DOCSLIB.ORG

Reexamining the Phylogeny of Clinically Relevant Candida Species

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Reexamining the Phylogeny of Clinically Relevant Candida Species RESEARCH ARTICLE Re-examining the phylogeny of clinically relevant Candida species and allied genera based on multigene analyses Clement K.M. Tsui1, Heide-Marie Daniel2, Vincent Robert3 & Wieland Meyer1,4 1Molecular Mycology Research Laboratory, Center for Infectious Diseases and Microbiology, Westmead Hospital, Westmead Millennium Institute, Westmead, NSW, Australia; 2BCCM/MUCL culture collection, Universite´ Catholique de Louvain, Unite´ de Microbiologie, Louvain-la-Neuve, Belgium; 3Centraalbureau voor Schimmelcultures, Utrecht, The Netherlands; and 4Western Clinical School, Department of Medicine, The University of Sydney, Sydney, Australia Correspondence: Wieland Meyer, Molecular Abstract Mycology Research Laboratory, Center for Infectious Diseases and Microbiology, Yeasts of the artificial genus Candida include plant endophytes, insect symbionts, Westmead Hospital, Westmead Millennium and opportunistic human pathogens. Phylogenies based on rRNA gene and actin Institute, Westmead, NSW 2145, Australia. sequences confirmed that the genus is not monophyletic, and the relationships Tel.: 161 2 98456895; fax: 161 2 98915317; among Candida species and allied teleomorph genera are not clearly resolved. e-mail: [email protected] Protein-coding genes have been useful to resolve taxonomic positions among a broad range of fungi. Over 70 taxa of the genus Candida and its allied sexually Received 10 August 2007; revised 18 November reproducing genera were therefore selected, and their phylogenetic relationships 2007; accepted 20 November 2007. were investigated using nuclear sequences of the largest subunit and second largest First published online 31 January 2008. subunit of RNA polymerase II gene, actin, the second subunit of the mitochondrial DOI:10.1111/j.1567-1364.2007.00342.x cytochrome oxidase gene, and D1/D2 LSU rRNA gene. The DNA sequences were analysed by maximum parsimony and Bayesian inference, resulting in the Editor: Teun Boekhout recognition of six major phylogenetic groups (A–F). Group A contains six facultative pathogenic Candida species, which seem to have derived from Keywords nonpathogenic species, while Group B contains species of Clavispora, Metschniko- Ascomycetous yeasts; Candida ; wia, and Pichia guilliermondii. Species of Debaryomyces form an independent Debaryomyces ; Pichia ; Saccharomyces ; group C that is related to groups A and B. Pichia fermentans and other phylogeny. environmental species are concentrated in Group D. Group E, containing Pichia anomala, may be a sibling to group F, which is represented by the Saccharomyces species complex. place the clinically relevant species in their evolutionary Introduction context. Members of the polyphyletic genus Candida are ubiquitous The genus Candida comprises a wide range of phylogen- in numerous natural and artificial habitats (Kurtzman & etically unrelated anamorphic fungi. These species were Fell, 1998). These single-celled fungi have been the subjects classified into one artificial genus due to the lack of of clinical research because many Candida species are distinctive characters that would allow their assignment to a facultative pathogens in humans and have become pressing more natural genus (Meyer et al., 1998). Indeed, for many concerns in public health with the increase of immunosup- Candida species, connections with known teleomorphic pressed patients. Other members of the genus Candida or ascomycete genera have been established using a single-gene their teleomorph counterparts have an ancient history in phylogeny (Kurtzman & Robnett, 1998). However, taxono- food production and some are currently used in indus- mists have restrained from the erection of new genera for trial processes, being listed as ‘Generally Regarded As Safe’ ascomycetous yeasts in many cases because of their unre- (GRAS) organisms by the FDA of the USA (http:// solved phylogeny. Therefore, the current classification is in www.gpoaccess.gov/cfr/index.html). Because of these close large part artificial and unsatisfactory. Multiple gene phylo- links, a phylogenetic analysis needs to integrate species of genies have started to establish new genera in phylogeneti- clinical, applied and environmental relevance. Here, species cally well-circumscribed groups (Kurtzman & Robnett, 2003; of these different orientations were included with the aim to Suh et al., 2006). To revise additional well-circumscribed FEMS Yeast Res 8 (2008) 651–659 c 2008 Federation of European Microbiological Societies Published by Blackwell Publishing Ltd. All rights reserved 652 C.K.M. Tsui et al. groups, a greater resolution at the backbone of the phyloge- analysed with the goal of dividing Candida species into netic tree is necessary. A more natural classification system well-supported clades and consolidating the phylogenetic should be able to accommodate novel species in their positions of the taxa with an unresolved status. appropriate genera and to predict significant characteristics within genera or larger groups. Materials and methods A better knowledge on the evolutionary relationships of Candida species is vital to understand the ecology, clinical Taxon sampling, DNA extraction, and PCR relevance, and diagnosis of these yeasts. The sequences of the amplification D1/D2 region of the large subunit (LSU) of the ribosomal Seventy isolates including numerous type strains were gene complex (rRNA gene) have been used widely in yeast studied (Table 1). The taxon sampling represented a large phylogeny. But D1/D2 LSU sequences alone were not able diversity of Saccharomycetales and included two potentially to resolve the inter-generic relationships (Kurtzman & basal taxa: Yarrowia lipolytica and Zygoascus hellenicus. Robnett, 1997, 1998). They were also unable to distinguish These taxa represented distinct evolutionary lineages by the a number of closely related species such as Pichia guillier- composition of their cell wall polysaccharides (Weijman & mondii and Pichia caribbica, Candida mucifera, and Stepha- Golubev, 1988; Phaff, 1998; Suzuki, 2002) and 18S rRNA noascus ciferrii, as well as Kluyveromyces marxianus and gene analysis (Prillinger et al., 2002). All cultures are Kluyveromyces lactis (Daniel & Meyer, 2003). Previous maintained in the Australian Medical Fungal Culture research showed that actin gene sequences offered a better Collection at the Westmead Hospital/University of Sydney. phylogenetic resolution among Candida species. Four major Cultures were grown and DNA was extracted as described well-supported groups were established (Daniel et al., 2001). previously (Meyer et al., 1997). The extracted DNA was However, in a follow-up study, most branches in the tree stored at À 20 1C until future use. Fragments of the RPB1 of an expanded taxon data set lacked significant statistical and RPB2 genes were amplified using the primer sequences support (Daniel, 2003). Because the results of single gene published in Diezmann et al. (2004). A fragment of the analyses do not provide sufficient information to resolve the COX2 gene was amplified with the primers published by phylogeny of the ascomycetous yeasts and because single Kurtzman & Robnett (2003) or primers CO2F1 (50-GGT gene trees could be misleading (Rokas et al., 2003), multi- ATW CAK GAA TTA TAY GA-30) and CO2R1 (50-CAS ATT gene analyses have been conducted to clarify the phyloge- CWA RTT TKG TWG GCA T-30) designed during the netic relationships of the genus Candida and its allied genera current study. The PCR was performed in volumes of 25 mL and to improve the branch resolutions (Kurtzman & Rob- containing 75 mM Tris-HCl, 1.5 mM MgCl , 7.5 pmol of nett, 2003; Diezmann et al., 2004). These investigations, 2 each primer, 1 U Taq (AmpliTaq, Applied Biosystems), and however, sampled only single families or were restricted to 20 ng of genomic DNA. The reactions were carried out in a the common clinically relevant species. Suh et al. (2006) PTC-100 Thermal Cycler (MJ Research Inc., Watertown, have defined the lack of protein-coding gene sequences for MA) using the following programme: 5-min denaturation at several major branches of yeasts. 95 1C, and 30–35 cycles of: 95 1C for 30 s, 54 1C for 30 s In the present study, additional sequence data were (or 55 1C for RPB2), 72 1C for 45 s, a final extension at 72 1C generated for the expanded taxon sampling set (Daniel, for 7 min, and a 4 1C soak. The PCR product was then 2003), and sequences for four of the nine clades that were purified using the GFX PCR DNA and Gel Band purification without alternative data to rRNA gene sequences were kit (Amersham Biosciences, Buckinghamshire, UK) and provided (Suh et al., 2006). In previous studies, the sequenced using the ABI PRISMs BigDyes Terminator occurrence of genome duplication in the evolution of the v3.1 Cycle Sequencing Kit (PE Applied Biosystems, Foster Saccharomyces species and Candida glabrata was revealed City, CA) with the amplification primers in both forward (e.g. Dujon, 2006). According to current knowledge, this and reverse directions. duplication concerned a subgroup of the well-circumscribed Saccharomyces clade, and potential gene paralogues would Phylogenetic analyses not influence the basal branching of the phylogenetic tree, which was the subject of the current study. With this fact in Sequences were edited in SEQUENCHER 4.1 (Gene codes mind we carefully selected genes that are commonly used to corporation), and their identity was verified by BLAST study fungal phylogeny, using primers that do not amplify searches (with significant scores with an e-value o 0.001)
Load more

Recommended publications
  • Genome Diversity and Evolution in the Budding Yeasts (Saccharomycotina)
    | YEASTBOOK GENOME ORGANIZATION AND INTEGRITY Genome Diversity and Evolution in the Budding Yeasts (Saccharomycotina) Bernard A. Dujon*,†,1 and Edward J. Louis‡,§ *Department Genomes and Genetics, Institut Pasteur, Centre National de la Recherche Scientifique UMR3525, 75724-CEDEX15 Paris, France, †University Pierre and Marie Curie UFR927, 75005 Paris, France, ‡Centre for Genetic Architecture of Complex Traits, and xDepartment of Genetics, University of Leicester, LE1 7RH, United Kingdom ORCID ID: 0000-0003-1157-3608 (E.J.L.) ABSTRACT Considerable progress in our understanding of yeast genomes and their evolution has been made over the last decade with the sequencing, analysis, and comparisons of numerous species, strains, or isolates of diverse origins. The role played by yeasts in natural environments as well as in artificial manufactures, combined with the importance of some species as model experimental systems sustained this effort. At the same time, their enormous evolutionary diversity (there are yeast species in every subphylum of Dikarya) sparked curiosity but necessitated further efforts to obtain appropriate reference genomes. Today, yeast genomes have been very informative about basic mechanisms of evolution, speciation, hybridization, domestication, as well as about the molecular machineries underlying them. They are also irreplaceable to investigate in detail the complex relationship between genotypes and phenotypes with both theoretical and practical implications. This review examines these questions at two distinct levels offered by the broad evolutionary range of yeasts: inside the best-studied Saccharomyces species complex, and across the entire and diversified subphylum of Saccharomycotina. While obviously revealing evolutionary histories at different scales, data converge to a remarkably coherent picture in which one can estimate the relative importance of intrinsic genome dynamics, including gene birth and loss, vs.
    [Show full text]
  • Identification and Phylogeny of Ascomycetous Yeasts from Analysis
    Antonie van Leeuwenhoek 73: 331–371, 1998. 331 © 1998 Kluwer Academic Publishers. Printed in the Netherlands. Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences Cletus P. Kurtzman∗ & Christie J. Robnett Microbial Properties Research, National Center for Agricultural Utilization Research, Agricultural Research Ser- vice, U.S. Department of Agriculture, Peoria, Illinois 61604, USA (∗ author for correspondence) E-mail: [email protected] Received 19 June 1998; accepted 19 June 1998 Key words: Ascomycetous yeasts, phylogeny, ribosomal DNA, systematics Abstract Approximately 500 species of ascomycetous yeasts, including members of Candida and other anamorphic genera, were analyzed for extent of divergence in the variable D1/D2 domain of large subunit (26S) ribosomal DNA. Divergence in this domain is generally sufficient to resolve individual species, resulting in the prediction that 55 currently recognized taxa are synonyms of earlier described species. Phylogenetic relationships among the ascomycetous yeasts were analyzed from D1/D2 sequence divergence. For comparison, the phylogeny of selected members of the Saccharomyces clade was determined from 18S rDNA sequences. Species relationships were highly concordant between the D1/D2 and 18S trees when branches were statistically well supported. Introduction lesser ranges of nDNA relatedness than those found among heterothallic species. Disadvantages of nDNA reassociation studies in- Procedures commonly used for yeast identification clude the need for pairwise comparisons of all isolates rely on the appearance of cellular morphology and dis- under study and that resolution is limited to the ge- tinctive reactions on a standardized set of fermentation netic distance of sister species, i.e., closely related and assimilation tests.
    [Show full text]
  • Fungal Ecology 33 (2018) 1E12
    Fungal Ecology 33 (2018) 1e12 Contents lists available at ScienceDirect Fungal Ecology journal homepage: www.elsevier.com/locate/funeco Decaying Picea abies log bark hosts diverse fungal communities * Igor Kazartsev a, b, c, Ekaterina Shorohova a, b, d, , Ekaterina Kapitsa a, b, Helena Kushnevskaya a, e a Forest Research Institute of the Karelian Research Centre, Russian Academy of Science, Pushkinskaya Str. 11, Petrozavodsk, 185910, Russia b Saint-Petersburg State Forest Technical University, Institutsky Str. 5, St. Petersburg, 194021, Russia c All-Russian Institute of Plant Protection, Podbelskogo Shosse 3, St. Petersburg, 196608, Russia d Natural Resources Institute Finland (Luke), Latokartanonkaari 9, FI-00790, Helsinki, Finland e Saint-Petersburg State University, University Embankment 7-9, St Petersburg, 199034, Russia article info abstract Article history: We examined taxonomic composition of fungal communities in Picea abies log bark using next gener- Received 20 June 2017 ation sequencing. Three successional stages along gradients of log attributes were identified. In the initial Received in revised form stage, the communities were composed by yeasts, plant pathogens and cosmopolitan saprotrophic fungi 19 October 2017 with broad substrate utilization. In the intermediate stage, bark was colonized mainly by saprotrophs Accepted 20 December 2017 common in decaying wood, symbionts of epixylic plants and nematode-trapping fungi. The final stage was characterized by the dominance of mycorrhizal fungi. Wood-decaying fungi occurred in all stages. Corresponding Editor: Jacob Heilmann- However, their sporadic appearance in bark samples suggests that they are not essential for bark Clausen decomposition. Our results provide an insight into the hidden diversity of wood-inhabiting communities e fungal communities, associated with decomposition of bark as a component of coarse woody debris.
    [Show full text]
  • Candida Species
    Introduction Introduction ulvovaginal candidiasis (VVC) is a disease caused by V the abnormal growth of yeast-like fungi on the mucosa of the female genital tract (Souza et al., 2009). Although Candida species occur as normal vaginal flora, opportunistic conditions such as diabetes, pregnancy and other immune depressants in the host enable them to proliferate and cause infection (Pam et al., 2012). There are approximately 200 Candida species, among which are Candida albicans, glabrata, tropicalis, stellatoidea, parapsilosis, catemilata, ciferri, guilliermondii, haemulonii, kefyr and krusei. Candida albicans is the most common species (Pam et al., 2012). The most frequent cause of VVC is Candida albicans. Non-Candida albicans species of Candida, predominantly Candida glabrata, are responsible for the remainder of cases (Ge et al., 2010). It is estimated that 75% of women experience at least one episode of vulvovaginal candidiasis throughout their life and 40-50% of them have at least one recurrence (González et al., 2011). Most patients with symptomatic VVC may be readily diagnosed on the basis of microscopic examination of vaginal 1 Introduction secretions. Culture is a more sensitive method of diagnosis than vaginal smears, especially in a suspected patient with a negative result for microscopy (Khosravi et al., 2011). Antifungal agents that are used for treatment of VVC include imidazole antifungals (e.g., butoconazole, clotrimazole, and miconazole), triazole antifungals (eg, fluconazole, terconazole), and polyene antifungals (e.g., nystatin) (Abdelmonem et al., 2012). The azoles, particularly fluconazole, remain among the most common antifungal drugs used for prophylaxis and treatment (Pietrella et al., 2011). It is recommended in various guidelines as the first drug of choice because it is less toxic and can be taken as a single oral dose (Pam et al., 2012).
    [Show full text]
  • Inhibition of MRN Activity by a Telomere Protein Motif
    ARTICLE https://doi.org/10.1038/s41467-021-24047-2 OPEN Inhibition of MRN activity by a telomere protein motif Freddy Khayat1,6, Elda Cannavo2,6, Majedh Alshmery1, William R. Foster1, Charly Chahwan 1,4, Martino Maddalena1,5, Christopher Smith 1, Antony W. Oliver 1, Adam T. Watson1, Antony M. Carr 1, ✉ Petr Cejka2,3 & Alessandro Bianchi 1 The MRN complex (MRX in Saccharomyces cerevisiae, made of Mre11, Rad50 and Nbs1/Xrs2) 1234567890():,; initiates double-stranded DNA break repair and activates the Tel1/ATM kinase in the DNA damage response. Telomeres counter both outcomes at chromosome ends, partly by keeping MRN-ATM in check. We show that MRX is disabled by telomeric protein Rif2 through an N- terminal motif (MIN, MRN/X-inhibitory motif). MIN executes suppression of Tel1, DNA end- resection and non-homologous end joining by binding the Rad50 N-terminal region. Our data suggest that MIN promotes a transition within MRX that is not conductive for endonuclease activity, DNA-end tethering or Tel1 kinase activation, highlighting an Achilles’ heel in MRN, which we propose is also exploited by the RIF2 paralog ORC4 (Origin Recognition Complex 4) in Kluyveromyces lactis and the Schizosaccharomyces pombe telomeric factor Taz1, which is evolutionarily unrelated to Orc4/Rif2. This raises the possibility that analogous mechanisms might be deployed in other eukaryotes as well. 1 Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK. 2 Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Universitàdella Svizzera italiana (USI), Bellinzona, Switzerland. 3 Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland.
    [Show full text]
  • A Curated Ortholog Database for Yeasts and Fungi Spanning 600 Million Years of Evolution
    bioRxiv preprint doi: https://doi.org/10.1101/237974; this version posted October 8, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. AYbRAH: a curated ortholog database for yeasts and fungi spanning 600 million years of evolution Kevin Correia1, Shi M. Yu1, and Radhakrishnan Mahadevan1,2,* 1Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada, ON 2Institute of Biomaterials and Biomedical Engineering, University of Toronto, Ontario, Canada Corresponding author: Radhakrishnan Mahadevan∗ Email address: [email protected] ABSTRACT Budding yeasts inhabit a range of environments by exploiting various metabolic traits. The genetic bases for these traits are mostly unknown, preventing their addition or removal in a chassis organism for metabolic engineering. To help understand the molecular evolution of these traits in yeasts, we created Analyzing Yeasts by Reconstructing Ancestry of Homologs (AYbRAH), an open-source database of predicted and manually curated ortholog groups for 33 diverse fungi and yeasts in Dikarya, spanning 600 million years of evolution. OrthoMCL and OrthoDB were used to cluster protein sequence into ortholog and homolog groups, respectively; MAFFT and PhyML were used to reconstruct the phylogeny of all homolog groups. Ortholog assignments for enzymes and small metabolite transporters were compared to their phylogenetic reconstruction, and curated to resolve any discrepancies. Information on homolog and ortholog groups can be viewed in the AYbRAH web portal (https://kcorreia.github. io/aybrah/) to review ortholog groups, predictions for mitochondrial localization and transmembrane domains, literature references, and phylogenetic reconstructions.
    [Show full text]
  • Bandoniozyma Gen. Nov., a Genus of Fermentative and Non-Fermentative Tremellaceous Yeast Species
    Bandoniozyma gen. nov., a Genus of Fermentative and Non-Fermentative Tremellaceous Yeast Species Patricia Valente1,2*., Teun Boekhout3., Melissa Fontes Landell2, Juliana Crestani2, Fernando Carlos Pagnocca4, Lara Dura˜es Sette4,5, Michel Rodrigo Zambrano Passarini5, Carlos Augusto Rosa6, Luciana R. Branda˜o6, Raphael S. Pimenta7, Jose´ Roberto Ribeiro8, Karina Marques Garcia8, Ching-Fu Lee9, Sung-Oui Suh10,Ga´bor Pe´ter11,De´nes Dlauchy11, Jack W. Fell12, Gloria Scorzetti12, Bart Theelen3, Marilene H. Vainstein2 1 Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal do Rio Grande do Sul, Porto Alegre - RS, Brazil, 2 Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre – RS, Brazil, 3 Centraalbureau voor Schimmelcultures Fungal Biodiversity Centre, Utrecht, The Netherlands, 4 Departamento de Bioquı´mica e Microbiologia, Sa˜o Paulo State University, Rio Claro - SP, Brazil, 5 Colec¸a˜o Brasileira de Micro-organismos de Ambiente e Indu´stria, Divisa˜o de Recursos Microbianos-Centro Pluridisciplinar de Pesquisas Quimicas, Biologicas e Agricolas, Universidade Estadual de Campinas, Campinas – SP, Brazil, 6 Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte – MG, Brazil, 7 Laborato´rio de Microbiologia Ambiental e Biotecnologia, Campus Universita´rio de Palmas, Universidade Federal do Tocantins, Palmas - TO, Brazil, 8 Instituto de Microbiologia Prof. Paulo de Goes, Universidade Federal do Rio de Janeiro, Rio de Janeiro - RJ, Brazil, 9 Department of Applied
    [Show full text]
  • Searching for Telomerase Rnas in Saccharomycetes
    bioRxiv preprint doi: https://doi.org/10.1101/323675; this version posted May 16, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Article TERribly Difficult: Searching for Telomerase RNAs in Saccharomycetes Maria Waldl 1,†, Bernhard C. Thiel 1,†, Roman Ochsenreiter 1, Alexander Holzenleiter 2,3, João Victor de Araujo Oliveira 4, Maria Emília M. T. Walter 4, Michael T. Wolfinger 1,5* ID , Peter F. Stadler 6,7,1,8* ID 1 Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria; {maria,thiel,romanoch}@tbi.univie.ac.at, michael.wolfi[email protected] 2 BioInformatics Group, Fakultät CB Hochschule Mittweida, Technikumplatz 17, D-09648 Mittweida, Germany; [email protected] 3 Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany 4 Departamento de Ciência da Computação, Instituto de Ciências Exatas, Universidade de Brasília; [email protected], [email protected] 5 Center for Anatomy and Cell Biology, Medical University of Vienna, Währingerstraße 13, 1090 Vienna, Austria 6 German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Competence Center for Scalable Data Services and Solutions, and Leipzig Research Center for Civilization Diseases, University Leipzig, Germany 7 Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany 8 Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501 * Correspondence: MTW michael.wolfi[email protected]; PFS [email protected] † These authors contributed equally to this work.
    [Show full text]
  • Complete DNA Sequence of Kuraishia Capsulata Illustrates Novel Genomic Features Among Budding Yeasts (Saccharomycotina)
    GBE Complete DNA Sequence of Kuraishia capsulata Illustrates Novel Genomic Features among Budding Yeasts (Saccharomycotina) Lucia Morales1,BenjaminNoel2,BetinaPorcel2, Marina Marcet-Houben3,4, Marie-Francoise Hullo1, Christine Sacerdot1,8, Fredj Tekaia1,Ve´ronique Leh-Louis5, Laurence Despons5, Varun Khanna1, Jean-Marc Aury2,Vale´rie Barbe2,ArnaudCouloux2, Karen Labadie2, Eric Pelletier2, Jean-Luc Souciet6, Teun Boekhout7, Toni Gabaldon3,4, Patrick Wincker2, and Bernard Dujon1,* 1Institut Pasteur, Unite´ de Ge´ne´tique Mole´culaire des Levures, CNRS UMR3525, Univ. P. M. Curie UFR927, Paris, France 2Commissariat a` l’Energie Atomique, Institut de Ge´nomique/Ge´noscope, Evry, France 3Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain 4Universitat Pompeu Fabra (UPF), Barcelona, Spain 5Univ. de Strasbourg, CNRS UPR9002, Architecture et Re´activite´ de l’ARN, Institut de Biologie Mole´culaire et Cellulaire du CNRS, Strasbourg, France 6Univ. de Strasbourg, CNRS UMR7156, Institut de Botanique, Strasbourg, France 7CBS Fungal Biodiversity Centre, KNAW, Utrecht, Netherlands 8Present address: Institut de Biologie (IBENS), Ecole Normale Supe´rieure, 46 rue d’Ulm, Paris, France *Corresponding author: E-mail: [email protected]. Accepted: November 27, 2013 Data deposition: Assembled sequences as well as reads have been deposited at European Nucleotide Archive under the accession CBUD020000001–CBUD020000057 (contigs) and HG793125–HG793131 (scaffolds). Abstract The numerous yeast genome sequences presently available provide a rich source of information for functional as well as evolutionary genomics but unequally cover the large phylogenetic diversity of extant yeasts. We present here the complete sequence of the nuclear genome of the haploid-type strain of Kuraishia capsulata (CBS1993T), a nitrate-assimilating Saccharomycetales of uncertain taxon- omy, isolated from tunnels of insect larvae underneath coniferous barks and characterized by its copious production of extracellular polysaccharides.
    [Show full text]
  • ( 12 ) United States Patent
    US010398154B2 (12 ) United States Patent ( 10 ) Patent No. : US 10 , 398 , 154 B2 Embree et al. ( 45 ) Date of Patent: * Sep . 3 , 2019 (54 ) MICROBIAL COMPOSITIONS AND ( 58 ) Field of Classification Search METHODS OF USE FOR IMPROVING MILK None PRODUCTION See application file for complete search history . (71 ) Applicant: ASCUS BIOSCIENCES , INC ., San Diego , CA (US ) (56 ) References Cited ( 72 ) Inventors: Mallory Embree, San Diego , CA (US ) ; U . S . PATENT DOCUMENTS Luke Picking , San Diego , CA ( US ) ; 3 , 484 , 243 A 12 / 1969 Anderson et al . Grant Gogul , Cardiff , CA (US ) ; Janna 4 ,559 , 298 A 12 / 1985 Fahy Tarasova , San Diego , CA (US ) (Continued ) (73 ) Assignee : Ascus Biosciences , Inc. , San Diego , FOREIGN PATENT DOCUMENTS CA (US ) CN 104814278 A 8 / 2015 ( * ) Notice : Subject to any disclaimer , the term of this EP 0553444 B1 3 / 1998 patent is extended or adjusted under 35 U .S . C . 154 (b ) by 0 days. (Continued ) This patent is subject to a terminal dis OTHER PUBLICATIONS claimer . Borling , J , Master' s thesis, 2010 . * (21 ) Appl. No .: 16 / 029, 398 ( Continued ) ( 22 ) Filed : Jul. 6 , 2018 Primary Examiner - David W Berke- Schlessel (65 ) Prior Publication Data ( 74 ) Attorney , Agent, or Firm — Cooley LLP US 2018 /0325966 A1 Nov . 15 , 2018 ( 57 ) ABSTRACT Related U . S . Application Data The disclosure relates to isolated microorganisms — includ (63 ) Continuation of application No. ing novel strains of the microorganisms - microbial consor PCT/ US2014 /012573 , filed on Jan . 6 , 2017 . tia , and compositions comprising the same . Furthermore , the disclosure teaches methods of utilizing the described micro (Continued ) organisms, microbial consortia , and compositions compris (51 ) Int.
    [Show full text]
  • Candida Pellucida Fungal Planet Description Sheets 369
    368 Persoonia – Volume 44, 2020 Candida pellucida Fungal Planet description sheets 369 Fungal Planet 1068 – 29 June 2020 Candida pellucida A.M. Glushakova, M.A. Tomashevskaya & Kachalkin, sp. nov. Etymology. The name refers to Exomias pellucidus from which the ex-type Notes — Analysis of the ITS-D1/D2 regions of the surveyed strain was isolated. yeasts suggested that they were conspecific and represented Classification — Debaryomycetaceae, Saccharomycetales, a hitherto undescribed species of the Candida/Lodderomyces Saccharomycetes. clade. Based on the NCBI GenBank nucleotide database, the best hits using the ITS sequence are Candida viswanathii On glucose peptone yeast extract agar (GPYA) and 5 % malt CBS 7889 (GenBank KY102513; 90.24 % similar, 18 subst. extract agar (MEA), after 7 d at 25 °C, streak is white-cream, and 23 gaps) and Candida viswanathii ATCC 22981T (Gen- semi-glistening, with a smooth surface and entire margin. Bank NR_138345; 88.07 % similar, 24 subst. and 36 gaps), Cells are ovoid to elongate (2–6 × 5–8 μm) and occur singly using LSU it is Candida viswanathii CBS 4024T (GenBank or in pairs, dividing by polar and multilateral budding. Rare KY106885; 98.20 % similar, 9 subst.), using SSU it is Candida pseudohyphae are produced on potato dextrose agar (PDA) labiduridarum NRRL Y-27940T (GenBank NG_063271; 99.88 % and cornmeal agar (CMA). Ascospores and true hyphae have similar, 2 subst.), using TEF1 it is Candida dubliniensis CD36T not been observed during 4 wk at 10 and 25 °C in culture (GenBank XM_002417390; 95.67 % similar, 19 subst.) and (pure cultures and in mating test) grown on GPYA, MEA, PDA, using RPB1 it is Candida viswanathii CBS 4024T (GenBank CMA and yeast nitrogen base with 0.5 % glucose (YNB) agar.
    [Show full text]
  • DNA Barcoding Analysis of More Than 1000 Marine Yeast Isolates Reveals Previously Unrecorded Species
    bioRxiv preprint doi: https://doi.org/10.1101/2020.08.29.273490; this version posted September 6, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. DNA barcoding analysis of more than 1000 marine yeast isolates reveals previously unrecorded species Chinnamani PrasannaKumar*1,2, Shanmugam Velmurugan2,3, Kumaran Subramanian4, S. R. Pugazhvendan5, D. Senthil Nagaraj3, K. Feroz Khan2,6, Balamurugan Sadiappan1,2, Seerangan Manokaran7, Kaveripakam Raman Hemalatha8, Bhagavathi Sundaram Sivamaruthi9, Chaiyavat Chaiyasut9 1Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Panaji, Goa-403004, India 2Centre of Advance studies in Marine Biology, Annamalai University, Parangipettai, Tamil Nadu- 608502, India 3Madawalabu University, Bale, Robe, Ethiopia 4Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Tamil Nadu-600119, India 5Department of Zoology, Arignar Anna Government Arts College, Cheyyar, Tamil Nadu- 604407, India 6Research Department of Microbiology, Sadakathullah Appa College, Rahmath Nagar, Tirunelveli Tamil Nadu -627 011 7Center for Environment & Water, King Fahd University of Petroleum and Minerals, Dhahran-31261, Saudi Arabia 8Department of Microbiology, Annamalai university, Annamalai Nagar, Chidambaram, Tamil Nadu- 608 002, India 9Innovation Center for Holistic Health, Nutraceuticals, and Cosmeceuticals, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand. *Corresponding author email: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.08.29.273490; this version posted September 6, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
    [Show full text]