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Liu F, Hu ZD, Zhao XM, Zhao WN, Feng ZX, Yurkov A, Alwasel S, Boekhout T, Bensch K, Hui FL, Bai FY, Wang QM. Phylogenomic analysis of the Candida auris-Candida haemuli clade and related taxa in the Metschnikowiaceae, and proposal of thirteen new genera, fifty-five new combinations and nine new species. PERSOONIA 2024; 52:22-43. [PMID: 39161632 PMCID: PMC11319837 DOI: 10.3767/persoonia.2024.52.02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 03/12/2024] [Indexed: 08/21/2024]
Abstract
Candida is a polyphyletic genus of asexually reproducing yeasts in the Saccharomycotina with more than 400 species that occur in almost all families of the subclass and its name is strongly connected with the infectious disease candidiasis. During the last two decades, approximately half of the Candida species have been reassigned into more than 36 already existing genera and 14 newly proposed genera, but the polyphyletic feature of the genus largely remained. Candida auris is an important, globally emerging opportunistic pathogen that has caused life-threatening outbreaks in healthcare facilities worldwide. This species belongs to the Candida auris-Candida haemuli (CAH) clade in the Metschnikowiaceae, a clade that contains multidrug-resistant clinically relevant species, but also species isolated from natural environments. The clade is phylogenetically positioned remotely from the type species of the genus Candida that is Candida vulgaris (currently interpreted as a synonym of Candida tropicalis) and belongs to the family Debaryomycetaceae. Although previous phylogenetic and phylogenomic studies confirmed the position of C. auris in the Metschnikowiaceae, these analyses failed to resolve the position of the CAH clade within the family and its delimitation from the genera Clavispora and Metschnikowia. To resolve the position of the CAH clade, phylogenomic and comparative genomics analyses were carried out to address the phylogenetic position of C. auris and related species in the Metschnikowiaceae using several metrics, such as the average amino acid identity (AAI) values, the percentage of conserved proteins (POCP) and the presence-absence patterns of orthologs (PAPO). Based on those approaches, 13 new genera are proposed for various Candida and Hyphopichia species, including members of the CAH clade in the Metschnikowiaceae. As a result, C. auris and related species are reassigned to the genus Candidozyma. Fifty-five new combinations and nine new species are introduced and this will reduce the polyphyly of the genus Candida. Citation: Liu F, Hu Z-D, Zhao X-M, et al. 2024. Phylogenomic analysis of the Candida auris-Candida haemuli clade and related taxa in the Metschnikowiaceae, and proposal of thirteen new genera, fifty-five new combinations and nine new species. Persoonia 52: 22-43. https://doi.org/10.3767/persoonia.2024.52.02 .
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Affiliation(s)
- F. Liu
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, Hebei, China
| | - Z.-D. Hu
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, Hebei, China
| | - X.-M. Zhao
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, Hebei, China
| | - W.-N. Zhao
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, Hebei, China
| | - Z.-X. Feng
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, Hebei, China
| | - A. Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - S. Alwasel
- College of Sciences, King Saud University, Riyadh, Saudi Arabia
| | - T. Boekhout
- College of Sciences, King Saud University, Riyadh, Saudi Arabia
- The Yeasts Foundation, Amsterdam, The Netherlands
| | - K. Bensch
- Westerdijk Institute of Fungal Biodiversity, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - F.-L. Hui
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, China
| | - F.-Y. Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Q.-M. Wang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, Hebei, China
- Hebei Basic Science Center for Biotic Interaction, Hebei University, Baoding 071002, Hebei, China
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Hebei University, Baoding 071002, Hebei, China
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Opulente DA, LaBella AL, Harrison MC, Wolters JF, Liu C, Li Y, Kominek J, Steenwyk JL, Stoneman HR, VanDenAvond J, Miller CR, Langdon QK, Silva M, Gonçalves C, Ubbelohde EJ, Li Y, Buh KV, Jarzyna M, Haase MAB, Rosa CA, Čadež N, Libkind D, DeVirgilio JH, Hulfachor AB, Kurtzman CP, Sampaio JP, Gonçalves P, Zhou X, Shen XX, Groenewald M, Rokas A, Hittinger CT. Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts. Science 2024; 384:eadj4503. [PMID: 38662846 PMCID: PMC11298794 DOI: 10.1126/science.adj4503] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 03/22/2024] [Indexed: 05/03/2024]
Abstract
Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to very broad (generalists). Two general paradigms have been proposed to explain this variation: (i) trade-offs between performance efficiency and breadth and (ii) the joint influence of extrinsic (environmental) and intrinsic (genomic) factors. We assembled genomic, metabolic, and ecological data from nearly all known species of the ancient fungal subphylum Saccharomycotina (1154 yeast strains from 1051 species), grown in 24 different environmental conditions, to examine niche breadth evolution. We found that large differences in the breadth of carbon utilization traits between yeasts stem from intrinsic differences in genes encoding specific metabolic pathways, but we found limited evidence for trade-offs. These comprehensive data argue that intrinsic factors shape niche breadth variation in microbes.
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Affiliation(s)
- Dana A. Opulente
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
- Biology Department Villanova University, Villanova, PA 19085, USA
| | - Abigail Leavitt LaBella
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- North Carolina Research Center (NCRC), Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 150 Research Campus Drive, Kannapolis, NC 28081, USA
| | - Marie-Claire Harrison
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - John F. Wolters
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Chao Liu
- College of Agriculture and Biotechnology and Centre for Evolutionary & Organismal Biology, Zhejiang University, Hangzhou 310058, China
| | - Yonglin Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Jacek Kominek
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
- LifeMine Therapeutics, Inc., Cambridge, MA 02140, USA
| | - Jacob L. Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hayley R. Stoneman
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
- University of Colorado - Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Jenna VanDenAvond
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Caroline R. Miller
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Quinn K. Langdon
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Margarida Silva
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Carla Gonçalves
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Emily J. Ubbelohde
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Yuanning Li
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Kelly V. Buh
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Martin Jarzyna
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- Graduate Program in Neuroscience and Department of Biology, Washington University School of Medicine, St. Louis, MO 63130, USA
| | - Max A. B. Haase
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
- Vilcek Institute of Graduate Biomedical Sciences and Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Carlos A. Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Neža Čadež
- Food Science and Technology Department, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Diego Libkind
- Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC), Universidad Nacional del Comahue, CONICET, CRUB, Quintral 1250, San Carlos de Bariloche, 8400, Río Negro, Argentina
| | - Jeremy H. DeVirgilio
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, IL 61604, USA
| | - Amanda Beth Hulfachor
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Cletus P. Kurtzman
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, IL 61604, USA
| | - José Paulo Sampaio
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Paula Gonçalves
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Xiaofan Zhou
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Xing-Xing Shen
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- College of Agriculture and Biotechnology and Centre for Evolutionary & Organismal Biology, Zhejiang University, Hangzhou 310058, China
| | | | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
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Franco-Duarte R, Čadež N, Rito T, Drumonde-Neves J, Dominguez YR, Pais C, Sousa MJ, Soares P. Whole-Genome Sequencing and Annotation of the Yeast Clavispora santaluciae Reveals Important Insights about Its Adaptation to the Vineyard Environment. J Fungi (Basel) 2022; 8:jof8010052. [PMID: 35049992 PMCID: PMC8781136 DOI: 10.3390/jof8010052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 11/16/2022] Open
Abstract
Clavispora santaluciae was recently described as a novel non-Saccharomyces yeast species, isolated from grapes of Azores vineyards, a Portuguese archipelago with particular environmental conditions, and from Italian grapes infected with Drosophila suzukii. In the present work, the genome of five Clavispora santaluciae strains was sequenced, assembled, and annotated for the first time, using robust pipelines, and a combination of both long- and short-read sequencing platforms. Genome comparisons revealed specific differences between strains of Clavispora santaluciae reflecting their isolation in two separate ecological niches—Azorean and Italian vineyards—as well as mechanisms of adaptation to the intricate and arduous environmental features of the geographical location from which they were isolated. In particular, relevant differences were detected in the number of coding genes (shared and unique) and transposable elements, the amount and diversity of non-coding RNAs, and the enzymatic potential of each strain through the analysis of their CAZyome. A comparative study was also conducted between the Clavispora santaluciae genome and those of the remaining species of the Metschnikowiaceae family. Our phylogenetic and genomic analysis, comprising 126 yeast strains (alignment of 2362 common proteins) allowed the establishment of a robust phylogram of Metschnikowiaceae and detailed incongruencies to be clarified in the future.
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Affiliation(s)
- Ricardo Franco-Duarte
- CBMA, Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, 4710-057 Braga, Portugal; (T.R.); (C.P.); (M.J.S.); (P.S.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
- Correspondence: or
| | - Neža Čadež
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, 101, 1000 Ljubljana, Slovenia;
| | - Teresa Rito
- CBMA, Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, 4710-057 Braga, Portugal; (T.R.); (C.P.); (M.J.S.); (P.S.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| | - João Drumonde-Neves
- IITAA—Institute of Agricultural and Environmental Research and Technology, University of Azores, 9700-042 Angra do Heroísmo, Portugal;
| | | | - Célia Pais
- CBMA, Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, 4710-057 Braga, Portugal; (T.R.); (C.P.); (M.J.S.); (P.S.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| | - Maria João Sousa
- CBMA, Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, 4710-057 Braga, Portugal; (T.R.); (C.P.); (M.J.S.); (P.S.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| | - Pedro Soares
- CBMA, Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, 4710-057 Braga, Portugal; (T.R.); (C.P.); (M.J.S.); (P.S.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
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Thompson SRL, Lee DK, Lachance MA, Smith DR. Mutational Effects of Mobile Introns on the Mitochondrial Genomes of Metschnikowia Yeasts. Front Genet 2021; 12:785218. [PMID: 34804133 PMCID: PMC8601654 DOI: 10.3389/fgene.2021.785218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 10/19/2021] [Indexed: 11/25/2022] Open
Abstract
It has been argued that DNA repair by homologous recombination in the context of endonuclease-mediated cleavage can cause mutations. To better understand this phenomenon, we examined homologous recombination following endonuclease cleavage in a native genomic context: the movement of self-splicing introns in the mitochondrial genomes of Metschnikowia yeasts. Self-splicing mitochondrial introns are mobile elements, which can copy and paste themselves at specific insertion sites in mitochondrial DNA using a homing endonuclease in conjunction with homologous recombination. Here, we explore the mutational effects of self-splicing introns by comparing sequence variation within the intron-rich cox1 and cob genes from 71 strains (belonging to 40 species) from the yeast genus Metschnikowia. We observed a higher density of single nucleotide polymorphisms around self-splicing-intron insertion sites. Given what is currently known about the movement of organelle introns, it is likely that their mutational effects result from the high binding affinity of endonucleases and their interference with repair machinery during homologous recombination (or, alternatively, via gene conversion occurring during the intron insertion process). These findings suggest that there are fitness costs to harbouring self-splicing, mobile introns and will help us better understand the risks associated with modern biotechnologies that use endonuclease-mediated homologous recombination, such as CRISPR-Cas9 gene editing.
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Affiliation(s)
- Scout R L Thompson
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Dong Kyung Lee
- Department of Biology, University of Western Ontario, London, ON, Canada
| | | | - David Roy Smith
- Department of Biology, University of Western Ontario, London, ON, Canada
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Abstract
While sequencing and characterizing the mitochondrial genomes of 71 strains from the yeast genus Metschnikowia [1] (close cousin to the model species Candida albicans), we uncovered one of the most extreme examples of mitochondrial genome architectural diversity observed to date. These Metschnikowia mitochondrial DNAs (mtDNAs) capture nearly the entire known gene-size and intron-content range for cox1 and cob across all eukaryotic life and show remarkable differences in structure and noncoding content. This genomic variation can be seen both among species and between strains of the same species, raising the question: why are Metschnikowia mitogenomes so malleable?
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Lachance MA, Lee DK, Hsiang T. Delineating yeast species with genome average nucleotide identity: a calibration of ANI with haplontic, heterothallic Metschnikowia species. Antonie Van Leeuwenhoek 2020; 113:2097-2106. [PMID: 33048250 DOI: 10.1007/s10482-020-01480-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 10/02/2020] [Indexed: 11/24/2022]
Abstract
We determined pairwise average nucleotide identity (ANI) values for the genomes of 71 strains assigned to 36 Metschnikowia species, 28 of which were represented by multiple isolates selected to represent the range of genetic diversity of the species, and most of which were defined on the basis of reproductive isolation. Similar to what has been proposed for prokaryote species delineation, an ANI value of 95% emerged as a good guideline for the delineation of yeast species, although some overlap exists, whereby members of a reproductive community could have slightly lower values (e.g., 94.3% for M. kamakouana), and representatives of distinct sister species could give slightly higher values (e.g., 95.2% for the sister species M. drakensbergensis and M. proteae). Unlike what is observed in prokaryotes, a sizeable gap between intraspecific and interspecific ANI values was not encountered. Given the ease with which yeast draft genomes can now be obtained, ANI values are poised to become the new standard upon which yeast species may be delineated on genetic distance. As borderline cases exist, however, the delineation of yeast species will continue to require careful evaluation of all available data. We also explore the often-neglected distinction between phylogenetic relatedness and sequence identity through the analysis of a tree constructed from ANI' (100 - ANI) values.
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Affiliation(s)
- Marc-André Lachance
- Department of Biology, University of Western Ontario, London, Ontario, N6A 5B7, Canada.
| | - Dong Kyung Lee
- Department of Biology, University of Western Ontario, London, Ontario, N6A 5B7, Canada
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
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Takashima M, Suh SO, Bai FY, Sugita T. Takashi Nakase's last tweet: what is the current direction of microbial taxonomy research? FEMS Yeast Res 2020; 19:5670643. [PMID: 31816016 DOI: 10.1093/femsyr/foz066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Accepted: 12/07/2019] [Indexed: 12/14/2022] Open
Abstract
During the last few decades, type strains of most yeast species have been barcoded using the D1/D2 domain of their LSU rRNA gene and internal transcribed spacer (ITS) region. Species identification using DNA sequences regarding conspecificity in yeasts has also been studied. Most yeast species can be identified according to the sequence divergence of their ITS region or a combination of the D1/D2 and ITS regions. Studies that have examined intraspecific diversity have used multilocus sequence analyses, whereas the marker regions used in this analysis vary depending upon taxa. D1/D2 domain and ITS region sequences have been used as barcodes to develop primers suitable for the detection of the biological diversity of environmental DNA and the microbiome. Using these barcode sequences, it is possible to identify relative lineages and infer their gene products and function, and how they adapt to their environment. If barcode sequence was not variable enough to identify a described species, one could investigate the other biological traits of these yeasts, considering geological distance, environmental circumstances and isolation of reproduction. This article is dedicated to late Dr Takashi Nakase (1939-2018).
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Affiliation(s)
- Masako Takashima
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba 305-0074, Japan.,Department of Microbiology, Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose, Tokyo 204-8588, Japan
| | - Sung-Oui Suh
- Manufacturing Science and Technology, American Type Culture Collection (ATCC), 10801 University Blvd., Manassas, VA 20110, USA
| | - Feng-Yan Bai
- Institute of Microbiology, State Key Laboratory of Mycology, Chinese Academy of Sciences, Beijing 100101, China
| | - Takashi Sugita
- Department of Microbiology, Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose, Tokyo 204-8588, Japan
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Lee DK, Santos ARDO, Hsiang T, Rosa CA, Lachance MA. Catching speciation in the act-act 2: Metschnikowia lacustris sp. nov., a sister species to Metschnikowia dekortorum. Antonie Van Leeuwenhoek 2020; 113:753-762. [PMID: 32100143 DOI: 10.1007/s10482-020-01395-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 02/12/2020] [Indexed: 10/24/2022]
Abstract
The isolation of a single yeast strain in the clade containing Metschnikowia dekortorum, in the Amazon biome of Brazil, incited us to re-examine the species boundaries within the clade. The strain (UFMG-CM-Y6306) was difficult to position relative to neighbouring species using standard barcode sequences (ITS-D1/D2 rRNA gene region). Mating took place freely with α strains of M. bowlesiae, M. dekortorum, and M. similis, but two-spored asci, indicative of a fertile meiotic progeny, were formed abundantly only with certain strains of M. dekortorum. Accordingly, we examined mating success among every phylotype in the clade and constructed a phylogeny based on a concatenation of 100 of the largest orthologous genes annotated in draft genomes. The analyses confirmed membership of the Amazonian isolate in M. dekortorum, but also indicated that the species should be subdivided into two. As a result, we retain three original members of M. dekortorum in the species, together with the new isolate, and reassign six isolates recovered from Mesoamerican lacustrine habitats to Metschnikowia lacustris sp. nov. The type is UWOPS 12-619.2T (isotype CBS 16250T). MycoBank: MB 833751.
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Affiliation(s)
- Dong Kyung Lee
- Department of Biology, University of Western Ontario, London, ON, N6A 5B7, Canada
| | | | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Carlos A Rosa
- Departamento de Microbiologia, ICB, Universidade Federal de Minas Gerais, C.P. 486, Belo Horizonte, MG, Brazil
| | - Marc-André Lachance
- Department of Biology, University of Western Ontario, London, ON, N6A 5B7, Canada.
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Santos ARDO, Lee DK, Ferreira AG, do Carmo MC, Rondelli VM, Barros KO, Hsiang T, Rosa CA, Lachance MA. The yeast community of Conotelus sp. (Coleoptera: Nitidulidae) in Brazilian passionfruit flowers (Passiflora edulis) and description of Metschnikowia amazonensis sp. nov., a large-spored clade yeast. Yeast 2020; 37:253-260. [PMID: 32017239 DOI: 10.1002/yea.3453] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/12/2019] [Accepted: 11/15/2019] [Indexed: 11/11/2022] Open
Abstract
Species of the nitidulid beetle Conotelus found in flowers of Convolvulaceae and other plants across the New World and in Hawaii consistently harbour a yeast community dominated by one or more large-spored Metschnikowia species. We investigated the yeasts found in beetles and flowers of cultivated passionfruit in Rondônia state, in the Amazon biome of Brazil, where a Conotelus species damages the flowers and hinders fruit production. A sample of 46 beetles and 49 flowers yielded 86 and 83 yeast isolates, respectively. Whereas the flower community was dominated by Kodamaea ohmeri and Kurtzmaniella quercitrusa, the major yeasts recovered from beetles were Wickerhamiella occidentalis, which is commonly isolated from this community, and a novel species of large-spored Metschnikowia in the arizonensis subclade, which we describe here as Metschnikowia amazonensis sp. nov. Phylogenetic analyses based on barcode sequences (ITS-D1/D2) and a multigene alignment of 11,917 positions (genes ura2, msh6, and pmt2) agreed to place the new species as a sister to Metschnikowia arizonensis, a rare species known only from one locality in Arizona. The two form sterile asci when mated, which is typical of related members of the clade. The α pheromone of the new species is unique but typical of the subclade. The type of M. amazonensis sp. nov. is UFMG-CM-Y6309T (ex-type CBS 16156T , mating type a), and the designated allotype (mating type α) is UFMG-CM-Y6307A (CBS 16155A ). MycoBank MB 833560.
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Affiliation(s)
| | - Dong Kyung Lee
- Department of Biology, University of Western Ontario, London, Ontario, Canada
| | | | - Marina Conceição do Carmo
- Departamento de Agronomia e Entomologia, Universidade Federal Rural de Pernambuco, Recife, Pernambuco, Brazil
| | - Vando Miossi Rondelli
- Departamento de Agronomia, Universidade Federal de Rondônia, Rolim de Moura, Rondônia, Brazil
| | - Katharina O Barros
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Carlos A Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Marc-André Lachance
- Department of Biology, University of Western Ontario, London, Ontario, Canada
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10
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Takashima M, Sugita T. Draft Genome Analysis of Trichosporonales Species That Contribute to the Taxonomy of the Genus Trichosporon and Related Taxa. Med Mycol J 2019; 60:51-57. [PMID: 31155572 DOI: 10.3314/mmj.19.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Many nomenclatural changes, including proposals of new taxa, have been carried out in fungi to adapt to the "One fungus = One name" (1F=1N) principle. In yeasts, while some changes have been made in response to 1F=1N, most have resulted from two other factors: i) an improved understanding of biological diversity due to an increase in number of known species, and ii) progress in the methods for analyzing and evaluating biological diversity. The method for constructing a backbone tree, which is a basal tree used to infer phylogeny, has also progressed from single-gene trees to multi-locus trees and further, to genome trees. This paper describes recent advances related to the contribution of genomic data to taxonomy, using the order Trichosporonales as an example.
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Affiliation(s)
- Masako Takashima
- Japan Collection of Microorganisms, RIKEN BioResource Research Center
| | - Takashi Sugita
- Department of Microbiology, Meiji Pharmaceutical University
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11
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Metschnikowia miensis f.a., sp. nov., isolated from flowers in Mie prefecture, Japan. Antonie van Leeuwenhoek 2019; 113:321-329. [PMID: 31637663 DOI: 10.1007/s10482-019-01340-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 09/30/2019] [Indexed: 10/25/2022]
Abstract
Four yeast strains (RIFY 10001T, RIFY 10002, RIFY 10003, and RIFY 10004) were isolated from flowers growing in fields of mustard and broad beans in Japan. Ascospore formation was not observed. Sequence analysis of the D1/D2 domain of the large subunit ribosomal RNA (LSU rRNA) gene of the four strains indicated that they belong to the genus Metschnikowia and are closely related to Metschnikowia hawaiiana strain CBS 9146T and Metschnikowia orientalis strain CBS 10331T. The D1/D2 domain of the LSU rRNA gene and internal transcribed spacer regions of strain RIFY 10001T were 85.7% identical to those of M. hawaiiana strain CBS 9146T. All four strains were distinguished from the M. hawaiiana strain CBS 9146T by their inability to ferment glucose. Hence, these four strains are novel species and were named as Metschnikowia miensis (holotype: RIFY 10001T; isotypes: NBRC 112445T = CBS 14749T).
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12
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Pawlikowska E, James SA, Breierova E, Antolak H, Kregiel D. Biocontrol capability of local Metschnikowia sp. isolates. Antonie Van Leeuwenhoek 2019; 112:1425-1445. [PMID: 31111331 PMCID: PMC6748895 DOI: 10.1007/s10482-019-01272-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 05/03/2019] [Indexed: 12/16/2022]
Abstract
This study set out to isolate and identify epiphytic yeasts producing pulcherrimin, and to evaluate their potential as biological control agents (BCAs). We isolated Metschnikowia sp. strains from flowers and fruits collected in Poland. The plant material had been collected between April to September 2017 from two small orchards where traditional organic management is employed. We identified the essential phenotypic features of the yeast, including assimilation and enzymatic profiles, stress resistance, adhesion properties, and antimicrobial activity against various fungi involved in crop and/or food spoilage. Yeast screening was performed using YPD agar supplemented with chloramphenicol and Fe(III) ions. Taxonomic classification was determined by sequence analysis of the D1/D2 domains of the large subunit rRNA gene. The isolates were identified as Metschnikowia andauensis and Metschnikowia sinensis. The yeast isolates were further characterized based on their enzymatic and assimilation profiles, as well as their growth under various stress conditions. In addition, the hydrophobicity and adhesive abilities of the Metschnikowia isolates were determined using a MATH test and luminometry. Their antagonistic action against molds representing typical crop spoiling microflora was also evaluated. The assimilation profiles of the wild isolates were similar to those displayed by collection strains of M. pulcherrima. However, some of the isolates displayed more beneficial phenotypic properties, especially good growth under stress conditions. Several of the epiphytes grew well over a wider range of temperatures (8-30 °C) and pH levels (3-9), and additionally showed elevated tolerance to ethanol (8%), glucose (30%), and peroxides (50 mM). The hydrophobicity and adhesion of the yeast cells were strain- and surface-dependent. The tested yeasts showed potential for use as BCAs, with some exhibiting strong antagonism against molds belonging to the genera Alternaria, Botrytis, Fusarium, Rhizopus, and Verticillium, as well as against yeasts isolated as food spoilage microbiota.
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Affiliation(s)
- Ewelina Pawlikowska
- Institute of Fermentation Technology and Microbiology, Lodz University of Technology, Wolczanska 171/173, 90-924 Lodz, Poland
| | - Steve A. James
- Gut Microbes and Health, Quadram Institute Bioscience, Colney Lane, Norwich Research Park, Norwich, NR4 7UA UK
| | - Emilia Breierova
- Culture Collection of Yeasts (CCY), Institute of Chemistry, Slovak Academy of Sciences, Dúbravskácesta 9, 845 38 Bratislava, Slovakia
| | - Hubert Antolak
- Institute of Fermentation Technology and Microbiology, Lodz University of Technology, Wolczanska 171/173, 90-924 Lodz, Poland
| | - Dorota Kregiel
- Institute of Fermentation Technology and Microbiology, Lodz University of Technology, Wolczanska 171/173, 90-924 Lodz, Poland
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13
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Recognition and delineation of yeast genera based on genomic data: Lessons from Trichosporonales. Fungal Genet Biol 2019; 130:31-42. [DOI: 10.1016/j.fgb.2019.04.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 03/19/2019] [Accepted: 04/20/2019] [Indexed: 02/03/2023]
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14
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Chai CY, Huang LN, Cheng H, Liu WJ, Hui FL. Metschnikowia baotianmanensis f.a., sp. nov., a new yeast species isolated from the gut of the rhinoceros beetle Allomyrina dichotoma. Int J Syst Evol Microbiol 2019; 69:3087-3092. [PMID: 31329532 DOI: 10.1099/ijsem.0.003593] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four strains, NYNU 15610, NYNU 15612, NYNU 15613 and NYNU 15615, of a novel ascomycetous yeast were isolated from the gut of Allomyrina dichotoma (Coleoptera: Scarabeidae) collected from two different localities in Henan Province, Central PR China. The four strains shared identical sequences in both of the D1/D2 domains of the large subunit rRNA gene and the internal transcribed spacer regions. Sequence analyses revealed that this novel species represents a member of the genus Metschnikowia. It differed from its closest known species Metschnikowia zobellii, Metschnikowiaaustralis and Metschnikowia bicuspidata, by 8.4-9.2 % sequence divergence (33-40 nt substitutions and 7-12 gaps over 509 bases) in the D1/D2 sequences. The formation of ascospores was not observed on various sporulation media. In contrast to M. zobellii, M. australis and M. bicuspidata, the novel yeast species was unable to assimilate succinate, ethanol, ethylamine, cadaverine and 10 % NaCl plus 5 % glucose, but was able to grow in vitamin-free medium. The name Metschnikowia baotianmanensis f.a., sp. nov. is proposed to accommodate these strains, with NYNU 15613 as the holotype.
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Affiliation(s)
- Chun-Yue Chai
- School of Life Science and Technology, Nanyang Normal University, Nanyang 473061, PR China
| | - Lin-Na Huang
- School of Life Science and Technology, Nanyang Normal University, Nanyang 473061, PR China
| | - Han Cheng
- School of Life Science and Technology, Nanyang Normal University, Nanyang 473061, PR China
| | - Wen-Jing Liu
- School of Life Science and Technology, Nanyang Normal University, Nanyang 473061, PR China
| | - Feng-Li Hui
- School of Life Science and Technology, Nanyang Normal University, Nanyang 473061, PR China
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15
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Madden AA, Epps MJ, Fukami T, Irwin RE, Sheppard J, Sorger DM, Dunn RR. The ecology of insect-yeast relationships and its relevance to human industry. Proc Biol Sci 2019; 285:rspb.2017.2733. [PMID: 29563264 DOI: 10.1098/rspb.2017.2733] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 02/28/2018] [Indexed: 01/03/2023] Open
Abstract
Many species of yeast are integral to human society. They produce many of our foods, beverages and industrial chemicals, challenge us as pathogens, and provide models for the study of our own biology. However, few species are regularly studied and much of their ecology remains unclear, hindering the development of knowledge that is needed to improve the relationships between humans and yeasts. There is increasing evidence that insects are an essential component of ascomycetous yeast ecology. We propose a 'dispersal-encounter hypothesis' whereby yeasts are dispersed by insects between ephemeral, spatially disparate sugar resources, and insects, in turn, obtain the benefits of an honest signal from yeasts for the sugar resources. We review the relationship between yeasts and insects through three main examples: social wasps, social bees and beetles, with some additional examples from fruit flies. Ultimately, we suggest that over the next decades, consideration of these ecological and evolutionary relationships between insects and yeasts will allow prediction of where new yeast diversity is most likely to be discovered, particularly yeasts with traits of interest to human industry.
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Affiliation(s)
- Anne A Madden
- Department of Applied Ecology, North Carolina State University, David Clark Labs, 100 Brooks Avenue, Raleigh, NC 27607, USA
| | - Mary Jane Epps
- Department of Biology, Mary Baldwin University, 101 East Frederick Street, Staunton, VA 24401, USA
| | - Tadashi Fukami
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305, USA
| | - Rebecca E Irwin
- Department of Applied Ecology, North Carolina State University, David Clark Labs, 100 Brooks Avenue, Raleigh, NC 27607, USA
| | - John Sheppard
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, 400 Dan Allen Drive, Raleigh, NC 27606, USA
| | - D Magdalena Sorger
- Department of Applied Ecology, North Carolina State University, David Clark Labs, 100 Brooks Avenue, Raleigh, NC 27607, USA.,Research & Collections, North Carolina Museum of Natural Sciences, 11 West Jones Street, Raleigh, NC 27601, USA
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, David Clark Labs, 100 Brooks Avenue, Raleigh, NC 27607, USA.,Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, 2100 Copenhagen Ø, Denmark.,German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
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16
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Development of a Transformation Method for Metschnikowia borealis and other CUG-Serine Yeasts. Genes (Basel) 2019; 10:genes10020078. [PMID: 30678093 PMCID: PMC6409616 DOI: 10.3390/genes10020078] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 01/09/2019] [Accepted: 01/18/2019] [Indexed: 11/16/2022] Open
Abstract
Yeasts belonging to the Metschnikowia genus are particularly interesting for the unusual formation of only two needle-shaped ascospores during their mating cycle. Presently, the meiotic process that can lead to only two spores from a diploid zygote is poorly understood. The expression of fluorescent nuclear proteins should allow the meiotic process to be visualized in vivo; however, no large-spored species of Metschnikowia has ever been transformed. Accordingly, we aimed to develop a transformation method for Metschnikowia borealis, a particularly large-spored species of Metschnikowia, with the goal of enabling the genetic manipulations required to study biological processes in detail. Genetic analyses confirmed that M. borealis, and many other Metschnikowia species, are CUG-Ser yeasts. Codon-optimized selectable markers lacking CUG codons were used to successfully transform M. borealis by electroporation and lithium acetate, and transformants appeared to be the result of random integration. Mating experiments confirmed that transformed-strains were capable of generating large asci and undergoing recombination. Finally, random integration was used to transform an additional 21 yeast strains, and all attempts successfully generated transformants. The results provide a simple method to transform many yeasts from an array of different clades and can be used to study or develop many species for various applications.
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17
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Kijpornyongpan T, Urbina H, Suh SO, Luangsa-ard J, Aime MC, Blackwell M. TheSuhomycesclade: from single isolate to multiple species to disintegrating sex loci. FEMS Yeast Res 2018; 19:5212297. [DOI: 10.1093/femsyr/foy125] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 11/27/2018] [Indexed: 12/25/2022] Open
Affiliation(s)
- Teeratas Kijpornyongpan
- Department of Botany and Plant Pathology, Purdue University, 915 W State St, West Lafayette IN 47907-2054, USA
| | - Hector Urbina
- Department of Botany and Plant Pathology, Purdue University, 915 W State St, West Lafayette IN 47907-2054; Florida Department of Agriculture & Consumer Services, Division of Plant Industry, Gainesville, Florida 32608-7100, USA
| | - Sung-Oui Suh
- Manufacturing Science and Technology Program, ATCC, 10801 University Boulevard, Manassas, VA 20110-2209, USA
| | - Jennifer Luangsa-ard
- Microbe Interaction and Ecology Laboratory, BIOTEC, 113 Thailand Science Park, Phahonyothin Rd., Klong Nueng, Klong Luang, Pathum Thani 12120, Thailand
| | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, 915 W State St, West Lafayette IN 47907-2054, USA
| | - Meredith Blackwell
- Department of Biological Sciences, Louisiana State University; Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
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18
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Pizarro D, Divakar PK, Grewe F, Leavitt SD, Huang JP, Dal Grande F, Schmitt I, Wedin M, Crespo A, Lumbsch HT. Phylogenomic analysis of 2556 single-copy protein-coding genes resolves most evolutionary relationships for the major clades in the most diverse group of lichen-forming fungi. FUNGAL DIVERS 2018. [DOI: 10.1007/s13225-018-0407-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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19
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O’Brien CE, McCarthy CGP, Walshe AE, Shaw DR, Sumski DA, Krassowski T, Fitzpatrick DA, Butler G. Genome analysis of the yeast Diutina catenulata, a member of the Debaryomycetaceae/Metschnikowiaceae (CTG-Ser) clade. PLoS One 2018; 13:e0198957. [PMID: 29944657 PMCID: PMC6019693 DOI: 10.1371/journal.pone.0198957] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 05/28/2018] [Indexed: 11/18/2022] Open
Abstract
Diutina catenulata (Candida catenulata) is an ascomycetous yeast that has been isolated from humans, animals and environmental sources. The species is a contaminant of dairy products, and has been linked to superficial and invasive infections in both humans and animals. Previous phylogenetic analyses have assigned the species to the Saccharomycetales, but failed to identify its specific clade. Here, we report the genome sequence of an environmental isolate of D. catenulata. Examination of the tRNA repertoire and coding potential of this species shows that it translates the CUG codon as serine and not leucine. In addition, two phylogenetic analyses using 204 ubiquitous gene family alignments and 3,826 single-copy genes both confirm the placement of the species in the Debaryomycetaceae/Metschnikowiaceae, or CTG-Ser clade. The sequenced isolate contains an MTLα idiomorph. However, unlike most MTL loci in related species, poly (A) polymerase (PAP) is not adjacent to MTLα1.
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Affiliation(s)
- Caoimhe E. O’Brien
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Charley G. P. McCarthy
- Department of Biology, Genome Evolution Laboratory, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Annie E. Walshe
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Dennis R. Shaw
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Deirdre A. Sumski
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Tadeusz Krassowski
- School of Medicine, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - David A. Fitzpatrick
- Department of Biology, Genome Evolution Laboratory, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Geraldine Butler
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
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20
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Haase MAB, Kominek J, Langdon QK, Kurtzman CP, Hittinger CT. Genome sequence and physiological analysis of Yamadazyma laniorum f.a. sp. nov. and a reevaluation of the apocryphal xylose fermentation of its sister species, Candida tenuis. FEMS Yeast Res 2018; 17:3737663. [PMID: 28419220 DOI: 10.1093/femsyr/fox019] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Accepted: 04/11/2017] [Indexed: 11/12/2022] Open
Abstract
Xylose fermentation is a rare trait that is immensely important to the cellulosic biofuel industry, and Candida tenuis is one of the few yeasts that has been reported with this trait. Here we report the isolation of two strains representing a candidate sister species to C. tenuis. Integrated analysis of genome sequence and physiology suggested the genetic basis of a number of traits, including variation between the novel species and C. tenuis in lactose metabolism due to the loss of genes encoding lactose permease and β-galactosidase in the former. Surprisingly, physiological characterization revealed that neither the type strain of C. tenuis nor this novel species fermented xylose in traditional assays. We reexamined three xylose-fermenting strains previously identified as C. tenuis and found that these strains belong to the genus Scheffersomyces and are not C. tenuis. We propose Yamadazyma laniorum f.a. sp. nov. to accommodate our new strains and designate its type strain as yHMH7 (=CBS 14780 = NRRL Y-63967T). Furthermore, we propose the transfer of Candida tenuis to the genus Yamadazyma as Yamadazyma tenuis comb. nov. This approach provides a roadmap for how integrated genome sequence and physiological analysis can yield insight into the mechanisms that generate yeast biodiversity.
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Affiliation(s)
- Max A B Haase
- Laboratory of Genetics, Genome Center of Wisconsin, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53706, USA.,DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jacek Kominek
- Laboratory of Genetics, Genome Center of Wisconsin, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53706, USA.,DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Quinn K Langdon
- Laboratory of Genetics, Genome Center of Wisconsin, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Cletus P Kurtzman
- National Center for Agricultural Utilization Research, ARS-USDA, 1815 North University St., Peoria, IL 61604, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, Genome Center of Wisconsin, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53706, USA.,DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
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21
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de Vega C, Albaladejo RG, Lachance MA. Metschnikowia maroccana f.a., sp. nov., a new yeast species associated with floral nectar from Morocco. Int J Syst Evol Microbiol 2018; 68:2028-2035. [PMID: 29688165 DOI: 10.1099/ijsem.0.002784] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Wild flowers, and in particular, nectar of flowers, have been shown to be a rich reservoir of yeast biodiversity. In a taxonomic study of yeasts recovered from floral nectar in Morocco, nine strains were found to represent a novel species. Morphological and physiological characteristics and sequence analyses of the D1/D2 region of the large subunit rRNA gene as well as the internal transcribed spacer region showed that the novel species belonged to the genus Metschnikowia. The name Metschnikowia maroccana f.a., sp. nov. (EBDCdVMor24-1T=CBS 15053T=NRRL Y-63972T) is proposed to accommodate this new species. Metschnikowia maroccana was isolated from floral nectar of Teucrium pseudochamaepitys, Teucrium polium and Gladiolus italicus. The ascosporic state of the novel species was not found. Metschnikowia maroccana was phylogenetically distinct from any currently recognized species and forms a well-supported subclade (bootstrap value 81 %) containing species associated with flowers and flower-visiting insects, including Metschnikowia gruessii, Metschnikowia lachancei and Metschnikowia vanudenii. The close genealogical relationship of M. maroccana with the M. gruessii clade is also consistent with the striking similarity of their 'aeroplane' cells morphologies and the lack of utilization of the α-glucoside trehalose. The ecology of these novel species and its probable endemicity are discussed.
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Affiliation(s)
- Clara de Vega
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avenida de Américo Vespucio s/n, 41092 Sevilla, Spain
| | - Rafael G Albaladejo
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, C/ Profesor García González 2, 41012 Sevilla, Spain
| | - Marc-André Lachance
- Department of Biology, University of Western Ontario, London, ON N6A 5B7, Canada
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22
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Metschnikowia mating genomics. Antonie van Leeuwenhoek 2018; 111:1935-1953. [DOI: 10.1007/s10482-018-1084-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 04/05/2018] [Indexed: 01/29/2023]
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23
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Piombo E, Sela N, Wisniewski M, Hoffmann M, Gullino ML, Allard MW, Levin E, Spadaro D, Droby S. Genome Sequence, Assembly and Characterization of Two Metschnikowia fructicola Strains Used as Biocontrol Agents of Postharvest Diseases. Front Microbiol 2018; 9:593. [PMID: 29666611 PMCID: PMC5891927 DOI: 10.3389/fmicb.2018.00593] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 03/15/2018] [Indexed: 01/08/2023] Open
Abstract
The yeast Metschnikowia fructicola was reported as an efficient biological control agent of postharvest diseases of fruits and vegetables, and it is the bases of the commercial formulated product "Shemer." Several mechanisms of action by which M. fructicola inhibits postharvest pathogens were suggested including iron-binding compounds, induction of defense signaling genes, production of fungal cell wall degrading enzymes and relatively high amounts of superoxide anions. We assembled the whole genome sequence of two strains of M. fructicola using PacBio and Illumina shotgun sequencing technologies. Using the PacBio, a high-quality draft genome consisting of 93 contigs, with an estimated genome size of approximately 26 Mb, was obtained. Comparative analysis of M. fructicola proteins with the other three available closely related genomes revealed a shared core of homologous proteins coded by 5,776 genes. Comparing the genomes of the two M. fructicola strains using a SNP calling approach resulted in the identification of 564,302 homologous SNPs with 2,004 predicted high impact mutations. The size of the genome is exceptionally high when compared with those of available closely related organisms, and the high rate of homology among M. fructicola genes points toward a recent whole-genome duplication event as the cause of this large genome. Based on the assembled genome, sequences were annotated with a gene description and gene ontology (GO term) and clustered in functional groups. Analysis of CAZymes family genes revealed 1,145 putative genes, and transcriptomic analysis of CAZyme expression levels in M. fructicola during its interaction with either grapefruit peel tissue or Penicillium digitatum revealed a high level of CAZyme gene expression when the yeast was placed in wounded fruit tissue.
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Affiliation(s)
- Edoardo Piombo
- Department of Agricultural, Forestry and Food Sciences, University of Torino, Turin, Italy
- Centre of Competence for the Innovation in the Agro-environmental Sector, University of Torino, Turin, Italy
| | - Noa Sela
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Michael Wisniewski
- United States Department of Agriculture – Agricultural Research Service, Kernersville, WV, United States
| | - Maria Hoffmann
- Division of Microbiology, United States Food and Drug Administration, College Park, MD, United States
| | - Maria L. Gullino
- Department of Agricultural, Forestry and Food Sciences, University of Torino, Turin, Italy
- Centre of Competence for the Innovation in the Agro-environmental Sector, University of Torino, Turin, Italy
| | - Marc W. Allard
- Division of Microbiology, United States Food and Drug Administration, College Park, MD, United States
| | - Elena Levin
- Department of Postharvest Science, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Davide Spadaro
- Department of Agricultural, Forestry and Food Sciences, University of Torino, Turin, Italy
- Centre of Competence for the Innovation in the Agro-environmental Sector, University of Torino, Turin, Italy
| | - Samir Droby
- Department of Postharvest Science, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
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Affiliation(s)
- Kenneth H. Wolfe
- School of Medicine, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Geraldine Butler
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
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Canto A, Herrera CM, Rodriguez R. Nectar-living yeasts of a tropical host plant community: diversity and effects on community-wide floral nectar traits. PeerJ 2017; 5:e3517. [PMID: 28717591 PMCID: PMC5511698 DOI: 10.7717/peerj.3517] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 06/07/2017] [Indexed: 11/24/2022] Open
Abstract
We characterize the diversity of nectar-living yeasts of a tropical host plant community at different hierarchical sampling levels, measure the associations between yeasts and nectariferous plants, and measure the effect of yeasts on nectar traits. Using a series of hierarchically nested sampling units, we extracted nectar from an assemblage of host plants that were representative of the diversity of life forms, flower shapes, and pollinator types in the tropical area of Yucatan, Mexico. Yeasts were isolated from single nectar samples; their DNA was identified, the yeast cell density was estimated, and the sugar composition and concentration of nectar were quantified using HPLC. In contrast to previous studies from temperate regions, the diversity of nectar-living yeasts in the plant community was characterized by a relatively high number of equally common species with low dominance. Analyses predict highly diverse nectar yeast communities in a relatively narrow range of tropical vegetation, suggesting that the diversity of yeasts will increase as the number of sampling units increases at the level of the species, genera, and botanical families of the hosts. Significant associations between specific yeast species and host plants were also detected; the interaction between yeasts and host plants impacted the effect of yeast cell density on nectar sugars. This study provides an overall picture of the diversity of nectar-living yeasts in tropical host plants and suggests that the key factor that affects the community-wide patterns of nectar traits is not nectar chemistry, but rather the type of yeasts interacting with host plants.
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Affiliation(s)
- Azucena Canto
- Centro de Investigacion Cientifica de Yucatan, A.C., Merida, Yucatan, Mexico
| | | | - Rosalina Rodriguez
- Centro de Investigacion Cientifica de Yucatan, A.C., Merida, Yucatan, Mexico
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Draft Genome Sequence of
Metschnikowia australis
Strain UFMG-CM-Y6158, an Extremophile Marine Yeast Endemic to Antarctica. GENOME ANNOUNCEMENTS 2017; 5:5/20/e00328-17. [PMID: 28522704 PMCID: PMC5477319 DOI: 10.1128/genomea.00328-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here we report the draft genome sequence of Metschnikowia australis strain UFMG-CM-Y6158, a yeast endemic to Antarctica. We isolated the strain from the marine seaweed Acrosiphonia arcta (Chlorophyta). The genome is 14.3 Mb long and contains 4,442 predicted protein-coding genes.
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27
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Lachance MA. Metschnikowia: half tetrads, a regicide and the fountain of youth. Yeast 2016; 33:563-574. [DOI: 10.1002/yea.3208] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 07/27/2016] [Accepted: 08/25/2016] [Indexed: 11/07/2022] Open
Affiliation(s)
- Marc-André Lachance
- Department of Biology; University of Western Ontario; London Ontario Canada N6A 5B7
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28
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Abstract
Yeast systematics has wholeheartedly embraced the phylogenetic approach. Central to this has been the unspoken convention that taxa at all ranks be strictly monophyletic. This can result in a proliferation of small genera and instances of nomenclatural instability, counter to the expected benefit of phylogenetic systematics. But the literature abounds with examples, at all taxonomic levels, where paraphyly is a reality that can no longer be ignored. The very concepts of Bacteria or Archaea, under the constraint of monophyly, are in peril. It is therefore desirable to effect a shift in practices that will recognize the existence of paraphyletic taxa.
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Affiliation(s)
- Marc-André Lachance
- Department of Biology, University of Western Ontario, London, Ontario N6A5B7, Canada
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