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Phylogenomics of the Zygomycetes - Fungal Genetics 2015
The document discusses exploring the phylogeny and genome evolution of zygomycete lineages through phylogenomics. The goals are to facilitate fungal genome sequencing across the kingdom fungi, produce a genome-scale phylogeny of fungi, create genome reference datasets, and obtain data from non-model organisms.
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Phylogenomics of the Zygomycetes - Fungal Genetics 2015
- 1. Fungal Genetics 2015 Phylogenomicsof the Zygomycete lineages: Exploring phylogeny and genome evolution Jason Stajich @hyphaltip @zygolife @stajichlab
- 2. 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
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- 4. Zygomycetes Diverse, early branchinglineages that could contain transition states for zoosporic to Dikarya and multicellular states “Conundrum of the fungi” because the placement of the groups has varied
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- 6. Date Spinellus fusiger onMycena capillaripes Darvin DeShazer
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- 9. Date Entomophthora muscae onhouse fly Gryganskyi et al 2013; DOI: 10.1371/journal.pone.0071168
- 10. s s ung host hyphae parasite hyphae S.dispora! rhizoids merosporangium sporangiophore Katy Lazarus
- 11. A–E. Mucorales. Zygosporesof 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
- 12. ARTICLES Reconstructing the earlyevolution of Fungi using a six-gene phylogeny Timothy Y. James1 , Frank Kauff1 , Conrad L. Schoch2 *, P. Brandon Matheny3 *, Vale´rie Hofstetter1 *, Cymon J. Cox1 {, Gail Celio4 , Ce´cile Gueidan1 , Emily Fraker1 , Jolanta Miadlikowska1 , H. Thorsten Lumbsch5 , Alexandra Rauhut6 , Vale´rie 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 Schu¨ßler9 , 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 Lu¨cking5 , Burkhard Bu¨del6 , David M. Geiser32 , Andre´ Aptroot33 , Paul Diederich34 , Imke Schmitt5 {, Matthias Schultz35 , Rebecca Yahr1 {, David S. Hibbett3 , Franc¸ois 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 extant phylum Chytridiomycota (chytrids). Current classifications assume that chytrids form an early-diverging clade within the kingdom Fungi and imply a single loss of the spore flagellum, leading to the diversification of terrestrial fungi. Here we develop phylogenetic hypotheses for Fungi using data from six gene regions and nearly 200 species. Our results indicate that there may have been at least four independent losses of the flagellum in the kingdom Fungi. These losses of swimming spores coincided with the evolution of new mechanisms of spore dispersal, such as aerial dispersal in mycelial groups and polar tube eversion in the microsporidia (unicellular forms that lack mitochondria). The enigmatic microsporidia seem to be derived from an endoparasitic chytrid ancestor similar to Rozella allomycis, on the earliest diverging branch of the fungal phylogenetic tree. Fungi, Viridiplantae and Animalia are all large clades descended from unicellular, flagellated, aquatic forms that radiated extensively on land. For both plants and animals, biologists have developed unified hypotheses regarding the evolution of morphology and ecology from ancestral 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 with highly derived sexual mechanisms at the tips of the plant phylo- geny1,2 . Similarly, animals seem to have evolved increasingly complex tissue systems and development from a simple, flagellated, protist- like ancestor similar to extant Choanoflagellida3 . *These authors contributed equally to this work. 1 Department of Biology, Duke University, Durham, North Carolina 27708-0338, USA. 2 Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331- 2902, USA. 3 Department of Biology, Clark University, Worcester, Massachusetts 01610, USA. 4 Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108, USA. 5 Field Museum of Natural History, Chicago, Illinois 60605-2496, USA. 6 Fachbereich Biologie, Abteilung Pflanzeno¨kologie und Systematik, 67653 Kaiserslautern, Germany. 7 Institute of Systematic Botany, New York Botanical Garden, Bronx, New York 10458-6126, USA. 8 University Program in Genetics and Genomics, Duke University, Durham, North Carolina 27708-0338, USA. 9 Institute of Botany, Darmstadt University of Technology, D-64287 Darmstadt, Germany. 10 Department of Biological Sciences, University of Maine, Orono, Maine 04469, USA. 11 National Center for Agricultural Utilization Research, USDA Agricultural Research Service, Peoria, Illinois 61604, USA. 12 Department of Plant Biology, University of Georgia, Athens, Georgia 30605, USA. 13 Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama 35487, USA. 14 Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA. 15 Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045-7534, USA. 16 Institute of Biological Sciences, University of Wales, Aberystwyth, Ceredigion SY23 3DA, UK. 17 Institute of Grassland and Environmental Research, Plas Gogerddan, Aberystwyth, Ceredigion SY23 3EB, UK. 18 United States Plant, Soil and Nutrition Laboratory, USDA-ARS Plant Protection Research Unit, Ithaca, New York 14853-2901, USA. 19 Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia 26506-6057, USA. 20 TechnoSuruga, Chiyoda-ku, Tokyo 101-0052, Japan. 21 Systematic Botany and Mycology Laboratory, USDA Agricultural Research Service, Beltsville, Maryland 20705, USA. 22 Department of Plant Pathology, Washington State University, Pullman, Washington 99164, USA. 23 Harvard University Herbaria, Cambridge, Massachusetts 02138, USA. 24 Biodiversity (Mycology and Botany), Agriculture and Agri-Food Canada, Ottawa, Ontario K1A 0C6, Canada. 25 Institute of Marine Sciences, University of North Carolina at Chapel Hill, Morehead City, North Carolina 28557, USA. 26 Mid-Columbia Agricultural Research and Extension Center, Oregon State University, Hood River, Oregon 97031, USA. 27 Centraalbureau voor Schimmelcultures, Fungal Biodiversity Centre, 3508 AD Utrecht, The Netherlands. 28 Botany Department, University of Tennessee, Knoxville, Tennessee 37996, USA. 29 Faculty of Agriculture, Okayama University, Okayama 700-8530, Japan. 30 Institut fu¨r Biologie, Universita¨t Kassel, D-34132 Kassel, Germany. 31 Department of Botany, Brandon University, Brandon, Manitoba R7A 6A9, Canada. 32 Department of Plant Pathology, Penn State University, University Park, Pennsylvania 16802, USA. 33 Adviesbureau voor Bryologie en Lichenologie, NL-3762 XK Soest, The Netherlands. 34 Muse´e national d’histoire naturelle, L-2160 Luxembourg. 35 Biozentrum Klein Flottbek und Botanischer Garten, Universita¨t Hamburg, Systematik der Pflanzen, D-22609 Hamburg, Germany. {Present addresses: Biometry and Molecular Research, Department of Zoology, Natural History Museum, London SW7 5BD, UK (C.J.C.); Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, 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 Comparative Genomics, University of Iowa, Iowa City, Iowa 52242, USA (Z.W.); Leibniz Institute for Natural Product Research and Infection Biology, Hans-Kno¨ll-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 818 NaturePublishing Group©2006 ‘Chytridiomycota’: euchytrids ‘Zygomycota’ microsporidia 139 Glomus mosseae 845 Glomus intraradices 574 Geosiphon pyriformis 141 Mortierella verticillata 144 Umbelopsis ramanniana 184 Phycomyces blakesleeanus 1241 Rhizopus oryzae 136 Dimargaris bacillispora 140 Coemansia reversa 1062 Orphella aff. haysii 29 Smittium culisetae 185 Spiromyces aspiralis 142 Rhopalomyces elegans 145 Piptocephalis corymbifera 28 Entomophthora muscae 19 Physoderma maydis 18 Coelomomyces stegomyiae 24 Polychytrium aggregatum 27 Cladochytrium replicatum 21 Batrachochytrium dendrobatidis 689 Rhizophydium macroporosum 43 Rhizophlyctis rosea 182 Spizellomyces punctatus 635 Synchytrium macrosporum 25 Monoblepharella sp. 26 Hyaloraphidium curvatum 1068 Encephalitozoon cuniculi 1089 Antonospora locustae Ciona intestinalis Homo sapiens ‘Zygomycota’: Mucormycotina Fungi Y Y Cyanidioschyzon merolae Arabidopsis thaliana Phytophthora sojae Thalassiosira pseudonana Monosiga brevicollis Cryptosporidium parvum Toxoplasma gondii Dictyostelium discoideum Drosophila melanogaster Caenorhabditis elegans 297 Rozella allomycis Y 300 Allomyces arbusculus 20 Rhizoclosmatium sp. 638 Neocallimastix sp. 137 Conidiobolus coronatus ‘Zygomycota’: Entomophthorales 301 Basidiobolus ranarum 633 Olpidium brassicae 844 Paraglomus occultum 539 Endogone pisiformis 659 Ramichloridium ancep 669 Exophiala pisciphila 684 Agonimia sp. 91 Dermatocarpon miniatum 661 Endocarpon pallidulum 697 Staurothele frustulenta 342 Pyrgillus javanicus 387 Pyrenula pseudobufo 891 Peltula umbilicata 892 Peltula auriculata 896 Lichinella iodopulchra 101 Anisomeridium polypori 1036 Trematosphaeria heterospora 1037 Westerdykella cylindrica 283 Pyrenophora phaeocomes 54 Cochliobolus heterostrophus 940 Pleospora herbarum 110 Trypethelium sp. 274 Dothidea sambuci 921 Dothidea insculpta 939 Capnodium coffeae 355 Dendrographa minor 126 Roccella fuciformis 80 Simonyella variegata 148 Cheilymenia stercorea 62 Scutellinia scutellata 65 Aleuria aurantia 949 Pyronema domesticum 50 Sarcoscypha coccinea 152 Caloscypha fulgens 176 Gyromitra californica 179 Disciotis sp. 60 Morchella aff. esculenta 66 Helvella compressa 181 Ascobolus crenulatus 507 Peziza vesiculosa 71 Peziza proteana 905 Orbilia vinosa 906 Orbilia auricolor 1069 Saccharomyces cerevisiae 1070 Saccharomyces castellii 1073 Candida glabrata 1071 Kluyveromyces waltii 1072 Ashbya gossypii 1075 Kluyveromyces lactis 1074 Candida albicans 1269 Candida tropicalis 1270 Candida guilliermondii Pezizomycotina Metazoa Glomeromycota --/85 ‘Chytridiomycota’: Blastocladiales ... Rhodophyta Stramenopiles Apicomplexa Mycetozoa Choanoflagellida ‘Chytridiomycota’ ‘Chytridiomycota’ 100/94 100/93 100/94 S S S S S S S S S S S O M M M P P A A A A A A I I H H O O P A H A H H S S S S A P S A S M S S S S S S S S S S S S S S S S S S S S S S S P P P P A A A A L L L L L L L L L L S S H Sa Ascomycota A D Assembling Fungal Tree Of Life - AFTOL (2006) Molecular-based phylogeny resolving major relationships of Fungi. Rozella and Microsporidia as earliest lineages of Fungi
- 13. Phylogeny of theZygomycota based on nuclear ribosomal sequence data Merlin M. White1,2 Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045-7534 Timothy Y. James Department of Biology, Duke University, Durham, North Carolina 27708 Kerry O’Donnell NCAUR, ARS, USDA, Peoria, Illinois 61604 Matı´as J. Cafaro Department of Biology, University of Puerto Rico at Mayagu¨ez, Mayagu¨ez, Puerto Rico 00681 Yuuhiko Tanabe Laboratory of Intellectual Fundamentals for Environmental Studies, National Institute for Environmental Studies, Ibaraki 305-8506, Japan Junta Sugiyama Tokyo Office, TechnoSuruga Co. Ltd., 1-8-3, Kanda Ogawamachi, 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 phylum is polyphyletic; two of four orders of Trichomycetes are related to the Mesomycetozoa (protists) that diverged near the fungal/animal split. Current circumscription of the Zygomycota includes only orders with representatives that produce zygospores. We present a molecular-based phylogeny including recognized representatives of the Zygomycetes and Trichomycetes with a combined dataset for nuclear rRNA 18S (SSU), 5.8S and 28S (LSU) genes. Tree reconstruction by Bayesian analyses suggests the Zygomycota is paraphyletic. Although 12 clades were identified only some of these correspond to the nine orders of Zygomycota currently recognized. A large superordinal clade, comprising the Dimargaritales, Harpellales, Kickxellales and Zoopagales, grouping together many symbiotic fungi, also is identified in part 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 closel related to the Ascomycota + Basidiomycota Glomeromycota. The final major group, the insec associated Entomophthorales, appears to be poly phyletic. In the present analyses Basidiobolus an Neozygites group within Zygomycota but not with th Entomophthorales. Clades are discussed with specia reference to traditional classifications, mapping mor phological characters and ecology, where possible, a a snapshot of our current phylogenetic perspective o the Zygomycota. Key words: Asellariales, basal lineages, Chytridio mycota, Fungi, molecular systematics, opisthokon INTRODUCTION Most studies suggest that the phylum Zygomycota i not monophyletic and the classification of the entir phylum is in flux. The Zygomycota currently i divided into two classes, the Zygomycetes an Trichomycetes. However molecular phylogenies sug gest that neither group is natural (i.e. monophyletic) Two orders previously classified as Trichomycetes, th Amoebidiales and Eccrinales, are not fungi (Benn and O’Donnell 2000, Cafaro 2005). Furthermor Microsporidia, animal pathogens previously consid ered to be protists, might have evolved within th Zygomycota (but see Tanabe et al 2005) (Keeling et a 2000, Forget et al 2002, Keeling 2003). One signif cant recent change has been the removal of th glomeralean arbuscular mycorrhizal (AM) fungi from Zygomycota and their reclassification as a separat phylum, the Glomeromycota (Schu¨ßler et al 2001). Members of the Zygomycota have been considere a primitive and early diverging lineage of the Fung because they lack complex fruiting structures an most representatives have coenocytic aseptate hypha during all or part of their life cycle. Zygomycota ofte might be overlooked even by mycologists, but the can be encountered as near as the kitchen, disguise as moldy bread or fruit (James and O’Donnell 2004) Some are beneficial, such as Rhizopus, used in severa traditional fermented foods, including tempeh an cassava. Most species of the Zygomycota are saprobic but some species are facultative pathogens of plants animals (including humans) or even other fungi. Th Trichomycetes are obligate endosymbionts of arthro pods. Indeed members of the Zygomycota ar1 Corresponding Author. E-mail: MerlinWhite@boisestate.edu This paper is dedicated to the great many students of the ‘‘lower Fungi’’—past and present—who helped introduce us to this wonderfully eclectic and diverse group that we can only hope to highlight 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
- 14. Improving ‘Zygomycete’ Tree ofLife • 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
- 15. Hypotheses and questionsfrom 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
- 16. Yarrowia lipolytica Encephalitozoon cuniculi Spizellomycespunctatus Aspergillus fumigatus Batrachochytrium dendrobatidis Thalassiosira pseudonana Pythium 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 maydis Sporobolomyces 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 James et al. Cur Biol 2013 Rozella TY James CDC microsporidia 6,350 genes Whole genome phylogeny from 200 proteins
- 17. ~80 Zygomycete genomes 51protein coding genes ~20k filtered positions RAxML PROTGAMMALichtheimia_ramosa_B5399 Conidiobolus_coronatus_NRRL_28638.Conco1 Martensiomyces_pterosporus.Marpt1 Rhizomucor_variabilis_B7584 Rhizophagus_irregularis_DAOM_181602 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 Lichtheimia_corymbifera_FSU_9682 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 Mortierella_verticillata_NRRL_6337 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 Rozella_allomycis_CSF55 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 99 100 79 100 100 83 100 70 70 67 100 100 100 100 100 100 100 100 100 100 97 100 98 100 100 100 82 89 100 82 100 100 46 60 22 68 81 100 100 100 100 100 100 100 93 100 100 100 100 100 100 46 29 100 100 96 100 100 100 98 100 100 Microsporidia Dikarya Chytridiomycota + Blastocladiomycota Rhizopus microsporus Rhizopus oryzae & Rhizopus delemar
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- 19. Potential new cladewith Umbelopsis It has been grouped with both Mortierellomycotina & Mucormycotina Lichtheimia_ramosa_B5399 Rhizomucor_variabilis_B7584 Rhizophagus_irregularis_DAOM_181602 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 Lichtheimia_corymbifera_FSU_9682 Mortierella_elongata_AG-77.Morel1 Mycotypha_africana_NRRL2978 Spinellus_fusiger_NRRL22323 Cunninghamella_bertholletiae_175 Umbelopsis_ramanniana.Umbra1 Mucor_B8987 Pilobolus_umbonatus_NRRL6349 Cunninghamella_elegans_B9769 Mucor_circinelloides.Mucci2 Mortierella_verticillata_NRRL_6337 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 Apophysomyces_elegans_B7760 Mucor_racemosus_B9645 Mucor_irregularis_B50 Lichtheimia_hyalospora_FSU_10163.Lichy1 Rhizomucor_miehei_CAU432 Saksenaea_vasiformis_B4078 Thamindium_elegans_NRRL2467 R_microB9738 Absidia_repens_NRRL1336 Blakesea_trispora_NRRL2456 Phycomyces_blakesleeanus.Phybl2 Circinella_umbellata_NRRL1351 Syncephalastrum_monosporum_B8922 Mortierella_alpina_B6842 Mucor_velutinosus_B5328 Umbelopsis_isabellina_B7317 Cunninghamella_echinulata_NRRL1382 Micromucor_ramannianus_NRRL5844 Chaetocladium_jonesii_NRRL2343 100 100 100 70 100 100 100 100 46 100 99 100 100 100 70 70 67 100 100 100 100 100 100 100 100 100 97 100 98 100 82 89 100 100 46 60 22 68 81 100 100 100 100 100 93 100 100 100 100 100 46 29 100 100 100 98 100 100 Dikarya Rhizopus microsporus Rhizopus oryzae & Rhizopus delemar
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- 21. Genome skimming basedphylogenomics ✤ 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)
- 22. 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 Code http://github.com/stajichlab/Phyling exonerate Cap3 FASTX
- 23.
- 24. Conidiobolus_coronatus_NRRL_28638.Conco1 Rhizomucor_variabilis_B7584 Rhizophagus_irregularis_DAOM_181602 Hesseltinella_vesiculosa_NRRL_3301.Hesve Cokeromyces_recurvatus_NRRL2243 Echinosporandium_transversale_NRRL3116 Zygorhynchus_heterogamus_NRRL1489 R_stol_My Cokeromyces_recurvatus_B5483 Mortierella_elongata_AG-77.Morel1 Mycotypha_africana_NRRL2978 Cunninghamella_bertholletiae_175 Mucor_B8987 Pilobolus_umbonatus_NRRL6349 Cunninghamella_elegans_B9769 Mucor_circinelloides.Mucci2 Ramicandelaber_brevisporus.Ramb Mortierella_verticillata_NRRL_6337 Hessentinella_vesiculosa_NRRL3301 Mucor_1006PhL Mucor_indicus_B7402 Parasitella_parasitica_NRRL2501 Conidiobolus_thromboides_FSU_785.Conth1 Conidiobolus_incongruus_B7586 Spiromyces_aspiralis_NRRL22631 Thamindium_elegans_NRRL2467 Absidia_repens_NRRL1336 Blakesea_trispora_NRRL2456 Mortierella_alpina_B6842 Mucor_velutinosus_B5328 Cunninghamella_echinulata_NRRL1382 Chaetocladium_jonesii_NRRL2343 100 100 70 100 100 100 100 100 100 100 97 89 100 100 100 46 22 81 100 100 100 100 93 100 100 100 46 29 100 96 100Identical placement oftaxa 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.
- 25. Linderina_pennispora_NRRL3781 Pilobolus_umbonatus_NRRL6349 Thamindium_elegans_NRRL2467 Circinella_umbellata_NRRL1351 Cokeromyces_recurvatus_NRRL2243 Cunninghamella_echinulata_NRRL1382 Micromucor_ramannianus_NRRL5844 Mycotypha_africana_NRRL2978 Absidia_repens_NRRL1336 Blakesea_trispora_NRRL2456 Spiromyces_aspiralis_NRRL22631 Radiomyces_spectabilis_NRRL2753 Spinellus_fusiger_NRRL22323 Echinosporandium_transversale_NRRL3116 Zygorhynchus_heterogamus_NRRL1489 Hessentinella_vesiculosa_NRRL3301 Parasitella_parasitica_NRRL2501 Chaetocladium_jonesii_NRRL2343 Syncephalastrum_racemosum_NRRL2496 Total Bases 0e+00 1e+06 2e+06 3e+06 4e+06 Variability in coveragefrom multiplex samples Overall coverage varies because of differences or bias in how concentration is made with multiplexing
- 26.
- 27. Conclusions ✤ Early stageof 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
- 28. 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)