the Mesomycetozoa (protists) thatdiverged near the fungal/animal split. Currentcircumscription of the Zygomycota includes onlyorders with representatives that produce zygospores.We present a molecular-based phylogeny includingrecognized representatives of the Zygomycetes andTrichomycetes with a combined dataset for nuclearrRNA 18S (SSU), 5.8S and 28S (LSU) genes. Treereconstruction by Bayesian analyses suggests theZygomycota is paraphyletic. Although 12 clades wereidentified only some of these correspond to the nineorders of Zygomycota currently recognized. A largesuperordinal clade, comprising the Dimargaritales,Harpellales, Kickxellales and Zoopagales, groupingtogether many symbiotic fungi, also is identified inpart by a unique septal structure. Although Harpel-lales and Kickxellales are not monophyletic, these

lineages are distinct from the Mucorales, Endogo-nales and Mortierellales, which appear more closelyrelated to the Ascomycota + Basidiomycota +Glomeromycota. The final major group, the insect-associated Entomophthorales, appears to be poly-phyletic. In the present analyses Basidiobolus andNeozygites group within Zygomycota but not with theEntomophthorales. Clades are discussed with specialreference to traditional classifications, mapping mor-phological characters and ecology, where possible, asa snapshot of our current phylogenetic perspective ofthe Zygomycota.

Key words: Asellariales, basal lineages, Chytridio-mycota, Fungi, molecular systematics, opisthokont

INTRODUCTION

Most studies suggest that the phylum Zygomycota isnot monophyletic and the classification of the entirephylum is in flux. The Zygomycota currently isdivided into two classes, the Zygomycetes andTrichomycetes. However molecular phylogenies sug-gest that neither group is natural (i.e. monophyletic).Two orders previously classified as Trichomycetes, theAmoebidiales and Eccrinales, are not fungi (Bennyand O’Donnell 2000, Cafaro 2005). FurthermoreMicrosporidia, animal pathogens previously consid-ered to be protists, might have evolved within theZygomycota (but see Tanabe et al 2005) (Keeling et al2000, Forget et al 2002, Keeling 2003). One signifi-cant recent change has been the removal of theglomeralean arbuscular mycorrhizal (AM) fungi fromZygomycota and their reclassification as a separatephylum, the Glomeromycota (Schußler et al 2001).

Members of the Zygomycota have been considereda primitive and early diverging lineage of the Fungibecause they lack complex fruiting structures andmost representatives have coenocytic aseptate hyphaeduring all or part of their life cycle. Zygomycota oftenmight be overlooked even by mycologists, but theycan be encountered as near as the kitchen, disguisedas moldy bread or fruit (James and O’Donnell 2004).Some are beneficial, such as Rhizopus, used in severaltraditional fermented foods, including tempeh andcassava. Most species of the Zygomycota are saprobic,but some species are facultative pathogens of plants,animals (including humans) or even other fungi. TheTrichomycetes are obligate endosymbionts of arthro-pods. Indeed members of the Zygomycota areubiquitous in nature, in a seemingly endless varietyof interactions.

2 Current Address: Department of Biology, Boise State University,Boise, Idaho 83725-1515 (as of Jan 2007)

1 Corresponding Author. E-mail: [email protected]

This paper is dedicated to the great many students of the ‘‘lowerFungi’’—past and present—who helped introduce us to thiswonderfully eclectic and diverse group that we can only hope tohighlight herein.

Accepted for publication 10 October 2006.

Mycologia, 98(6), 2006, pp. 872–884.# 2006 by The Mycological Society of America, Lawrence, KS 66044-8897

872

Improving ‘Zygomycete’ Tree of Life

• NSF funded Genealogy of Life project - ZyGoLife http://zygolife.org (*site down till Saturday)

• Improve understanding of relationships of these fungi by deep sampling of genome ‘backbone’ (100 more) and SSU/or light genome sequencing for 1000s of ‘leaves’

• Integrate fossil evidence for divergence time estimates

• Increased sampling from Environmental and Single-cell approaches

• Encyclopedia of Life pages for all Zygo species

• Capture images and cellular and cell wall structure for all major lineages

Improved Zygomyete Relationships inferred from whole genome

data

0.1

Coemansia

Batrachochytrium

Conidiobolus coronatus

Homo

Spizellomyces

Rhizophagus

Aspergillus

Monosiga

Allomyces

Mucor

Gonopodya

Rhizopus

Dictyostelium

Piromyces

Conidiobolus thromboides

Cryptococcus

Ustilago

Neurospora

Schizosaccharomyces

Backusella

Umbelopsis

Mortierella verticillata

Puccinia

Rozella

Catenaria

Mortierella elongata

Lichtheimia

Phycomyces

Coprinopsis

Arabidopsis

Blastocladiomycota

Chytridiomycota

Kickxellomycotina

Entomopthoromycota

Mucormycotina

Basidiomycota

Ascomycota

Mortierellomycotina

Glomeromycota

http://zygolife.org

Hypotheses and questions from genomic data

✤ What is structure of clades within Zygos: EKZ & MMG

✤ Where do difficult-to-place taxa belong? Olpidium, Endogene

✤ What is the diversity of the Entomophthoromycota?

✤ Trait evolution and genome content - how does ecology influence genome content

Yarrowia lipolytica

Encephalitozoon cuniculi

Spizellomyces punctatus

Aspergillus fumigatus

Batrachochytrium dendrobatidis

Thalassiosira pseudonanaPythium ultimum

Sclerotinia sclerotiorum

Saccharomyces cerevisiae

Piromyces sp.

Capsaspora owczarzaki

Cryptococcus neoformans var. grubii

Drosophila melanogaster

Monosiga brevicollis

Rozella allomycis

Antonospora locustae

Dictyostelium discoideum

Neurospora crassa

Phycomyces blakesleeanus

Cyanidoschyzon merolae

Coprinopsis cinerea

Vavraia culicis

Enterocytozoon bieneusi

Nematocida parisii ERTm1

Schizosaccharomyces pombe

Ashbya gossypii

Rhizopus oryzae

Toxoplasma gondii

Wallemia sebi

Hydra magnipapillata

Allomyces macrogynus

Encephalitozoon intestinalis

Chlamydomonas reinhardtii

Ustilago maydisSporobolomyces roseus

Mortierella verticillata

Nosema ceranae

Ciona intestinalis

Homalophlyctis polyrhiza

Ascomycota

Basidiomycota

Mucoromycotina

Chytridiomycota sensu lato

Cryptomycota +microsporidia

Dikarya

99/100

23/100

87/96

3/100

46/100

0.3

)LJXUH��

James et al. Cur Biol 2013

Rozella

TY James

CDCmicr

ospo

ridia6,350 genes

Whole genome phylogeny from 200 proteins

~80 Zygomycete genomes 51 protein coding genes~20k filtered positions

RAxML PROTGAMMA

0.2

Lichtheimia_ramosa_B5399

Conidiobolus_coronatus_NRRL_28638.Conco1

Martensiomyces_pterosporus.Marpt1

Rhizomucor_variabilis_B7584


Hesseltinella_vesiculosa_NRRL_3301.Hesve

Cokeromyces_recurvatus_NRRL2243

Echinosporandium_transversale_NRRL3116

Apophysomyces_trapeziformis_B9324

Zygorhynchus_heterogamus_NRRL1489

R_stol_My

Thermomucor_indicae-seudaticae_HACC_243

Cokeromyces_recurvatus_B5483

Syncephalastrum_racemosum_B6101


Mortierella_elongata_AG-77.Morel1

Basidiobolus_meristosporus_B9252

Mycotypha_africana_NRRL2978

Coemansia_reversa_NRRL_1564.Coere1

Spinellus_fusiger_NRRL22323

Cunninghamella_bertholletiae_175

Umbelopsis_ramanniana.Umbra1

Mucor_B8987

Pilobolus_umbonatus_NRRL6349

Cunninghamella_elegans_B9769

Mucor_circinelloides.Mucci2

Ramicandelaber_brevisporus.Rambr1


Radiomyces_spectabilis_NRRL2753

Syncephalastrum_racemosum_NRRL2496

R_stolB9770

Hessentinella_vesiculosa_NRRL3301

Rhizopus_stolonifer_B9770

Backusella_circina_FSU_941.Bacci1

Mucor_1006PhL

Mucor_indicus_B7402

Parasitella_parasitica_NRRL2501

Conidiobolus_thromboides_FSU_785.Conth1

Apophysomyces_elegans_B7760

Mucor_racemosus_B9645

Mucor_irregularis_B50

Lichtheimia_hyalospora_FSU_10163.Lichy1

Conidiobolus_incongruus_B7586

Linderina_pennispora_NRRL3781

Spiromyces_aspiralis_NRRL22631


Arabidopsis_thaliana

Rhizomucor_miehei_CAU432

Saksenaea_vasiformis_B4078

Thamindium_elegans_NRRL2467

Toxopasma_gondii_ME49.assembly

R_microB9738

Absidia_repens_NRRL1336

Piptocephalis_cylindrospora.Pipcy2

Blakesea_trispora_NRRL2456

Phycomyces_blakesleeanus.Phybl2

Circinella_umbellata_NRRL1351

Syncephalastrum_monosporum_B8922

Mortierella_alpina_B6842

Mucor_velutinosus_B5328

Umbelopsis_isabellina_B7317

Piromyces_sp_E2.PirE2_1

Cunninghamella_echinulata_NRRL1382

Micromucor_ramannianus_NRRL5844

Chaetocladium_jonesii_NRRL2343

100

100

100

70

100

100

100

100

46

100

99

10079

100

100

83

10070

70

67

100

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97

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82

89

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46

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22

68

81

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93

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29

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Microsporidia

DikaryaChytridiomycota + Blastocladiomycota

Rhizopus microsporus

Rhizopus oryzae & Rhizopus delemar

Mucormycotina

MortierellomycotinaGlomeromycota

M-M-G Clade

0.2











R_stol_My












Mucor_B8987








R_stolB9770




Mucor_1006PhL

Mucor_indicus_B7402
















R_microB9738














100

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82

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Microsporidia




Potential new clade with Umbelopsis

It has been grouped with both Mortierellomycotina &

Mucormycotina

0.2











R_stol_My












Mucor_B8987








R_stolB9770




Mucor_1006PhL

Mucor_indicus_B7402
















R_microB9738














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93

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Microsporidia




Entomophthoromycota

Kickxellomycotina

Zoopagomycotina

E-K-Z clade

0.2











R_stol_My












Mucor_B8987








R_stolB9770




Mucor_1006PhL

Mucor_indicus_B7402
















R_microB9738














100

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82

89

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46

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22

68

81

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93

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Microsporidia




Genome skimming based phylogenomics

✤ Sample lightly (5-10x coverage) with Illumina, IonTorrent

✤ Extract reads based on a set of targeted marker loci, quick assembly of these reads, scaffold them based on the marker

✤ Alternatively do draft genome assembly

✤ Extract best ORF by protein to genome alignments (splice-site aware)

Date

6-frame translated(proteins)

Raw Sequencing Reads (genomic or

transcriptomic)

Reads grouped matching each marker query

HMMs of phylogenetic

marker proteins

Contigs for each marker

Assembly of reads (PHRAP)

Predicted protein for

each marker gene

Genewise

HMMER

Multiple alignment for each marker gene and ~300

fungi

Concatenated alignment & phylogenetic

tree

Gene tree for each marker

PHYling pipeline

PHYling PipelineCode http://github.com/stajichlab/Phyling

exonerate

Cap3

FASTX

http://github.com/stajichlab/Phyling

0.2











R_stol_My












Mucor_B8987








R_stolB9770




Mucor_1006PhL

Mucor_indicus_B7402
















R_microB9738














100

100

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100

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46

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67

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68

81

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Microsporidia




19 of the taxa are actually genome skimming sequence

(1-4M reads)

0.2











R_stol_My












Mucor_B8987








R_stolB9770




Mucor_1006PhL

Mucor_indicus_B7402
















R_microB9738














100

100

100

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46

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83

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46

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Microsporidia




Identical placement of taxa from genome skimming or complete assembly Genome skimming taxa from the same strain or same species are sister taxa in the tree supporting that PHYling can extract sufficient data from unassembled reads to provide good placement.




















Total Bases

0e+00

1e+06

2e+06

3e+06

4e+06

Variability in coverage from multiplex samples Overall coverage varies because of differences or bias in how concentration is made with multiplexing

Date

−1.0

−0.5

0.0

0.5

1.0

Linderina_pennisp

ora_NRRL3781

Mycotypha_africana_N

RRL2978

Pilobolus_um

bonatus_NR

RL6349

Blakesea_trispora_N

RRL2456

Cokeromyces_recurvatus_NR

RL2243

Cunningham

ella_echinulata_NRRL1382

Syncephalastrum_racem

osum

_NRR

L2496

Radiom

yces_spectabilis_N

RRL2753

Zygorhynchus_heterogam

us_N

RRL1489

R_microB9738


Spinellus_fusig

er_N

RRL22323

Mucor_racem

osus_B

9645

Absidia_repens_N

RRL1336

Spiromyces_aspiralis_N

RRL22631

Echinosporandium

_transversale_NRRL3116

Mucor_velutinosus_B

5328

Mortierella_verticillata_N

RRL_6337

Mucor_indicus_B

7402



Umbelopsis_isabellin

a_B7

317

Mucor_B8987

Rhizomucor_variabilis_B

7584

Mucor_1006P

hLMortierella_elongata_AG

.77.Morel1

Wallemia_sebi_CBS

_633.66

R_oryz21789

Neurospora_crassa_OR7

4ASyncephalastrum_racem

osum

_B6101

R_oryzB7

407


R_oryz18148

Backusella_circina_FS

U_941.Bacci1

Syncephalastrum_m

onosporum_B8922

R_oryz21396

R_oryz99133

Mucor_ram

osissimus_97.1192

Rhizo

pus_delemar_R

A_99.880

Umbelopsis_

ramanniana.Umbra1

Circinella_umbellata_N

RRL1351

R_stolB9770

R_oryz13440

R_del

R_oryz99892

R_micro_rhiz

Rhizopus_microsporus_var_rhizopodiform

us_B

7455

Cunningham

ella_bertholletiae_175

Rhizopus_oryzae_99.892


770

Cunningham

ella_elegans_B9769

R_micro

Basid

iobolus_meristosporus_B9

252

R_oryzHUMC02


483

Hesseltinella_vesiculosa_NRRL_3301.Hesve1

Coem

ansia

_reversa_N

RRL_1564.Coere1

Rhizomucor_m

iehei_CA

U432

R_del21447

Microm

ucor_ram

annianus_N

RRL5844

Apophysomyces_trapeziformis_

B9324

R_del21446

Apophysomyces_elegans_B

7760

Phycom

yces_blakesle

eanus.Phybl2

Lichtheimia_ram

osa_B5

399

R_stol_M

yThermom

ucor_indica

e.seudaticae_H

ACC_

243

Ramica

ndelaber_brevisporus.Ram

br1


586

Saksenaea_vasiformis_B

4078

Lichtheimia_hyalospora_FS

U_10163.Lichy1

Rozella_allomycis_C

SF55

R_del21477

Parasitella_parasitica_N

RRL2501

Cryptococcus_neoformans_var_neoformans_JEC21

R_micro_chin

Rhizopus_microsporus_var._chinensis_CCTC

C_M

201021

Catenaria_anguillulae_PL

171.Catan1

Lichtheimia_corym

bifera_FSU

_9682

Batrachochytrium

_dendrobatidis_

JAM81.Batde5

Conidiobolus_thromboides_FSU

_785.Conth1


Tham

indium

_elegans_N

RRL2467

Rhizophagus_irregularis_DAO

M_181602.Gloin1

Chaetocla

dium

_jonesii_NR

RL2343

Encephalitozoon_intestinalis_

ATCC_50506.Encin1

Encephalitozoon_hellem_ATC

C_50504.Enche1


Encephalitozoon_cuniculi_GB.M1.En

ccu1

Encephalitozoon_rom

aleae_SJ.2008.En

cro1

Mucor_irregularis_B

50No

sema_ceranae_BR

L01.Nosce1

Monosiga_brevico

llisNe

matocida_parisii_ER

Tm1.Nem

pa1


R_azyg

Relative capture & length of marker genesNormalized length differences of all marker genes per species vs the model length - some species

Better

Worse

Microsporidia

Conclusions

✤ Early stage of project to collect and integrate data to understand evolution of the “Zygomycetes”

✤ Support for monophyletic EKZ and MMG clades - to be named.

✤ Genome Skimming for Phylogenomics works well

✤ Testing how this can replace some barcoding strategies

✤ Open to collaboration, contribution of species to the sampling, student contributions to EOL pages

Acknowledgements -‐ Team ZyGo!

Stajich lab Peng Liu

Jinfeng Chen Ousmane Cisse Rod Olarte

Steven Ahrendt Yizhou Wang Na Jeong

Tim James (U Michigan) Joey Spatafora (Oregon State)

Robert Roberson (Arizona State) Kerry O’Donnell (USDA-NCAUR)

Merlin White (Boise State) Rytas Vilgalys (Duke)

Matthew Smith & Gerry Benny (U Florida)Nicolas Corradi (U Ottawa)

Mary Berbee (U British Columbia) Thomas Taylor (U Kansas)

Poster #520 (Friday)

Katy Lazarus Andrii Gryganskyi (Lambert)

Greg Bonito (Michigan State)