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Supporting Information Bender et al. 10.1073/pnas.0802779105 Table S1. Species names and calculated numeric values pertaining to Fig. 1 Mitochondrially Nuclear encoded Nuclear encoded Species name encoded methionine, % methionine, % methionine, corrected, % Animals Primates Cebus albifrons 6.76 Cercopithecus aethiops 6.10 Colobus guereza 6.73 Gorilla gorilla 5.46 Homo sapiens 5.49 2.14 2.64 Hylobates lar 5.33 Lemur catta 6.50 Macaca mulatta 5.96 Macaca sylvanus 5.96 Nycticebus coucang 6.07 Pan paniscus 5.46 Pan troglodytes 5.38 Papio hamadryas 5.99 Pongo pygmaeus 5.04 Tarsius bancanus 6.74 Trachypithecus obscurus 6.18 Other mammals Acinonyx jubatus 6.86 Artibeus jamaicensis 6.43 Balaena mysticetus 6.04 Balaenoptera acutorostrata 6.17 Balaenoptera borealis 5.96 Balaenoptera musculus 5.78 Balaenoptera physalus 6.02 Berardius bairdii 6.01 Bos grunniens 7.04 Bos taurus 6.88 2.26 2.70 Canis familiaris 6.54 Capra hircus 6.84 Cavia porcellus 6.41 Ceratotherium simum 6.06 Choloepus didactylus 6.23 Crocidura russula 6.17 Dasypus novemcinctus 7.05 Didelphis virginiana 6.79 Dugong dugon 6.15 Echinops telfairi 6.32 Echinosorex gymnura 6.86 Elephas maximus 6.84 Equus asinus 6.01 Equus caballus 6.07 Erinaceus europaeus 7.34 Eschrichtius robustus 6.15 Eumetopias jubatus 6.77 Felis catus 6.62 Halichoerus grypus 6.46 Hemiechinus auritus 6.83 Herpestes javanicus 6.70 Hippopotamus amphibius 6.50 Hyperoodon ampullatus 6.04 Inia geoffrensis 6.20 Bender et al. www.pnas.org/cgi/content/short/0802779105 1of10 Mitochondrially Nuclear encoded Nuclear encoded Species name encoded methionine, % methionine, % methionine, corrected, % Isoodon macrourus 6.00 Kogia breviceps 5.93 Lepus europaeus 6.26 Loxodonta africana 6.81 Macropus robustus 5.50 Macrotis lagotis 6.42 Megaptera novaeangliae 5.99 Metachirus nudicaudatus 6.61 Monodelphis domestica 6.62 Monodon monoceros 6.25 Muntiacus muntjak 6.59 Mus musculus 6.60 2.23 2.84 Notoryctes typhlops 5.71 Ochotona collaris 5.91 Ochotona princeps 5.99 Odobenus rosmarus 6.91 Ornithorhynchus anatinus 5.07 Orycteropus afer 5.83 Oryctolagus cuniculus 5.99 Ovis aries 6.83 Perameles gunnii 6.26 Phoca vitulina 6.56 Phocoena phocoena 6.33 Physeter catodon 6.25 Platanista minor 6.27 Pontoporia blainvillei 6.76 Procavia capensis 6.61 Pseudocheirus peregrinus 5.87 Rattus norvegicus 5.96 2.25 2.77 Rhinoceros unicornis 6.28 Sciurus vulgaris 6.04 Sus scrofa 6.98 Tachyglossus aculeatus 5.71 Talpa europaea 6.41 Tamandua tetradactyla 6.99 Tapirus terrestris 6.28 Tarsipes rostratus 6.08 Thryonomys swinderianus 7.43 Trichosurus vulpecula 5.88 Tupaia belangeri 6.47 Ursus americanus 6.43 Ursus arctos 6.14 Ursus maritimus 6.09 Vombatus ursinus 5.60 Zaglossus bruijni 5.44 Birds Anser albifrons 4.83 Arenaria interpres 4.75 Aythya americana 4.56 Branta canadensis 4.93 Buteo buteo 4.28 Ciconia boyciana 4.28 Ciconia ciconia 4.20 Corvus frugilegus 4.57 Diomedea melanophris 4.72 Dromaius novaehollandiae 4.54 Falco peregrinus 4.78 Gallus gallus 4.46 2.33 2.74 Gavia stellata 4.73 Struthio camelus 4.12 Reptiles Alligator mississippiensis 5.41 Bender et al. www.pnas.org/cgi/content/short/0802779105 2of10 Mitochondrially Nuclear encoded Nuclear encoded Species name encoded methionine, % methionine, % methionine, corrected, % Alligator sinensis 5.29 Bipes biporus 5.74 Caiman crocodilus 5.25 Chinemys reevesi 6.46 Chrysemys picta 6.30 Cordylus warreni 5.34 Iguana iguana 4.87 Pelomedusa subrufa 6.26 Sphenodon punctatus 6.22 Amphibians Ambystoma tigrinum 6.65 Andrias davidianus 6.53 Bombina bombina 4.86 Bombina orientalis 4.68 Ensatina eschscholtzii 6.87 Gyrinophilus porphyriticus 6.26 Hemidactylium scutatum 6.95 Kaloula pulchra 4.74 Phaeognathus hubrichti 6.67 Plethodon elongatus 6.83 Pseudotriton ruber 6.33 Xenopus laevis 5.18 Fish Acipenser transmontanus 4.60 Amia calva 4.87 Anguilla anguilla 5.53 Anguilla rostrata 5.56 Branchiostoma lanceolatum 5.40 Carassius auratus 4.67 Carpiodes carpio 4.50 Cololabis saira 4.34 Conger myriaster 5.63 Cyprinus carpio 4.64 Danio rerio 5.06 2.52 2.98 Esox lucius 4.21 Gadus morhua 4.73 Gambusia affinis 4.05 Gasterosteus aculeatus 4.13 Heterodontus francisci 4.29 Huso huso 4.47 Ictalurus punctatus 4.56 Lampetra fluviatilis 5.64 Lepidosiren paradoxa 5.05 Lophius americanus 3.97 Lota lota 4.34 Megalops cyprinoides 5.08 Mugil cephalus 3.96 Neoceratodus forsteri 5.74 Oncorhynchus clarkii 3.95 Oncorhynchus mykiss 3.95 Oncorhynchus tshawytscha 4.00 Osteoglossum bicirrhosum 4.63 Petromyzon marinus 5.72 Polyodon spathula 4.71 Polypterus senegalus 5.26 Salmo salar 4.05 Salvelinus fontinalis 4.08 Scomber scombrus 4.08 Scyliorhinus caniculus 4.58 Squalus acanthias 4.60 Tetraodon nigroviridis 4.08 2.18 2.75 Theragra chalcogramma 4.65 Bender et al. www.pnas.org/cgi/content/short/0802779105 3of10 Mitochondrially Nuclear encoded Nuclear encoded Species name encoded methionine, % methionine, % methionine, corrected, % Thunnus thynnus 4.16 Echinoderms Acanthaster brevispinus 2.02 Acanthaster planci 2.10 Arbacia lixula 2.65 Asterias amurensis 2.41 Asterina pectinifera 2.09 Astropecten polyacanthus 2.25 Cucumaria miniata 2.02 Florometra serratissima 2.00 Gymnocrinus richeri 2.21 Luidia quinalia 2.17 Ophiopholis aculeata 2.64 Ophiura lutkeni 2.78 Paracentrotus lividus 2.72 Phanogenia gracilis 2.10 Pisaster ochraceus 2.36 Strongylocentrotus purpuratus 2.80 Insects Aedes albopictus 6.94 Aleurochiton aceris 9.47 Aleurodicus dugesii 10.20 Anopheles gambiae 6.08 2.32 2.93 Anopheles quadrimaculatus A 6.14 Antheraea pernyi 7.05 Apis mellifera ligustica 9.28 Bactrocera oleae 5.57 Bemisia tabaci 9.23 Bombyx mandarina 7.87 Bombyx mori 7.81 Campanulotes bidentatus compar 6.44 Ceratitis capitata 5.47 Chrysomya putoria 6.00 Cochliomyia hominivorax 6.29 Coreana raphaelis 8.82 Crioceris duodecimpunctata 6.71 Dermatobia hominis 7.07 Drosophila mauritiana 6.11 Drosophila melanogaster 6.30 2.34 2.97 Drosophila sechellia 6.06 Drosophila simulans 6.14 Drosophila yakuba 5.82 Gomphiocephalus hodgsoni 6.85 Gryllotalpa orientalis 7.31 Haematobia irritans 6.40 Heterodoxus macropus 8.20 Homalodisca coagulata 8.97 Japyx solifugus 7.07 Lepidopsocid RS-2001 6.89 Locusta migratoria 7.59 Melipona bicolor 11.18 Neomaskellia andropogonis 10.21 Nesomachilis australica 5.63 Onychiurus orientalis 5.86 Ostrinia furnacalis 7.77 Ostrinia nubilalis 7.85 Pachypsylla venusta 7.70 Periplaneta fuliginosa 7.79 Petrobius brevistylis 5.74 Philaenus spumarius 8.59 Podura aquatica 6.35 Pteronarcys princeps 5.15 Bender et al. www.pnas.org/cgi/content/short/0802779105 4of10 Mitochondrially Nuclear encoded Nuclear encoded Species name encoded methionine, % methionine, % methionine, corrected, % Pyrocoelia rufa 8.54 Schizaphis graminum 8.51 Sclerophasma paresisensis 7.68 Tamolanica tamolana 7.15 Tetraleurodes acaciae 7.66 Tetrodontophora bielanensis 8.21 Thermobia domestica 5.78 Thrips imaginis 7.19 Trialeurodes vaporariorum 7.95 Triatoma dimidiata 6.86 Tribolium castaneum 6.35 Tricholepidion gertschi 6.50 Crustaceans Argulus americanus 8.25 Armillifer armillatus 7.09 Artemia franciscana 5.45 Callinectes sapidus 6.31 Cherax destructor 5.18 Daphnia pulex 3.99 Eriocheir sinensis 6.00 Geothelphusa dehaani 5.78 Gonodactylus chiagra 6.28 Harpiosquilla harpax 6.50 Hutchinsoniella macracantha 5.84 Lepeophtheirus salmonis 5.09 Lysiosquillina maculata 6.42 Macrobrachium rosenbergii 4.87 Marsupenaeus japonicus 5.28 Megabalanus volcano 5.51 Pagurus longicarpus 6.00 Panulirus japonicus 5.38 Penaeus monodon 5.95 Pollicipes polymerus 5.82 Portunus trituberculatus 6.24 Pseudocarcinus gigas 6.03 Speleonectes tulumensis 9.04 Squilla empusa 6.63 Squilla mantis 6.52 Tetraclita japonica 6.17 Tigriopus japonicus 4.09 Triops cancriformis 5.42 Triops longicaudatus 4.64 Vargula hilgendorfii 5.23 Arachnids Amblyomma triguttatum 8.74 Carios capensis 8.25 Centruroides limpidus 5.24 Habronattus oregonensis 9.71 Haemaphysalis flava 9.32 Heptathela hangzhouensis 7.85 Ixodes hexagonus 8.28 Ixodes holocyclus 9.47 Ixodes persulcatus 8.90 Ixodes uriae 9.08 Leptotrombidium akamushi 5.79 Leptotrombidium deliense 5.90 Leptotrombidium pallidum 5.81 Mesobuthus gibbosus 4.92 Ornithoctonus huwena 7.97 Ornithodoros moubata 8.07 Ornithodoros porcinus 8.29 Rhipicephalus sanguineus 8.94 Bender et al. www.pnas.org/cgi/content/short/0802779105 5of10 Mitochondrially Nuclear encoded Nuclear encoded Species name encoded methionine, % methionine, % methionine, corrected, % Varroa destructor 9.82 Nematodes Anisakis simplex 5.56 Ancylostoma duodenale 6.96 Ascaris suum 5.44 Brugia malayi 4.61 Caenorhabditis elegans 5.47 2.62 2.96 Cooperia oncophora 6.61 Dirofilaria immitis 4.46 Necator americanus 6.64 Onchocerca volvulus 4.43 Steinernema carpocapsae 5.04 Strelkovimermis spiculatus 9.84 Strongyloides stercoralis 3.51 Thaumamermis cosgrovei 7.82 Trichinella spiralis 8.29 Xiphinema americanum 5.78 Platyhelminthes Echinococcus multilocularis 2.76 Fasciola hepatica 2.98 Hymenolepis diminuta 2.82 Paragonimus westermani 2.62 Schistosoma japonicum 3.63 Schistosoma mansoni 3.69 Schistosoma mekongi 3.77 Taenia asiatica 2.92 Taenia crassiceps 3.10 Taenia solium 2.94 Molluscs Albinaria caerulea 7.39 Aplysia californica 5.04 Biomphalaria glabrata 7.15 Cepaea nemoralis 4.65 Crassostrea gigas 5.79 Crassostrea virginica 5.63 Graptacme eborea 7.77 Haliotis rubra 4.60 Ilyanassa obsoleta 5.11 Katharina tunicata 5.11 Lampsilis ornata 4.65 Loligo bleekeri 7.80 Lottia digitalis 5.01 Mytilus edulis 5.98 Mytilus galloprovincialis 6.00 Mytilus trossulus 6.25 Nautilus macromphalus 4.47 Octopus ocellatus 8.38 Octopus vulgaris 7.75 Placopecten magellanicus 4.17 Pupa strigosa
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    Evidence for Inter-Specific Recombination Among the Mitochondrial Genomes of Fusarium Species in the Gibberella Fujikuroi Comple

    Fourie et al. BMC Genomics 2013, 14:605 http://www.biomedcentral.com/1471-2164/14/605 RESEARCH ARTICLE Open Access Evidence for inter-specific recombination among the mitochondrial genomes of Fusarium species in the Gibberella fujikuroi complex Gerda Fourie1*, Nicolaas A van der Merwe2, Brenda D Wingfield2, Mesfin Bogale2, Bettina Tudzynski3, Michael J Wingfield1 and Emma T Steenkamp1 Abstract Background: The availability of mitochondrial genomes has allowed for the resolution of numerous questions regarding the evolutionary history of fungi and other eukaryotes. In the Gibberella fujikuroi species complex, the exact relationships among the so-called “African”, “Asian” and “American” Clades remain largely unresolved, irrespective of the markers employed. In this study, we considered the feasibility of using mitochondrial genes to infer the phylogenetic relationships among Fusarium species in this complex. The mitochondrial genomes of representatives of the three Clades (Fusarium circinatum, F. verticillioides and F. fujikuroi) were characterized and we determined whether or not the mitochondrial genomes of these fungi have value in resolving the higher level evolutionary relationships in the complex. Results: Overall, the mitochondrial genomes of the three species displayed a high degree of synteny, with all the genes (protein coding genes, unique ORFs, ribosomal RNA and tRNA genes) in identical order and orientation, as well as introns that share similar positions within genes. The intergenic regions and introns generally contributed significantly to the size differences and diversity observed among these genomes. Phylogenetic analysis of the concatenated protein-coding dataset separated members of the Gibberella fujikuroi complex from other Fusarium species and suggested that F. fujikuroi (“Asian” Clade) is basal in the complex.
  • The Abundance and Diversity of Fungi in a Hypersaline Microbial Mat from Guerrero Negro, Baja California, México

    The Abundance and Diversity of Fungi in a Hypersaline Microbial Mat from Guerrero Negro, Baja California, México

    Journal of Fungi Article The Abundance and Diversity of Fungi in a Hypersaline Microbial Mat from Guerrero Negro, Baja California, México Paula Maza-Márquez 1,*, Michael D. Lee 1,2 and Brad M. Bebout 1 1 Exobiology Branch, NASA Ames Research Center, Moffett Field, CA 94035, USA; [email protected] (M.D.L.); [email protected] (B.M.B.) 2 Blue Marble Space Institute of Science, Seattle, WA 98104, USA * Correspondence: [email protected] Abstract: The abundance and diversity of fungi were evaluated in a hypersaline microbial mat from Guerrero Negro, México, using a combination of quantitative polymerase chain reaction (qPCR) amplification of domain-specific primers, and metagenomic sequencing. Seven different layers were analyzed in the mat (Layers 1–7) at single millimeter resolution (from the surface to 7 mm in depth). The number of copies of the 18S rRNA gene of fungi ranged between 106 and 107 copies per g mat, being two logarithmic units lower than of the 16S rRNA gene of bacteria. The abundance of 18S rRNA genes of fungi varied significantly among the layers with layers 2–5 mm from surface contained the highest numbers of copies. Fifty-six fungal taxa were identified by metagenomic sequencing, classified into three different phyla: Ascomycota, Basidiomycota and Microsporidia. The prevalent genera of fungi were Thermothelomyces, Pyricularia, Fusarium, Colletotrichum, Aspergillus, Botrytis, Candida and Neurospora. Genera of fungi identified in the mat were closely related to genera known to have saprotrophic and parasitic lifestyles, as well as genera related to human and plant pathogens and fungi able to perform denitrification.
  • High-Level Classification of the Fungi and a Tool for Evolutionary Ecological Analyses

    High-Level Classification of the Fungi and a Tool for Evolutionary Ecological Analyses

    Fungal Diversity (2018) 90:135–159 https://doi.org/10.1007/s13225-018-0401-0 (0123456789().,-volV)(0123456789().,-volV) High-level classification of the Fungi and a tool for evolutionary ecological analyses 1,2,3 4 1,2 3,5 Leho Tedersoo • Santiago Sa´nchez-Ramı´rez • Urmas Ko˜ ljalg • Mohammad Bahram • 6 6,7 8 5 1 Markus Do¨ ring • Dmitry Schigel • Tom May • Martin Ryberg • Kessy Abarenkov Received: 22 February 2018 / Accepted: 1 May 2018 / Published online: 16 May 2018 Ó The Author(s) 2018 Abstract High-throughput sequencing studies generate vast amounts of taxonomic data. Evolutionary ecological hypotheses of the recovered taxa and Species Hypotheses are difficult to test due to problems with alignments and the lack of a phylogenetic backbone. We propose an updated phylum- and class-level fungal classification accounting for monophyly and divergence time so that the main taxonomic ranks are more informative. Based on phylogenies and divergence time estimates, we adopt phylum rank to Aphelidiomycota, Basidiobolomycota, Calcarisporiellomycota, Glomeromycota, Entomoph- thoromycota, Entorrhizomycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota and Olpidiomycota. We accept nine subkingdoms to accommodate these 18 phyla. We consider the kingdom Nucleariae (phyla Nuclearida and Fonticulida) as a sister group to the Fungi. We also introduce a perl script and a newick-formatted classification backbone for assigning Species Hypotheses into a hierarchical taxonomic framework, using this or any other classification system. We provide an example