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Liu F, Hu ZD, Yurkov A, Chen XH, Bao WJ, Ma Q, Zhao WN, Pan S, Zhao XM, Liu JH, Wang QM, Boekhout T. Saccharomycetaceae: delineation of fungal genera based on phylogenomic analyses, genomic relatedness indices and genomics-based synapomorphies. PERSOONIA 2024; 52:1-21. [PMID: 39161631 PMCID: PMC11319838 DOI: 10.3767/persoonia.2024.52.01] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/08/2024] [Indexed: 08/21/2024]
Abstract
A correct classification of fungi, including yeasts, is of prime importance to understand fungal biodiversity and to communicate about this diversity. Fungal genera are mainly defined based on phenotypic characteristics and the results of single or multigene-based phylogenetic analyses. However, because yeasts often have less phenotypic characters, their classification experienced a strong move towards DNA-based data, from short ribosomal sequences to multigene phylogenies and more recently to phylogenomics. Here, we explore the usefulness of various genomics-based parameters to circumscribe fungal genera more correctly taking the yeast domain as an example. Therefore, we compared the results of a phylogenomic analysis, average amino acid identity (AAI) values, the presence of conserved signature indels (CSIs), the percentage of conserved proteins (POCP) and the presence-absence patterns of orthologs (PAPO). These genome-based metrics were used to investigate their usefulness in demarcating 13 hitherto relatively well accepted genera in Saccharomycetaceae, namely Eremothecium, Grigorovia, Kazachstania, Kluyveromyces, Lachancea, Nakaseomyces, Naumovozyma, Saccharomyces, Tetrapisispora, Torulaspora, Vanderwaltozyma, Zygosaccharomyces and Zygotorulaspora. As a result, most of these genera are supported by the genomics-based metrics, but the genera Kazachstania, Nakaseomyces and Tetrapisispora were shown to be genetically highly diverse based on the above listed analyses. Considering the results obtained for the presently recognized genera, a range of 80-92 % POCP values and a range of 60-70 % AAI values might be valuable thresholds to discriminate genera in Saccharomycetaceae. Furthermore, the genus-specific genes identified in the PAPO analysis and the CSIs were found to be useful as synapomorphies to characterize and define genera in Saccharomycetaceae. Our results indicate that the combined monophyly-based phylogenomic analysis together with genomic relatedness indices and synapomorphies provide promising approaches to delineating yeast genera and likely those of filamentous fungi as well. The genera Kazachstania, Nakaseomyces and Tetrapisispora are revised and we propose eight new genera and 41 new combinations. Citation: Liu F, Hu Z-D, Yurkov A, et al. 2024. Saccharomycetaceae: delinaeation of fungal genera based on phylogenomic analyses, genomic relatedness indices and genomics-based synapomorphies. Persoonia 52: 1-21. https://doi.org/10.3767/persoonia.2024.52.01.
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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
| | - A. Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - X.-H. Chen
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, Hebei, China
| | - W.-J. Bao
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, Hebei, China
| | - Q. Ma
- 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
| | - S. Pan
- 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
| | - J.-H. Liu
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, Hebei, China
| | - Q.-M. Wang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, Hebei, China
- Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Hebei University, Baoding 071002, Hebei, China
- Hebei Basic Science Center for Biotic Interaction, Hebei University, Baoding 071002, Hebei, China
| | - T. Boekhout
- College of Sciences, King Saud University, Riyadh 11451, Saudi Arabia
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Tang J, Zhang L, Su J, Ye Q, Li Y, Liu D, Cui H, Zhang Y, Ye Z. Insights into Fungal Mitochondrial Genomes and Inheritance Based on Current Findings from Yeast-like Fungi. J Fungi (Basel) 2024; 10:441. [PMID: 39057326 PMCID: PMC11277600 DOI: 10.3390/jof10070441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/19/2024] [Accepted: 06/20/2024] [Indexed: 07/28/2024] Open
Abstract
The primary functions of mitochondria are to produce energy and participate in the apoptosis of cells, with them being highly conserved among eukaryotes. However, the composition of mitochondrial genomes, mitochondrial DNA (mtDNA) replication, and mitochondrial inheritance varies significantly among animals, plants, and fungi. Especially in fungi, there exists a rich diversity of mitochondrial genomes, as well as various replication and inheritance mechanisms. Therefore, a comprehensive understanding of fungal mitochondria is crucial for unraveling the evolutionary history of mitochondria in eukaryotes. In this review, we have organized existing reports to systematically describe and summarize the composition of yeast-like fungal mitochondrial genomes from three perspectives: mitochondrial genome structure, encoded genes, and mobile elements. We have also provided a systematic overview of the mechanisms in mtDNA replication and mitochondrial inheritance during bisexual mating. Additionally, we have discussed and proposed open questions that require further investigation for clarification.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Zihong Ye
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, China; (J.T.)
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Guo QC, Liu S, Hui FL. Spencermartinsiella henanensis fa., sp. nov., a novel yeast species isolated from rotting wood. Int J Syst Evol Microbiol 2024; 74. [PMID: 38190334 DOI: 10.1099/ijsem.0.006226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024] Open
Abstract
Two yeast strains (NYNU 211162 and NYNU 211275) were isolated from rotting wood collected in the Baotianman Nature Reserve, Henan Province, central China. Phylogenetic analysis of the D1/D2 domain of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region revealed that the strains represent a phylogenetically distinct species within the genus Spencermartinsiella. The name Spencermartinsiella henanensis fa., sp. nov. is proposed for this species with holotype CICC 33543T (Mycobank MB 851142). S. henanensis sp. nov. differed by only 3 nt (~0.5 %) substitutions from the closest known species S. europaea NCAIM Y.01817T in the D1/D2 domain, but by 33 nt (~6 %) substitutions, 34 nt (~3.8 %) substitutions, 30 nt (~5.6 %) substitutions and 75 nt (~9.9 %) substitutions in the ITS region and the partial TEF1, COXII and RPB2 genes. Additionally, S. henanensis sp. nov. can be physiologically distinguished from S. europaea by its ability to assimilate inulin, inability to assimilate ethylamine and cadaverine, and incapability of growth at 30 °C.
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Affiliation(s)
- Qi-Chao Guo
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, PR China
| | - Shan Liu
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, PR China
| | - Feng-Li Hui
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, PR China
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Liu S, Guo QC, An ZR, Hui FL. Danielozyma pruni sp. nov., an asexual yeast species isolated from insect frass. Int J Syst Evol Microbiol 2023; 73. [PMID: 37991229 DOI: 10.1099/ijsem.0.006124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023] Open
Abstract
Two strains (NYNU 218101 and NYNU 218104) of an asexual yeast species were isolated from insect frass collected in insect tunnels of red leaf plum trees in the Henan Province, central China. Molecular phylogenetic analysis of the D1/D2 domain of the large subunit rRNA gene and the internal transcribed spacer (ITS) region showed that these two strains belonged to the genus Danielozyma, with Danielozyma litseae as the closest known species. They differed from the type strain of D. litseae by 0.6 % substitutions (three substitutions and one gap) in the D1/D2 domain and by 5.1 % substitutions (19 substitutions and six gaps) in the ITS region, respectively. When compared with the partial ACT1, TEF1 and RPB1 gene sequences, they differed by 3 % (26 substitutions), 2.7 % (25 substitutions) and 9 %(54 substitutions) from D. litseae NRRL YB-3246T in these regions. Physiologically, they also differed from its closest known species D. litseae based on the ability to assimilate inulin and galactitol, as well as to grow in 0.1 % cycloheximide and its inability to ferment maltose and raffinose. In order to classify the two new isolates based on morphological and molecular evidence, we proposed the description of a novel species Danielozyma pruni sp. nov. with strain JCM 35735T as holotype (Mycobank MB 849101).
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Affiliation(s)
- Shan Liu
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, PR China
| | - Qi-Chao Guo
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, PR China
| | - Ze-Ren An
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, PR China
| | - Feng-Li Hui
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, PR China
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Csoma H, Kállai Z, Czentye K, Sipiczki M. Starmerella lactis-condensi, a yeast that has adapted to the conditions in the oenological environment. Int J Food Microbiol 2023; 401:110282. [PMID: 37329632 DOI: 10.1016/j.ijfoodmicro.2023.110282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 06/01/2023] [Accepted: 06/04/2023] [Indexed: 06/19/2023]
Abstract
The yeast Starmerella (Candida) lactis-condensi is considered a food contaminant microorganism. The aim of our research was to determine why St. lactis-condensi could become the dominant species of Essences, the top sweet wine speciality of Tokaj wine region in Hungary. We investigated the physiological properties of these yeasts based on parameters that may influence their ability to selectively proliferate and persist during maturation in wines with very high sugar content. These include glucose and fructose, alcohol, and sulphur tolerance. Our studies have shown that St. lactis-condensi is a fructophilic yeast that is able to adapt quickly to very high sugar concentrations (up to 500 g/L) in the Essences. The high glucose concentration inhibits its growth, as well as that of the St. bacillaris (Candida zemplinina) strains tested. The type and amount of sugars in the Essences, together with the sulphur and alcohol content, influence the composition of the dominant yeast biota. Analysis of (GTG)5 microsatellite in the nuclear genome and mtDNA-RFLP studies demonstrate that a diverse population of St. lactis-condensi occurs in the Tokaj wine region, in the Essences. This yeast species is characterised by both physiological and genetic biodiversity. GC-MS analysis of Essences colonised exclusively with these yeasts showed no deterioration in quality.
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Affiliation(s)
- Hajnalka Csoma
- Department of Genetics and Applied Microbiology, University of Debrecen, 4032 Debrecen, Hungary.
| | - Zoltán Kállai
- Research Institute for Viticulture and Oenology, Tarcal; Department of Oenological Microbiology, University of Debrecen, 4032 Debrecen, Hungary
| | - Kinga Czentye
- Department of Genetics and Applied Microbiology, University of Debrecen, 4032 Debrecen, Hungary
| | - Matthias Sipiczki
- Department of Genetics and Applied Microbiology, University of Debrecen, 4032 Debrecen, Hungary
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6
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Groenewald M, Hittinger C, Bensch K, Opulente D, Shen XX, Li Y, Liu C, LaBella A, Zhou X, Limtong S, Jindamorakot S, Gonçalves P, Robert V, Wolfe K, Rosa C, Boekhout T, Čadež N, éter G, Sampaio J, Lachance MA, Yurkov A, Daniel HM, Takashima M, Boundy-Mills K, Libkind D, Aoki K, Sugita T, Rokas A. A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina. Stud Mycol 2023; 105:1-22. [PMID: 38895705 PMCID: PMC11182611 DOI: 10.3114/sim.2023.105.01] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/12/2023] [Indexed: 06/21/2024] Open
Abstract
The subphylum Saccharomycotina is a lineage in the fungal phylum Ascomycota that exhibits levels of genomic diversity similar to those of plants and animals. The Saccharomycotina consist of more than 1 200 known species currently divided into 16 families, one order, and one class. Species in this subphylum are ecologically and metabolically diverse and include important opportunistic human pathogens, as well as species important in biotechnological applications. Many traits of biotechnological interest are found in closely related species and often restricted to single phylogenetic clades. However, the biotechnological potential of most yeast species remains unexplored. Although the subphylum Saccharomycotina has much higher rates of genome sequence evolution than its sister subphylum, Pezizomycotina, it contains only one class compared to the 16 classes in Pezizomycotina. The third subphylum of Ascomycota, the Taphrinomycotina, consists of six classes and has approximately 10 times fewer species than the Saccharomycotina. These data indicate that the current classification of all these yeasts into a single class and a single order is an underappreciation of their diversity. Our previous genome-scale phylogenetic analyses showed that the Saccharomycotina contains 12 major and robustly supported phylogenetic clades; seven of these are current families (Lipomycetaceae, Trigonopsidaceae, Alloascoideaceae, Pichiaceae, Phaffomycetaceae, Saccharomycodaceae, and Saccharomycetaceae), one comprises two current families (Dipodascaceae and Trichomonascaceae), one represents the genus Sporopachydermia, and three represent lineages that differ in their translation of the CUG codon (CUG-Ala, CUG-Ser1, and CUG-Ser2). Using these analyses in combination with relative evolutionary divergence and genome content analyses, we propose an updated classification for the Saccharomycotina, including seven classes and 12 orders that can be diagnosed by genome content. This updated classification is consistent with the high levels of genomic diversity within this subphylum and is necessary to make the higher rank classification of the Saccharomycotina more comparable to that of other fungi, as well as to communicate efficiently on lineages that are not yet formally named. Taxonomic novelties: New classes: Alloascoideomycetes M. Groenew., Hittinger, Opulente & A. Rokas, Dipodascomycetes M. Groenew., Hittinger, Opulente & A. Rokas, Lipomycetes M. Groenew., Hittinger, Opulente, A. Rokas, Pichiomycetes M. Groenew., Hittinger, Opulente & A. Rokas, Sporopachydermiomycetes M. Groenew., Hittinger, Opulente & A. Rokas, Trigonopsidomycetes M. Groenew., Hittinger, Opulente & A. Rokas. New orders: Alloascoideomycetes: Alloascoideales M. Groenew., Hittinger, Opulente & A. Rokas; Dipodascomycetes: Dipodascales M. Groenew., Hittinger, Opulente & A. Rokas; Lipomycetes: Lipomycetales M. Groenew., Hittinger, Opulente & A. Rokas; Pichiomycetes: Alaninales M. Groenew., Hittinger, Opulente & A. Rokas, Pichiales M. Groenew., Hittinger, Opulente & A. Rokas, Serinales M. Groenew., Hittinger, Opulente & A. Rokas; Saccharomycetes: Phaffomycetales M. Groenew., Hittinger, Opulente & A. Rokas, Saccharomycodales M. Groenew., Hittinger, Opulente & A. Rokas; Sporopachydermiomycetes: Sporopachydermiales M. Groenew., Hittinger, Opulente & A. Rokas; Trigonopsidomycetes: Trigonopsidales M. Groenew., Hittinger, Opulente & A. Rokas. New families: Alaninales: Pachysolenaceae M. Groenew., Hittinger, Opulente & A. Rokas; Pichiales: Pichiaceae M. Groenew., Hittinger, Opulente & A. Rokas; Sporopachydermiales: Sporopachydermiaceae M. Groenew., Hittinger, Opulente & A. Rokas. Citation: Groenewald M, Hittinger CT, Bensch K, Opulente DA, Shen X-X, Li Y, Liu C, LaBella AL, Zhou X, Limtong S, Jindamorakot S, Gonçalves P, Robert V, Wolfe KH, Rosa CA, Boekhout T, Čadež N, Péter G, Sampaio JP, Lachance M-A, Yurkov AM, Daniel H-M, Takashima M, Boundy-Mills K, Libkind D, Aoki K, Sugita T, Rokas A (2023). A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina. Studies in Mycology 105: 1-22. doi: 10.3114/sim.2023.105.01 This study is dedicated to the memory of Cletus P. Kurtzman (1938-2017), a pioneer of yeast taxonomy.
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Affiliation(s)
- M. Groenewald
- Westerdijk Fungal Biodiversity Institute, 3584 Utrecht, The
Netherlands;
| | - C.T. Hittinger
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic
Science Innovation, DOE Great Lakes Bioenergy Research Center, J. F. Crow
Institute for the Study of Evolution, University of Wisconsin-Madison,
Madison, WI 53726, USA;
| | - K. Bensch
- Westerdijk Fungal Biodiversity Institute, 3584 Utrecht, The
Netherlands;
| | - D.A. Opulente
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic
Science Innovation, DOE Great Lakes Bioenergy Research Center, J. F. Crow
Institute for the Study of Evolution, University of Wisconsin-Madison,
Madison, WI 53726, USA;
- Department of Biology, Villanova University, Villanova, PA
19085;
| | - X.-X. Shen
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou
310058, China;
| | - Y. Li
- Institute of Marine Science and Technology, Shandong University, Qingdao
266237, China;
| | - C. Liu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou
310058, China;
| | - A.L. LaBella
- Department of Bioinformatics and Genomics, The University of North
Carolina at Charlotte, Charlotte NC 28223, USA;
| | - X. Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease
Control, Integrative Microbiology Research Center, South China Agricultural
University, Guangzhou 510642, China;
| | - S. Limtong
- Department of Microbiology, Faculty of Science, Kasetsart University,
Bangkok 10900, Thailand;
| | - S. Jindamorakot
- Microbial Diversity and Utilization Research Team, National Center for
Genetic Engineering and Biotechnology, National Science and Technology
Development Agency, 113 Thailand Science Park, Khlong Nueng, Khlong Luang,
Pathum Thani 12120, Thailand;
| | - P. Gonçalves
- Associate Laboratory i4HB–Institute for Health and Bioeconomy,
NOVA School of Science and Technology, Universidade NOVA de Lisboa,
Caparica, Portugal;
- UCIBIO—Applied Molecular Biosciences Unit, Department of Life
Sciences, NOVA School of Science and Technology, Universidade NOVA de
Lisboa, Caparica, Portugal;
| | - V. Robert
- Westerdijk Fungal Biodiversity Institute, 3584 Utrecht, The
Netherlands;
| | - K.H. Wolfe
- Conway Institute and School of Medicine, University College Dublin,
Dublin 4, Ireland;
| | - C.A. Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de
Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil;
| | - T. Boekhout
- College of Sciences, King Saud University, Riyadh, Saudi
Arabia;
| | - N. Čadež
- Food Science and Technology Department, Biotechnical Faculty, University
of Ljubljana, Ljubljana, Slovenia;
| | - G. éter
- National Collection of Agricultural and Industrial Microorganisms,
Institute of Food Science and Technology, Hungarian University of
Agriculture and Life Sciences, H-1118, Budapest, Somlói út
14-16., Hungary;
| | - J.P. Sampaio
- UCIBIO, Departamento de Ciências da Vida, Faculdade de
Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516
Caparica, Portugal;
| | - M.-A. Lachance
- Department of Biology, University of Western Ontario, London, ON N6A
5B7, Canada;
| | - A.M. Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell
Cultures, 38124 Braunschweig, Germany;
| | - H.-M. Daniel
- BCCM/MUCL, Earth and Life Institute, Mycology Laboratory,
Université catholique de Louvain, 1348 Louvain-la-Neuve,
Belgium;
| | - M. Takashima
- Laboratory of Yeast Systematics, Tokyo NODAI Research Institute (TNRI),
Tokyo University of Agriculture, Sakuragaoka, Setagaya, Tokyo 156-8502,
Japan;
| | - K. Boundy-Mills
- Food Science and Technology, University of California Davis, Davis, CA,
95616, USA;
| | - D. Libkind
- Centro de Referencia en Levaduras y Tecnología Cervecera,
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;
| | - K. Aoki
- Laboratory of Yeast Systematics, Tokyo NODAI Research Institute (TNRI),
Tokyo University of Agriculture, Sakuragaoka, Setagaya, Tokyo 156-8502,
Japan;
| | - T. Sugita
- Laboratory of Microbiology, Meiji Pharmaceutical University, Noshio,
Kiyose, Tokyo 204-8588, Japan;
| | - A. Rokas
- Department of Biological Sciences and Evolutionary Studies Initiative,
Vanderbilt University, Nashville, TN 37235, USA
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Nualthaisong P, Sakolrak B, Panicharoen T, Limtong S, Khunnamwong P. Kodamaea samutsakhonensis f.a., sp. nov., a novel ascomycetous yeast species isolated from wild mushrooms in Thailand. Int J Syst Evol Microbiol 2023; 73. [PMID: 37167093 DOI: 10.1099/ijsem.0.005840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
Two strains of genus Kodamaea, representing a novel anamorphic yeast species, were isolated from two samples of Marasmiellus sp. collected in Thailand. Analysis of the sequences of the internal transcribed spacer (ITS) regions and the D1/D2 domains of the large subunit (LSU) rRNA gene showed that the two strains differed by 27-42 nucleotide substitutions in the D1/D2 domains of the LSU rRNA gene and 7-34 nucleotide substitutions in the ITS region of a group of related species, Kodamaea smagusa CBS 11430T, Kodamaea fungicola JCM 10142T, Kodamaea plutei ATCC MYA-4329T, Kodamaea lidongshanica SD5S01T and Kodamaea jinghongensis NYNU 167162T. Phylogenetic analysis based on the concatenated sequences of the ITS and the D1/D2 domains of the LSU rRNA gene showed that the two strains were placed in the Kodamaea clade and clearly separated from other recognized species of the genus. Therefore, the two strains were assigned as a novel species of the genus Kodamaea, for which we propose the name Kodamaea samutsakhonensis f.a., sp. nov. The holotype is TBRC 16043T (=DMKU-BP19T) and the isotype is PYCC 9354. The MycoBank number of the novel species is MB 846490.
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Affiliation(s)
- Panadda Nualthaisong
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Biodiversity Center Kasetsart University (BDCKU), Bangkok, 10900, Thailand
| | - Baramee Sakolrak
- Department of National Parks, Wildlife and Plant Conservation, Bangkok, 10900, Thailand
| | - Thitaya Panicharoen
- Division of Microbiology, Department of Science, Faculty of Science and Technology, Bansomdejchaopraya Rajabhat University, Bangkok, 10600, Thailand
| | - Savitree Limtong
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Biodiversity Center Kasetsart University (BDCKU), Bangkok, 10900, Thailand
- Academy of Science, Royal Society of Thailand, Bangkok, 10300, Thailand
| | - Pannida Khunnamwong
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Biodiversity Center Kasetsart University (BDCKU), Bangkok, 10900, Thailand
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8
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Kamilari E, Stanton C, Reen FJ, Ross RP. Uncovering the Biotechnological Importance of Geotrichum candidum. Foods 2023; 12:foods12061124. [PMID: 36981051 PMCID: PMC10048088 DOI: 10.3390/foods12061124] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/24/2023] [Accepted: 03/02/2023] [Indexed: 03/30/2023] Open
Abstract
Fungi make a fundamental contribution to several biotechnological processes, including brewing, winemaking, and the production of enzymes, organic acids, alcohols, antibiotics, and pharmaceuticals. The present review explores the biotechnological importance of the filamentous yeast-like fungus Geotrichum candidum, a ubiquitous species known for its use as a starter in the dairy industry. To uncover G. candidum's biotechnological role, we performed a search for related work through the scientific indexing internet services, Web of Science and Google Scholar. The following query was used: Geotrichum candidum, producing about 6500 scientific papers from 2017 to 2022. From these, approximately 150 that were associated with industrial applications of G. candidum were selected. Our analysis revealed that apart from its role as a starter in the dairy and brewing industries, this species has been administered as a probiotic nutritional supplement in fish, indicating improvements in developmental and immunological parameters. Strains of this species produce a plethora of biotechnologically important enzymes, including cellulases, β-glucanases, xylanases, lipases, proteases, and α-amylases. Moreover, strains that produce antimicrobial compounds and that are capable of bioremediation were identified. The findings of the present review demonstrate the importance of G. candidum for agrifood- and bio-industries and provide further insights into its potential future biotechnological roles.
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Affiliation(s)
- Eleni Kamilari
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland
- School of Microbiology, University College Cork, T12 YT20 Cork, Ireland
| | - Catherine Stanton
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland
- School of Microbiology, University College Cork, T12 YT20 Cork, Ireland
- Department of Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, P61 C996 Co. Cork, Ireland
| | - F Jerry Reen
- School of Microbiology, University College Cork, T12 YT20 Cork, Ireland
- Synthesis and Solid State Pharmaceutical Centre, University College Cork, T12 YT20 Cork, Ireland
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland
- School of Microbiology, University College Cork, T12 YT20 Cork, Ireland
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9
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Dlauchy D, Lee CF, Yurkov AM, Péter G. Diddensiella parasantjacobensis f.a., sp. nov., a yeast species from forest habitats. Int J Syst Evol Microbiol 2023; 73. [PMID: 36989131 DOI: 10.1099/ijsem.0.005763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023] Open
Abstract
Six conspecific yeast strains, representing an undescribed species, were isolated from rotten wood collected in different locations in Hungary and Germany and an additional one from fungal fruiting body in Taiwan. The seven strains share identical nucleotide sequences in the D1/D2 domain of the nuclear large subunit (LSU) rRNA gene. The Hungarian and Taiwanese isolates share identical internal transcribed spacer (ITS) sequences as well, while the two German isolates differ from them merely by three substitutions and four indels in this region. The investigated strains are very closely related to Diddensiella santjacobensis. Along their LSU D1/D2 domain they differ only by one substitution from the type strain of D. santjacobensis. However, in the ITS region of Hungarian and Taiwanese strains we detected 3.5 % divergence (nine substitutions and nine indels) between the undescribed species and D. santjacobensis, while the German strains differed by 13 substitutions and nine indels from D. santjacobensis. This ITS sequence divergence has raised the possibility that the strains investigated in this study may represent a different species from D. santjacobensis. This hypothesis was supported by comparisons of partial translation elongation factor 1-α (EF-1α) and cytochrome oxidase II (COX II) gene sequences. While no difference and 1-2 substitutions among the partial EF-1α and COX II gene sequences of the strains of the undescribed species, respectively, were detected; the undescribed species differ by about 4 % (36 substitutions) and 10 % (50-51 substitutions) from D. santjacobensis in these regions. Parsimony network analysis of the partial COX II gene sequences also separated the investigated strains from the type strain of D. santjacobensis. In this paper we propose Diddensiella parasantjacobensis f.a., sp. nov. (holotype: NCAIM Y.02121; isotypes: CBS 17819, DSM 114156) to accommodate the above-noted strains.
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Affiliation(s)
- Dénes Dlauchy
- National Collection of Agricultural and Industrial Microorganisms, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Somlói út 14-16., H-1118 Budapest, Hungary
| | - Ching-Fu Lee
- Institute of Analytical and Environmental Sciences, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 300044, Taiwan, ROC
| | - Andrey M Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Brunswick, Germany
| | - Gábor Péter
- National Collection of Agricultural and Industrial Microorganisms, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Somlói út 14-16., H-1118 Budapest, Hungary
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10
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Kidd SE, Abdolrasouli A, Hagen F. Fungal Nomenclature: Managing Change is the Name of the Game. Open Forum Infect Dis 2023; 10:ofac559. [PMID: 36632423 PMCID: PMC9825814 DOI: 10.1093/ofid/ofac559] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/18/2022] [Indexed: 01/09/2023] Open
Abstract
Fungal species have undergone and continue to undergo significant nomenclatural change, primarily due to the abandonment of dual species nomenclature in 2013 and the widespread application of molecular technologies in taxonomy allowing correction of past classification errors. These have effected numerous name changes concerning medically important species, but by far the group causing most concern are the Candida yeasts. Among common species, Candida krusei, Candida glabrata, Candida guilliermondii, Candida lusitaniae, and Candida rugosa have been changed to Pichia kudriavzevii, Nakaseomyces glabrata, Meyerozyma guilliermondii, Clavispora lusitaniae, and Diutina rugosa, respectively. There are currently no guidelines for microbiology laboratories on implementing changes, and there is ongoing concern that clinicians will dismiss or misinterpret laboratory reports using unfamiliar species names. Here, we have outlined the rationale for name changes across the major groups of clinically important fungi and have provided practical recommendations for managing change.
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Affiliation(s)
- Sarah E Kidd
- Correspondence: Sarah E. Kidd, BMedSc(Hons), PhD , National Mycology Reference Centre, SA Pathology, Frome Road, Adelaide, South Australia 5000, Australia ()
| | - Alireza Abdolrasouli
- Department of Medical Microbiology, King's College Hospital, London, United Kingdom,Department of Infectious Diseases, Imperial College London, London, United Kingdom
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands,Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands,Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
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11
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Ranade Y, Pathak P, Chandrashekar M, Saha S. Diversity Analysis of Culturable Epiphytic Microbial Consortia of Table Grape Berry Surface. FOOD BIOTECHNOL 2023. [DOI: 10.1080/08905436.2022.2163402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Yogita Ranade
- MIT School of Bioengineering Sciences & Research, MIT ADT University, Pune, India
| | - Pranav Pathak
- MIT School of Bioengineering Sciences & Research, MIT ADT University, Pune, India
| | | | - Sujoy Saha
- Plant Pathology, ICAR-National Research Centre for Grapes, Pune, India
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12
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Chai CY, Li Y, Yan ZL, Hui FL. Phylogenetic and genomic analyses of two new species of Clavispora (Metschnikowiaceae, Saccharomycetales) from Central China. Front Microbiol 2022; 13:1019599. [PMID: 36312955 PMCID: PMC9608443 DOI: 10.3389/fmicb.2022.1019599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 09/26/2022] [Indexed: 11/25/2022] Open
Abstract
Species in the genus Clavispora have previously been reported primarily in the northeast and northwest regions of China; the species diversity of Clavispora in central China is not currently clear. In this study, phylogenetic inferences of Clavispora based on sequences of a single-locus (LSU D1/D2) and a two-locus (LSU D1/D2 and ITS) were conducted. Two new species isolated from rotting wood in central China, namely Clavispora xylosa sp. nov. and Clavispora paralusitaniae sp. nov., were delimited and proposed based on morphological and molecular evidence. Cl. xylosa was closely related to C. thailandica CBS 10610T, but with 11.5% divergence in the LSU D1/D2 domains and 11.5% divergence in the ITS regions. Cl. paralusitaniae was a sister to Cl. lusitaniae CBS 6936T from which it differs with 4.7% divergence in the LSU D1/D2 domains and 5.4% divergence in the ITS regions. Description of Cl. xylosa sp. nov. and Cl. paralusitaniae sp. nov. was also supported by morphological comparisons and genomic analyses between the two new species and their closest relatives, C. thailandica CBS 10610T and Cl. lusitaniae CBS 6936T. These results indicate a potentially great diversity of Clavispora spp. inhabiting rotting wood in central China, ripe for future discovery.
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Affiliation(s)
- Chun-Yue Chai
- College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China
- Research Center of Henan Provincial Agricultural Biomass Resource Engineering and Technology, Nanyang Normal University, Nanyang, China
| | - Ying Li
- College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China
| | - Zhen-Li Yan
- State Key Laboratory of Motor Vehicle Biofuel Technology, Henan Tianguan Enterprise Group Co., Ltd, Nanyang, China
| | - Feng-Li Hui
- College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China
- Research Center of Henan Provincial Agricultural Biomass Resource Engineering and Technology, Nanyang Normal University, Nanyang, China
- *Correspondence: Feng-Li Hui,
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13
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Chai CY, Gao WL, Li Y, Yan ZL, Hui FL. Kodamaeahongheensis f.a., sp. nov., Kodamaeaovata f.a., sp. nov. and Kodamaeayamadae f.a., sp. nov., three new yeast species of Kodamaea (Saccharomycetales, Debaryomycetacae) from China. MycoKeys 2022; 89:121-137. [PMID: 36760829 PMCID: PMC9849074 DOI: 10.3897/mycokeys.89.81119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/15/2022] [Indexed: 11/12/2022] Open
Abstract
Kodamaea includes a growing number of interesting yeasts of the family Debaryomycetacae that are widely distributed in temperate, subtropical and tropical regions of different continents. During recent yeast collections in Henan and Yunnan Province in China, several isolates of Kodamaea were obtained from rotting wood, all of which represent undescribed taxa. Based on morphological and phylogenetic analyses (ITS and LSU rDNA), three new species are proposed: K.hongheensis f.a., sp. nov., K.ovata f.a., sp. nov. and K.yamadae f.a., sp. nov. In addition, sixteen Candida species, which are members of the Kodamaea clade based on phylogenetic analysis, are transferred to Kodamaea as new combinations. Our results indicate high species diversity of Kodamaea waiting to be discovered in rotting wood from tropical and subtropical China.
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Affiliation(s)
- Chun-Yue Chai
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, ChinaNanyang Normal UniversityNanyangChina,Research Center of Henan Provincial Agricultural Biomass Resource Engineering and Technology, Nanyang 473061, ChinaResearch Center of Henan Provincial Agricultural Biomass Resource Engineering and TechnologyNanyangChina
| | - Wan-Li Gao
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, ChinaNanyang Normal UniversityNanyangChina
| | - Ying Li
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, ChinaNanyang Normal UniversityNanyangChina
| | - Zhen-Li Yan
- State Key Laboratory of Motor Vehicle Biofuel Technology, Henan Tianguan Enterprise Group Co., Ltd., Nanyang 473000, ChinaState Key Laboratory of Motor Vehicle Biofuel TechnologyNanyangChina
| | - Feng-Li Hui
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, ChinaNanyang Normal UniversityNanyangChina,Research Center of Henan Provincial Agricultural Biomass Resource Engineering and Technology, Nanyang 473061, ChinaResearch Center of Henan Provincial Agricultural Biomass Resource Engineering and TechnologyNanyangChina
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Nutaratat P, Boontham W, Khunnamwong P. A Novel Yeast Genus and Two Novel Species Isolated from Pineapple Leaves in Thailand: Savitreella phatthalungensis gen. nov., sp. nov. and Goffeauzyma siamensis sp. nov. J Fungi (Basel) 2022; 8:jof8020118. [PMID: 35205872 PMCID: PMC8877625 DOI: 10.3390/jof8020118] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/21/2022] [Accepted: 01/23/2022] [Indexed: 02/05/2023] Open
Abstract
Four yeast strains, representing one genus and two novel anamorphic yeast species, were isolated from pineapple leaves collected in Thailand. Analysis of the sequences of the D1/D2 domains of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) regions showed the two strains (DMKU-PAL186 and DMKU-PAL178) were closely related to the type strains of the Protomyces and Taphrina species, but with high nucleotide divergence. Two strains (DMKU-PAL39 and DMKU-PAL18) were found to be closely related to the type strains of Goffeauzyma iberica, but with eight nucleotide substitutions in the D1/D2 domains and 26 nucleotide substitutions in the ITS regions. In phylogenetic analyses, the strains DMKU-PAL186 and DMKU-PAL178 formed a well-separated lineage from Protomyces and Taphrina genera, confirming that they represented a distinct genus, while the strains DMKU-PAL39 and DMKU-PAL18 represented a species in the genus Goffeauzyma, which was phylogenetically distinct from other recognized species of the genus. Based on molecular analyses and phenotypic characteristics, the names Savitreella gen. nov. (Taphrinomycetes, Ascomycota) and Savitreella phatthalungensis sp. nov. are proposed to accommodate the strains DMKU-PAL186 and DMKU-PAL178, and the name Goffeauzyma siamensis sp. nov. (Tremellomycetes, Basidiomycota) is proposed to accommodate the strains DMKU-PAL39 and DMKU-PAL18.
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Affiliation(s)
- Pumin Nutaratat
- Department of Biology, Faculty of Science, Thaksin University, Pa Phayom, Phatthalung 93210, Thailand;
- Microbial Technology for Agriculture, Food and Environment Research Center, Faculty of Science, Thaksin University, Pa Phayom, Phatthalung 93210, Thailand
| | - Wanatchaporn Boontham
- Program of Microbiology, Faculty of Science and Technology, Nakhon Pathom Rajabhat University, Nakhon Pathom 73000, Thailand;
| | - Pannida Khunnamwong
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Biodiversity Center, Kasetsart University (BDCKU), Bangkok 10900, Thailand
- Correspondence: ; Tel.: +66-2-562-5444
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15
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Khunnamwong P, Savarajara A, Jindamorakot S, Limtong S. Metahyphopichia suwanaadthiae sp. nov., an anamorphic yeast species in the order Saccharomycetales and reassignment of Candida silvanorum to the genus Metahyphopichia. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Seven yeast strains, representing a single novel anamorphic species, were isolated in Thailand. They consisted of five strains (DMKU-MRY16T, DMKU-SK18, DMKU-SK25, DMKU-SK30 and DMKU-SK32) obtained from five different mushrooms, and two strains (ST-224 and 11-14.2) derived from insect frass and soil, respectively. The pairwise sequence analysis indicated that all seven strains had identical sequences in the D1/D2 domains of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region. Metahyphopichia silvanorum was the most closely related species, but with 11.9–12.4% nucleotide substitutions in the D1/D2 domains of the LSU rRNA gene and 13.1–13.3% nucleotide substitutions in the ITS region. The phylogenetic analyses based on the concatenated sequences of the ITS region and the D1/D2 domains of the LSU rRNA gene showed that the seven strains form a well-separated subclade in a clade containing M. silvanorum and Metahyphopichia laotica with high bootstrap support. A phylogenetic analysis of a multilocus dataset including the small subunit (SSU) rRNA gene, the ITS region, the D1/D2 domains of the LSU rRNA gene, translation elongation factor 1-alpha gene, actin gene and the RNA polymerase II subunit 2 gene, confirmed the presence of the monophyletic clade that also includes M. silvanorum and M. laotica, and strongly supported the phylogenetic isolation of the seven strains from its neighbouring species. Therefore, the seven strains were assigned as a single novel species of the genus Metahyphopichia, according to their phylogenetic relationships. The name Metahyphopichia suwanaadthiae sp. nov. is proposed to accommodate the seven strains. The holotype is DMKU-MRY16T (TBRC 11775T=NBRC 114386T=PYCC 8655T). The MycoBank number of the novel species is MB 841280. In addition, Candida silvanorum is reassigned to the genus Metahyphopichia. The MycoBank number of M. silvanorum comb. nov. is MB 841279.
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Affiliation(s)
- Pannida Khunnamwong
- Biodiversity Center Kasetsart University (BDCKU), Bangkok 10900, Thailand
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Ancharida Savarajara
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sasitorn Jindamorakot
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Savitree Limtong
- Biodiversity Center Kasetsart University (BDCKU), Bangkok 10900, Thailand
- Academy of Science, The Royal Society of Thailand, Bangkok 10300, Thailand
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
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16
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Chaves ALS, Trilles L, Alves GM, Figueiredo-Carvalho MHG, Brito-Santos F, Coelho RA, Martins IS, Almeida-Paes R. A case-series of bloodstream infections caused by the Meyerozyma guilliermondii species complex at a reference center of oncology in Brazil. Med Mycol 2021; 59:235-243. [PMID: 32497174 DOI: 10.1093/mmy/myaa044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 05/06/2020] [Accepted: 05/12/2020] [Indexed: 12/12/2022] Open
Abstract
Bloodstream infections (BSI) caused by Candida species are the fourth cause of healthcare associated infections worldwide. Non-albicans Candida species emerged in the last decades as agents of serious diseases. In this study, clinical and microbiological aspects of six patients with BSI due to the Meyerozyma (Candida) guilliermondii species complex from an oncology reference center in Brazil, were evaluated. To describe demographic and clinical characteristics, medical records of the patients were reviewed. Molecular identification of the isolates was performed by ITS1-5.8S-ITS2 region sequencing. Antifungal susceptibility was evaluated by the EUCAST method and the minimal inhibitory concentrations (MIC) assessed according to the epidemiological cutoff values. Virulence associated phenotypes of the isolates were also studied. Ten isolates from the six patients were evaluated. Five of them were identified as Meyerozyma guilliermondii and the others as Meyerozyma caribbica. One patient was infected with two M. caribbica isolates with different genetic backgrounds. High MICs were observed for fluconazole and echinocandins. Non-wild type isolates to voriconazole appeared in one patient previously treated with this azole. Additionally, two patients survived, despite infected with non-wild type strains for fluconazole and treated with this drug. All isolates produced hemolysin, which was not associated with a poor prognosis, and none produced phospholipases. Aspartic proteases, phytase, and esterase were detected in a few isolates. This study shows the reduced antifungal susceptibility and a variable production of virulence-related enzymes by Meyerozyma spp. In addition, it highlights the poor prognosis of neutropenic patients with BSI caused by this emerging species complex. LAY ABSTRACT Our manuscript describes demographic, clinical and microbiological characteristics of patients with bloodstream infection by the Meyerozyma guilliermondii species complex at a reference center in oncology in Brazil.
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Affiliation(s)
- Alessandra Leal Silva Chaves
- Clinical Pathology Laboratory, HCI, National Cancer Institute, Rio de Janeiro, Brazil.,Mycology Laboratory, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Luciana Trilles
- Mycology Laboratory, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Gabriela Machado Alves
- Mycology Laboratory, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | | | - Fábio Brito-Santos
- Mycology Laboratory, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Rowena Alves Coelho
- Mycology Laboratory, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Ianick S Martins
- Nosocomial Infection Surveillance and Control Program, National Cancer Institute, Rio de Janeiro, Brazil.,Medical School of Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil
| | - Rodrigo Almeida-Paes
- Mycology Laboratory, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
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17
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Holič R, Šťastný D, Griač P. Sec14 family of lipid transfer proteins in yeasts. Biochim Biophys Acta Mol Cell Biol Lipids 2021; 1866:158990. [PMID: 34118432 DOI: 10.1016/j.bbalip.2021.158990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/31/2021] [Accepted: 06/02/2021] [Indexed: 11/25/2022]
Abstract
The hydrophobicity of lipids prevents their free movement across the cytoplasm. To achieve highly heterogeneous and precisely regulated lipid distribution in different cellular membranes, lipids are transported by lipid transfer proteins (LTPs) in addition to their transport by vesicles. Sec14 family is one of the most extensively studied groups of LTPs. Here we provide an overview of Sec14 family of LTPs in the most studied yeast Saccharomyces cerevisiae as well as in other selected non-Saccharomyces yeasts-Schizosaccharomyces pombe, Kluyveromyces lactis, Candida albicans, Candida glabrata, Cryptococcus neoformans, and Yarrowia lipolytica. Discussed are specificities of Sec14-domain LTPs in various yeasts, their mode of action, subcellular localization, and physiological function. In addition, quite few Sec14 family LTPs are target of antifungal drugs, serve as modifiers of drug resistance or influence virulence of pathologic yeasts. Thus, they represent an important object of study from the perspective of human health.
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Affiliation(s)
- Roman Holič
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Dominik Šťastný
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Peter Griač
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, Bratislava, Slovakia.
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18
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Toki W. A single case study of mycetangia-associated fungi and their abilities to assimilate wood-associated carbon sources in the ship timber beetle Elateroides flabellicornis (Coleoptera: Lymexylidae) in Japan. Symbiosis 2021. [DOI: 10.1007/s13199-021-00745-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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19
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Conti A, Corte L, Casagrande Pierantoni D, Robert V, Cardinali G. What Is the Best Lens? Comparing the Resolution Power of Genome-Derived Markers and Standard Barcodes. Microorganisms 2021; 9:microorganisms9020299. [PMID: 33540579 PMCID: PMC7912933 DOI: 10.3390/microorganisms9020299] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/22/2021] [Accepted: 01/29/2021] [Indexed: 02/07/2023] Open
Abstract
Fungal species delimitation was traditionally carried out with multicopy ribosomal RNA (rRNA) genes, principally for their ease of amplification. Since the efficacy of these markers has been questioned, single-copy protein-encoding genes have been proposed alone or in combination for Multi-Locus Sequence Typing (MLST). In this context, the role of the many sequences obtained with Next-Generation Sequencing (NGS) techniques, in both genomics and metagenomics, further pushes toward an analysis of the efficacy of NGS-derived markers and of the metrics to evaluate the marker efficacy in discriminating fungal species. This paper aims at proposing MeTRe (Mean Taxonomic Resolution), a novel index that could be used both for measuring marker efficacy and for assessing the actual resolution (i.e., the level of separation) between species obtained with different markers or their combinations. In this paper, we described and then employed this index to compare the efficacy of two rRNAs and four single-copy markers obtained from public databases as both an amplicon-based approach and genome-derived sequences. Two different groups of species were used, one with a pathogenic species of Candida that was characterized by relatively well-separated taxa, whereas the other, comprising some relevant species of the sensu stricto group of the genus Saccharomyces, included close species and interspecific hybrids. The results showed the ability of MeTRe to evaluate marker efficacy in general and genome-derived markers specifically.
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Affiliation(s)
- Angela Conti
- Department of Pharmaceutical Sciences, University of Perugia, 06121 Perugia, Italy; (A.C.); (L.C.); (D.C.P.)
| | - Laura Corte
- Department of Pharmaceutical Sciences, University of Perugia, 06121 Perugia, Italy; (A.C.); (L.C.); (D.C.P.)
| | | | - Vincent Robert
- Westerdjik Institute for Biodiversity, 3584 Utrecht, The Netherlands;
| | - Gianluigi Cardinali
- Department of Pharmaceutical Sciences, University of Perugia, 06121 Perugia, Italy; (A.C.); (L.C.); (D.C.P.)
- CEMIN Excellence Research Centre, 06123 Perugia, Italy
- Correspondence:
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20
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Čadež N, Dlauchy D, Tome M, Péter G. Novakomyces olei sp. nov., the First Member of a Novel Taphrinomycotina Lineage. Microorganisms 2021; 9:microorganisms9020301. [PMID: 33540601 PMCID: PMC7912804 DOI: 10.3390/microorganisms9020301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 01/27/2021] [Accepted: 01/29/2021] [Indexed: 01/25/2023] Open
Abstract
Taphrinomycotina is the smallest subphylum of the phylum Ascomycota. It is an assemblage of distantly related early diverging lineages of the phylum, comprising organisms with divergent morphology and ecology; however, phylogenomic analyses support its monophyly. In this study, we report the isolation of a yeast strain, which could not be assigned to any of the currently recognised five classes of Taphrinomycotina. The strain of the novel budding species was recovered from extra virgin olive oil and characterised phenotypically by standard methods. The ultrastructure of the cell wall was investigated by transmission electron microscopy. Comparisons of barcoding DNA sequences indicated that the investigated strain is not closely related to any known organism. Tentative phylogenetic placement was achieved by maximum-likelihood analysis of the D1/D2 domain of the nuclear LSU rRNA gene. The genome of the investigated strain was sequenced, assembled, and annotated. Phylogenomic analyses placed it next to the fission Schizosaccharomyces species. To accommodate the novel species, Novakomyces olei, a novel genus Novakomyces, a novel family Novakomycetaceae, a novel order Novakomycetales, and a novel class Novakomycetes is proposed as well. Functional analysis of genes missing in N. olei in comparison to Schizosaccharomyces pombe revealed that they are biased towards biosynthesis of complex organic molecules, regulation of mRNA, and the electron transport chain. Correlating the genome content and physiology among species of Taphrinomycotina revealed some discordance between pheno- and genotype. N. olei produced ascospores in axenic culture preceded by conjugation between two cells. We confirmed that N. olei is a primary homothallic species lacking genes for different mating types.
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Affiliation(s)
- Neža Čadež
- Food Science and Technology Department, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia; (N.Č.); (M.T.)
| | - Dénes Dlauchy
- National Collection of Agricultural and Industrial Microorganisms, Faculty of Food Science, Szent István University, Somlói út 14-16, H-1118 Budapest, Hungary;
| | - Miha Tome
- Food Science and Technology Department, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia; (N.Č.); (M.T.)
| | - Gábor Péter
- National Collection of Agricultural and Industrial Microorganisms, Faculty of Food Science, Szent István University, Somlói út 14-16, H-1118 Budapest, Hungary;
- Correspondence:
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Conti A, Casagrande Pierantoni D, Robert V, Cardinali G, Corte L. Homoplasy as an Auxiliary Criterion for Species Delimitation. Microorganisms 2021; 9:273. [PMID: 33525600 PMCID: PMC7911335 DOI: 10.3390/microorganisms9020273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/22/2021] [Accepted: 01/25/2021] [Indexed: 01/09/2023] Open
Abstract
Homoplasy is a sort of noise in phylogenetic reconstructions, due to the accumulation of backmutations, convergent evolution and horizontal gene transfer (HGT), which is considered the major trigger of homoplasy in microorganism for its massive presence. It is also known that homoplasy increases with the complexity of the tree with both real and simulated data. In this paper, we analyzed the variation of homoplasy with the two widely used taxonomic markers ITS and LSU in four taxonomic models characterized by differences in the intra-specific distances. An algorithm (HomoDist) was developed to analyze the homoplasy index (HI) variation upon addition of a single element (strain or species) in increasing distance from a starting element. This algorithm allows to follow changes of the consistency index (CI), complementary to the HI, with the increase of the number of taxa and with the increase of the distance among elements. Results show that homoplasy increases-as expected-with the number of taxa, but also as a function of the overall distance among species, often with an almost linear relationship between distance and HI. No HI change was observed in trees with few taxa spanning through short distances, indicating that this noise is not prohibitive in this context, although the analysis of the ratio between HI and distance can be recommended as a criterion for tree acceptance. The absence of large changes of the HI within the species, and its increase when new species are added by HomoDist, suggest that homoplasy variation can be used as an auxiliary test in distance-based species delimitation with any type of marker.
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Affiliation(s)
- Angela Conti
- Department of Pharmaceutical Sciences, University of Perugia, 06121 Perugia, Italy; (A.C.); (D.C.P.); (L.C.)
| | | | - Vincent Robert
- Westerdjik Institute for Biodiversity, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands;
| | - Gianluigi Cardinali
- Department of Pharmaceutical Sciences, University of Perugia, 06121 Perugia, Italy; (A.C.); (D.C.P.); (L.C.)
- CEMIN Excellence Research Centre, via Elce di Sotto 8, 06123 Perugia, Italy
| | - Laura Corte
- Department of Pharmaceutical Sciences, University of Perugia, 06121 Perugia, Italy; (A.C.); (D.C.P.); (L.C.)
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22
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Ohisa N, Sugawara Y, Mohri S. Breads Prepared by Using a Salt-tolerant Yeast Enrichment Culture and Dry Yeast. J JPN SOC FOOD SCI 2020. [DOI: 10.3136/nskkk.67.514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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23
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Valsalan R, Mathew D. Draft genome of Meyerozyma guilliermondii strain vka1: a yeast strain with composting potential. J Genet Eng Biotechnol 2020; 18:54. [PMID: 32996036 PMCID: PMC7524887 DOI: 10.1186/s43141-020-00074-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 09/17/2020] [Indexed: 11/30/2022]
Abstract
Background Meyerozyma guilliermondii is a yeast which could be isolated from a variety of environments. The vka1 strain isolated and purified from the organic compost was found to have composting potential. To better understand the genes assisting the composting potential in this yeast, whole genome sequencing and sequence annotation were performed. Results The genome of M. guilliermondii vka1 strain was sequenced using a hybrid approach, on Illumina Hiseq-2500 platform at 100× coverage followed by Nanopore platform at 20× coverage. The de novo assembly using dual-fold approach had given draft genome of 10.8 Mb size. The genome was found to contain 5385 genes. The annotation of the genes was performed, and the enzymes identified to have roles in the degradation of macromolecules are discussed in relation to its composting potential. Annotation of the genome assembly of the related strains had revealed the unique biodegradation related genes in this strain. Phylogenetic analysis using the rDNA region has confirmed the position of this strain in the Ascomycota family. Raw reads are made public, and the genome wide proteome profile is presented to facilitate further studies on this organism. Conclusions Meyerozyma guilliermondii vka1 strain was sequenced through hybrid approach and the reads were de novo assembled. Draft genome size and the number of genes in the strain were assessed and discussed in relation to the related strains. Scientific insights into the composting potential of this strain are also presented in relation to the unique genes identified in this strain.
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Affiliation(s)
- Ravisankar Valsalan
- Bioinformatics Centre, Kerala Agricultural University, KAU Post, Thrissur, Kerala State, 680 656, India
| | - Deepu Mathew
- Bioinformatics Centre, Kerala Agricultural University, KAU Post, Thrissur, Kerala State, 680 656, India.
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24
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Harrison PM. Variable absorption of mutational trends by prion-forming domains during Saccharomycetes evolution. PeerJ 2020; 8:e9669. [PMID: 32844065 PMCID: PMC7415223 DOI: 10.7717/peerj.9669] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/16/2020] [Indexed: 12/13/2022] Open
Abstract
Prions are self-propagating alternative states of protein domains. They are linked to both diseases and functional protein roles in eukaryotes. Prion-forming domains in Saccharomyces cerevisiae are typically domains with high intrinsic protein disorder (i.e., that remain unfolded in the cell during at least some part of their functioning), that are converted to self-replicating amyloid forms. S. cerevisiae is a member of the fungal class Saccharomycetes, during the evolution of which a large population of prion-like domains has appeared. It is still unclear what principles might govern the molecular evolution of prion-forming domains, and intrinsically disordered domains generally. Here, it is discovered that in a set of such prion-forming domains some evolve in the fungal class Saccharomycetes in such a way as to absorb general mutation biases across millions of years, whereas others do not, indicating a spectrum of selection pressures on composition and sequence. Thus, if the bias-absorbing prion formers are conserving a prion-forming capability, then this capability is not interfered with by the absorption of bias changes over the duration of evolutionary epochs. Evidence is discovered for selective constraint against the occurrence of lysine residues (which likely disrupt prion formation) in S. cerevisiae prion-forming domains as they evolve across Saccharomycetes. These results provide a case study of the absorption of mutational trends by compositionally biased domains, and suggest methodology for assessing selection pressures on the composition of intrinsically disordered regions.
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Affiliation(s)
- Paul M Harrison
- Department of Biology, McGill University, Monteal, Quebec, Canada
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25
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Jia RR, Lv SL, Chai CY, Hui FL. Three new Scheffersomyces species associated with insects and rotting wood in China. MycoKeys 2020; 71:87-99. [PMID: 32855604 PMCID: PMC7426279 DOI: 10.3897/mycokeys.71.56168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 07/18/2020] [Indexed: 11/12/2022] Open
Abstract
Three species of Scheffersomyces were identified during a diversity study of yeasts. All three are associated with insects and rotting wood in China. Phylogenetic analyses of a genomic dataset combining ITS and nrLSU revealed that these new collections are distinct from known species, thus three new species are introduced i.e. S. jinghongensis, S. paraergatensis, and S. anoplophorae. In our phylogenetic analyses, Scheffersomyces jinghongensis possesses a strong independent lineage and is closely related to S. titanus. S. paraergatensis is closely related to S. ergatensis, while S. anoplophorae is related to S. stambukii. Several differences in physiological traits and molecular data indicate that S. jinghongensis, S. paraergatensis, and S. anoplophorae are three newly identified species.
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Affiliation(s)
- Ran-Ran Jia
- School of Life Science and Technology, Nanyang Normal University, Nanyang 473061, China
| | - Shi-Long Lv
- School of Life Science and Technology, Nanyang Normal University, Nanyang 473061, China
| | - Chun-Yue Chai
- School of Life Science and Technology, Nanyang Normal University, Nanyang 473061, China
| | - Feng-Li Hui
- School of Life Science and Technology, Nanyang Normal University, Nanyang 473061, China
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26
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Kurylenko OO, Ruchala J, Dmytruk KV, Abbas CA, Sibirny AA. Multinuclear Yeast
Magnusiomyces (Dipodascus, Endomyces) magnusii
is a Promising Isobutanol Producer. Biotechnol J 2020; 15:e1900490. [DOI: 10.1002/biot.201900490] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/28/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Olena O. Kurylenko
- Department of Molecular Genetics and BiotechnologyInstitute of Cell BiologyNAS of Ukraine Lviv 79005 Ukraine
| | - Justyna Ruchala
- Department of Molecular Genetics and BiotechnologyInstitute of Cell BiologyNAS of Ukraine Lviv 79005 Ukraine
- Department of Microbiology and BiotechnologyUniversity of Rzeszow Rzeszow 35‐601 Poland
| | - Kostyantyn V. Dmytruk
- Department of Molecular Genetics and BiotechnologyInstitute of Cell BiologyNAS of Ukraine Lviv 79005 Ukraine
| | | | - Andriy A. Sibirny
- Department of Molecular Genetics and BiotechnologyInstitute of Cell BiologyNAS of Ukraine Lviv 79005 Ukraine
- Department of Microbiology and BiotechnologyUniversity of Rzeszow Rzeszow 35‐601 Poland
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27
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Mechanistic investigations in ultrasound-induced intensification of fermentative riboflavin production. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.biteb.2020.100380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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28
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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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29
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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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30
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Menoncin M, Bonatto D. Molecular and biochemical aspects ofBrettanomycesin brewing. JOURNAL OF THE INSTITUTE OF BREWING 2019. [DOI: 10.1002/jib.580] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Marcelo Menoncin
- Brewing Yeast Research Group, Biotechnology Center of the Federal University of Rio Grande do Sul, Department of Molecular Biology and Biotechnology; Federal University of Rio Grande do Sul; Porto Alegre RS Brazil
| | - Diego Bonatto
- Brewing Yeast Research Group, Biotechnology Center of the Federal University of Rio Grande do Sul, Department of Molecular Biology and Biotechnology; Federal University of Rio Grande do Sul; Porto Alegre RS Brazil
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31
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Stavrou AA, Lackner M, Lass-Flörl C, Boekhout T. The changing spectrum of Saccharomycotina yeasts causing candidemia: phylogeny mirrors antifungal susceptibility patterns for azole drugs and amphothericin B. FEMS Yeast Res 2019; 19:5510445. [DOI: 10.1093/femsyr/foz037] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 05/20/2019] [Indexed: 12/14/2022] Open
Affiliation(s)
- Aimilia A Stavrou
- Yeast Research, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Sciencepark 904, 1098XH Amsterdam, The Netherlands
| | - Michaela Lackner
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstrasse 41, 6020 Innsbruck, Austria
| | - Cornelia Lass-Flörl
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstrasse 41, 6020 Innsbruck, Austria
| | - Teun Boekhout
- Yeast Research, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Sciencepark 904, 1098XH Amsterdam, The Netherlands
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
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32
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Junker K, Chailyan A, Hesselbart A, Forster J, Wendland J. Multi-omics characterization of the necrotrophic mycoparasite Saccharomycopsis schoenii. PLoS Pathog 2019; 15:e1007692. [PMID: 31071195 PMCID: PMC6508603 DOI: 10.1371/journal.ppat.1007692] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 03/10/2019] [Indexed: 12/14/2022] Open
Abstract
Pathogenic yeasts and fungi are an increasing global healthcare burden, but discovery of novel antifungal agents is slow. The mycoparasitic yeast Saccharomycopsis schoenii was recently demonstrated to be able to kill the emerging multi-drug resistant yeast pathogen Candida auris. However, the molecular mechanisms involved in the predatory activity of S. schoenii have not been explored. To this end, we de novo sequenced, assembled and annotated a draft genome of S. schoenii. Using proteomics, we confirmed that Saccharomycopsis yeasts have reassigned the CTG codon and translate CTG into serine instead of leucine. Further, we confirmed an absence of all genes from the sulfate assimilation pathway in the genome of S. schoenii, and detected the expansion of several gene families, including aspartic proteases. Using Saccharomyces cerevisiae as a model prey cell, we honed in on the timing and nutritional conditions under which S. schoenii kills prey cells. We found that a general nutrition limitation, not a specific methionine deficiency, triggered predatory activity. Nevertheless, by means of genome-wide transcriptome analysis we observed dramatic responses to methionine deprivation, which were alleviated when S. cerevisiae was available as prey, and therefore postulate that S. schoenii acquired methionine from its prey cells. During predation, both proteomic and transcriptomic analyses revealed that S. schoenii highly upregulated and translated aspartic protease genes, probably used to break down prey cell walls. With these fundamental insights into the predatory behavior of S. schoenii, we open up for further exploitation of this yeast as a biocontrol yeast and/or source for novel antifungal agents.
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Affiliation(s)
- Klara Junker
- Yeast & Fermentation, Carlsberg Research Laboratory, Copenhagen, Denmark
| | - Anna Chailyan
- Yeast & Fermentation, Carlsberg Research Laboratory, Copenhagen, Denmark
| | - Ana Hesselbart
- Yeast & Fermentation, Carlsberg Research Laboratory, Copenhagen, Denmark
| | - Jochen Forster
- Yeast & Fermentation, Carlsberg Research Laboratory, Copenhagen, Denmark
| | - Jürgen Wendland
- Yeast & Fermentation, Carlsberg Research Laboratory, Copenhagen, Denmark
- Functional Yeast Genomics, Vrije Universiteit Brussel, Brussels, Belgium
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33
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Čadež N, Bellora N, Ulloa R, Hittinger CT, Libkind D. Genomic content of a novel yeast species Hanseniaspora gamundiae sp. nov. from fungal stromata (Cyttaria) associated with a unique fermented beverage in Andean Patagonia, Argentina. PLoS One 2019; 14:e0210792. [PMID: 30699175 PMCID: PMC6353571 DOI: 10.1371/journal.pone.0210792] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 01/03/2019] [Indexed: 11/19/2022] Open
Abstract
A novel yeast species was isolated from the sugar-rich stromata of Cyttaria hariotii collected from two different Nothofagus tree species in the Andean forests of Patagonia, Argentina. Phylogenetic analyses of the concatenated sequence of the rRNA gene sequences and the protein-coding genes for actin and translational elongation factor-1α indicated that the novel species belongs to the genus Hanseniaspora. De novo genome assembly of the strain CRUB 1928T yielded a 10.2-Mbp genome assembly predicted to encode 4452 protein-coding genes. The genome sequence data were compared to the genomes of other Hanseniaspora species using three different methods, an alignment-free distance measure, Kr, and two model-based estimations of DNA-DNA homology values, of which all provided indicative values to delineate species of Hanseniaspora. Given its potential role in a rare indigenous alcoholic beverage in which yeasts ferment sugars extracted from the stromata of Cytarria sp., we searched for the genes that may suggest adaptation of novel Hanseniaspora species to fermenting communities. The SSU1-like gene encoding a sulfite efflux pump, which, among Hanseniaspora, is present only in close relatives to the new species, was detected and analyzed, suggesting that this gene might be one factor that characterizes this novel species. We also discuss several candidate genes that likely underlie the physiological traits used for traditional taxonomic identification. Based on these results, a novel yeast species with the name Hanseniaspora gamundiae sp. nov. is proposed with CRUB 1928T (ex-types: ZIM 2545T = NRRL Y-63793T = PYCC 7262T; MycoBank number MB 824091) as the type strain. Furthermore, we propose the transfer of the Kloeckera species, K. hatyaiensis, K. lindneri and K. taiwanica to the genus Hanseniaspora as Hanseniaspora hatyaiensis comb. nov. (MB 828569), Hanseniaspora lindneri comb. nov. (MB 828566) and Hanseniaspora taiwanica comb. nov. (MB 828567).
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Affiliation(s)
- Neža Čadež
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, Ljubljana, Slovenia
| | - Nicolas Bellora
- Laboratorio de Microbiología Aplicada y Biotecnología, Instituto de Investigaciones en Biodiversidad y Medio-ambiente, Consejo Nacional de Investigaciones, Científicas y Técnicas (CONICET)-Universidad Nacional del Comahue, Bariloche, Argentina
| | - Ricardo Ulloa
- Laboratorio de Bioprocesos, Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas, Consejo Nacional de Investigaciones, Científicas y Técnicas (CONICET)-Universidad Nacional del Comahue, Neuquén, Argentina
| | - Chris Todd Hittinger
- Laboratory of Genetics, Genome Center of Wisconsin, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Diego Libkind
- Laboratorio de Microbiología Aplicada y Biotecnología, Instituto de Investigaciones en Biodiversidad y Medio-ambiente, Consejo Nacional de Investigaciones, Científicas y Técnicas (CONICET)-Universidad Nacional del Comahue, Bariloche, Argentina
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Bernardi B, Kayacan Y, Wendland J. Expansion of a Telomeric FLO/ALS-Like Sequence Gene Family in Saccharomycopsis fermentans. Front Genet 2018; 9:536. [PMID: 30542368 PMCID: PMC6277891 DOI: 10.3389/fgene.2018.00536] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 10/23/2018] [Indexed: 01/01/2023] Open
Abstract
Non-Saccharomyces species have been recognized for their beneficial contribution to fermented food and beverages based on their volatile compound formation and their ability to ferment glucose into ethanol. At the end of fermentation brewer's yeast flocculate which provides an easy means of separation of yeasts from green beer. Flocculation in Saccharomyces cerevisiae requires a set of flocculation genes. These FLO-genes, FLO1, FLO5, FLO9, FLO10, and FLO11, are located at telomeres and transcription of these adhesins is regulated by Flo8 and Mss11. Here, we show that Saccharomycopsis fermentans, an ascomycete yeast distantly related to S. cerevisiae, possesses a very large FLO/ALS-like Sequence (FAS) family encompassing 34 genes. Fas proteins are variable in size and divergent in sequence and show similarity to the Flo1/5/9 family. Fas proteins show the general build with a signal peptide, an N-terminal carbohydrate binding PA14 domain, a central region differing by the number of repeats and a C-terminus with a consensus sequence for GPI-anchor attachment. Like FLO genes in S. cerevisiae, FAS genes are mostly telomeric with several paralogs at each telomere. We term such genes that share evolutionary conserved telomere localization "telologs" and provide several other examples. Adhesin expression in S. cerevisiae and filamentation in Candida albicans is regulated by Flo8 and Mss11. In Saccharomycopsis we identified only a single protein with similarity to Flo8 based on sequence similarity and the presence of a LisH domain.
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Affiliation(s)
- Beatrice Bernardi
- Department of Bioengineering Sciences, Research Group of Microbiology, Functional Yeast Genomics, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Yeseren Kayacan
- Department of Bioengineering Sciences, Research Group of Microbiology, Functional Yeast Genomics, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Jürgen Wendland
- Department of Bioengineering Sciences, Research Group of Microbiology, Functional Yeast Genomics, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
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35
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Wachowska U, Irzykowski W, Jędryczka M. Agrochemicals: Effect on genetic resistance in yeasts colonizing winter wheat kernels. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 162:77-84. [PMID: 29990742 DOI: 10.1016/j.ecoenv.2018.06.042] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 06/09/2018] [Accepted: 06/14/2018] [Indexed: 05/27/2023]
Abstract
Crop protection agents are widely used in modern agriculture and exert direct effects on non-target microorganisms such as yeasts. Yeasts abundantly colonize wheat grain and affect its chemical composition. They can also limit pathogen growth. This study evaluated the sensitivity of yeast communities colonizing winter wheat kernels to benzimidazole, strobilurin, triazole and morpholine fungicides, trinexapac-ethyl, a commercial mixture of o-nitrophenol+p-nitrophenol+5-nitroguaiacol, and chitosan applied during the growing season of winter wheat and in vitro in a diffusion test. A molecular identification analysis of yeasts isolated from winter wheat kernels was performed, and nucleotide polymorphisms in the CYTb gene (G143A) conferring resistance to strobilurin fungicides in yeast cells were identified. The size of yeast communities increased during grain storage, and the total counts of endophytic yeasts were significantly (85%) reduced following intensive fungicide treatment (fenpropimorph, a commercial mixture of pyraclostrobin, epoxiconazole and thiophanate-methyl). This study demonstrated that agrochemical residues in wheat grain can drive selection of yeast communities for reduced sensitivity to xenobiotics. A mutation in the CYTb gene (G143A) was observed in all analyzed isolates of the following azoxystrobin-resistant species: Aureobasidium pullulans, Debaryomyces hansenii, Candida albicans and C. sake. Agrochemicals tested in vitro were divided into four classes of toxicity to yeasts: (1) tebuconazole and a commercial mixture of flusilazole and carbendazim - most toxic to yeasts; (2) fenpropimorph and a commercial mixture of pyraclostrobin and epoxyconazole; (3) propiconazole, chitosan, thiophanate-methyl and a commercial mixture of o-nitrophenol, p-nitrophenol and 5-nitroguaiacol; (4) trinexapac-ethyl and azoxystrobin - least toxic to yeasts. It was found that agrochemicals can have an adverse effect on yeast abundance and the composition of yeast communities, mostly due to differences in fungicide resistance between yeast species, including the clinically significant C. albicans.
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Affiliation(s)
- Urszula Wachowska
- Department of Entomology, Phytopathology and Molecular Diagnostics, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 17, 10-719 Olsztyn, Poland.
| | - Witold Irzykowski
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland
| | - Małgorzata Jędryczka
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland
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36
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Carvalho C, Tomás A, Libkind D, Imanishi Y, Sampaio JP. Zygotorulaspora chibaensis sp. nov. and Zygotorulaspora danielsina sp. nov., novel ascomycetous yeast species from tree bark and soil. Int J Syst Evol Microbiol 2018; 68:2633-2637. [DOI: 10.1099/ijsem.0.002889] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Cláudia Carvalho
- 1UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - André Tomás
- 1UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Diego Libkind
- 2Laboratorio de Microbiología Aplicada, Biotecnología y Bioinformática de Levaduras, Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC), CONICET - UNComahue, Av., San Carlos de Bariloche, Río Negro C.P. 8400, Argentina
| | - Yumi Imanishi
- 3Department of Biosciences, College of Science and Engineering, Kanto Gakuin University, Mutsuura-higashi 1-50-1, Kanazawa-ku, Yokohama 236-8501, Japan
| | - José Paulo Sampaio
- 1UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
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Draft Genome Sequences of Two Natural Isolates of the Yeast Barnettozyma californica from Ireland, UCD09 and UCD89. GENOME ANNOUNCEMENTS 2018; 6:6/25/e00548-18. [PMID: 29930057 PMCID: PMC6013596 DOI: 10.1128/genomea.00548-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
No genome sequence of a species from Barnettozyma, a yeast genus in the family Phaffomycetaceae, is currently available. We isolated two B. californica strains from soils in Ireland and generated draft sequences of their 11.7-Mb genomes. Single nucleotide polymorphism (SNP) analysis showed 20,490 differences between the strains and suggests that B. californica is haploid.
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Mühlhausen S, Schmitt HD, Pan KT, Plessmann U, Urlaub H, Hurst LD, Kollmar M. Endogenous Stochastic Decoding of the CUG Codon by Competing Ser- and Leu-tRNAs in Ascoidea asiatica. Curr Biol 2018; 28:2046-2057.e5. [PMID: 29910077 PMCID: PMC6041473 DOI: 10.1016/j.cub.2018.04.085] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 04/22/2018] [Accepted: 04/24/2018] [Indexed: 12/24/2022]
Abstract
Although the “universal” genetic code is now known not to be universal, and stop codons can have multiple meanings, one regularity remains, namely that for a given sense codon there is a unique translation. Examining CUG usage in yeasts that have transferred CUG away from leucine, we here report the first example of dual coding: Ascoidea asiatica stochastically encodes CUG as both serine and leucine in approximately equal proportions. This is deleterious, as evidenced by CUG codons being rare, never at conserved serine or leucine residues, and predominantly in lowly expressed genes. Related yeasts solve the problem by loss of function of one of the two tRNAs. This dual coding is consistent with the tRNA-loss-driven codon reassignment hypothesis, and provides a unique example of a proteome that cannot be deterministically predicted. Video Abstract
Ascoidea asiatica stochastically encodes CUG as leucine and serine It is the only known example of a proteome with non-deterministic features Stochastic encoding is caused by competing tRNALeu(CAG) and tRNASer(CAG) A. asiatica copes with stochastic encoding by avoiding CUG at key positions
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Affiliation(s)
- Stefanie Mühlhausen
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Hans Dieter Schmitt
- Department of Neurobiology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Kuan-Ting Pan
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Uwe Plessmann
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany; Bioanalytics Group, Department of Clinical Chemistry, University Medical Center Göttingen, Robert Koch Strasse 40, 37075 Göttingen, Germany
| | - Laurence D Hurst
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Martin Kollmar
- Group Systems Biology of Motor Proteins, Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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Colabella C, Corte L, Roscini L, Bassetti M, Tascini C, Mellor JC, Meyer W, Robert V, Vu D, Cardinali G. NGS barcode sequencing in taxonomy and diagnostics, an application in " Candida" pathogenic yeasts with a metagenomic perspective. IMA Fungus 2018; 9:91-105. [PMID: 30018874 PMCID: PMC6048569 DOI: 10.5598/imafungus.2018.09.01.07] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 05/10/2018] [Indexed: 11/29/2022] Open
Abstract
Species identification of yeasts and other Fungi is currently carried out with Sanger sequences of selected molecular markers, mainly from the ribosomal DNA operon, characterized by hundreds of tandem repeats of the 18S, ITS1, 5.8S, ITS2 and LSU loci. The ITS region has been recently proposed as a primary barcode marker making this region the most used one in taxonomy, phylogeny and diagnostics. The introduction of NGS is providing tools of high efficacy and relatively low cost to amplify two or more markers simultaneously with great sequencing depth. However, the presence of intra-genomic variability between the repeats requires specific analytical procedures and pipelines. In this study, 286 strains belonging to 11 pathogenic yeasts species were analysed with NGS of the region spanning from ITS1 to the D1/D2 domain of the LSU encoding ribosomal DNA. Results showed that relatively high heterogeneity can hamper the use of these sequences for the identification of single strains and even more of complex microbial mixtures. These observations point out that the metagenomics studies could be affected by species inflection at levels higher than currently expected.
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Affiliation(s)
- Claudia Colabella
- Microbiology Section, Department of Pharmaceutical Sciences, University of Perugia, 06121, Italy
| | - Laura Corte
- Microbiology Section, Department of Pharmaceutical Sciences, University of Perugia, 06121, Italy
| | - Luca Roscini
- Microbiology Section, Department of Pharmaceutical Sciences, University of Perugia, 06121, Italy
| | - Matteo Bassetti
- Infectious Diseases Division, Santa Maria Misericordia University Hospital, Udine, 33100, Italy
| | - Carlo Tascini
- Infectious Diseases Division, Cotugno Hospital Napoli, 80131, Italy
| | | | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School, Westmead Hospital, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Institute for Medical Research, Sydney, NSW 2006, Australia
| | - Vincent Robert
- Bioinformatics Unit, Westerdijk Fungal Biodiversity Institute, 3508 CT, Utrecht, Netherlands
| | - Duong Vu
- Bioinformatics Unit, Westerdijk Fungal Biodiversity Institute, 3508 CT, Utrecht, Netherlands
| | - Gianluigi Cardinali
- Microbiology Section, Department of Pharmaceutical Sciences, University of Perugia, 06121, Italy.,CEMIN Research Centre of Excellence, University of Perugia, Borgo 20 Giugno 74, 06121, Italy
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Kurtzman CP, Robnett CJ, Basehoar E, Ward TJ. Four new species of Metschnikowia and the transfer of seven Candida species to Metschnikowia and Clavispora as new combinations. Antonie van Leeuwenhoek 2018; 111:2017-2035. [DOI: 10.1007/s10482-018-1095-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 05/05/2018] [Indexed: 11/24/2022]
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de Vega C, Albaladejo RG, Guzmán B, Steenhuisen SL, Johnson SD, Herrera CM, Lachance MA. Flowers as a reservoir of yeast diversity: description of Wickerhamiella nectarea f.a. sp. nov., and Wickerhamiella natalensis f.a. sp. nov. from South African flowers and pollinators, and transfer of related Candida species to the genus Wickerhamiella as new combinations. FEMS Yeast Res 2018; 17:3966713. [PMID: 28810705 DOI: 10.1093/femsyr/fox054] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 07/13/2017] [Indexed: 11/14/2022] Open
Abstract
Flowers offer favourable microenvironments for yeast growth, and are increasingly recognised as a rich source of novel yeast species. Independent surveys of yeasts associated with flowers and pollinators in South Africa led to the discovery of 38 strains of two new species. Physiological profiles and analysis of the internal transcribed spacer and the D1/D2 domains of the large subunit rRNA gene showed that they represent two novel species that belong to the Wickerhamiella clade. We describe the species as Wickerhamiella nectarea f.a. sp. nov. (type strain EBDCdVSA11-1T, CBS 14162T, NRRL Y-63791T) and W. natalensis f.a. sp. nov. (type strain EBDCdVSA7-1T, CBS 14161T, NRRL Y-63790T). We extend the known range of flower-associated Wickerhamiella species to South Africa and discuss the ecology and phylogenetic relationships of the clade in relation to its host species and biogeography. Examination of growth characteristics supports that the Wickerhamiella clade exhibits a high degree of evolutionary lability, and that specialisation to different niches may occur rapidly. We review the current status of floral yeast biodiversity and nectar as a reservoir of species diversity, and the importance of pollinators and biogeography. In addition, 18 species formerly assigned to the genus Candida are reassigned formally to the genus Wickerhamiella.
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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
| | - Beatriz Guzmán
- Real Jardín Botánico, CSIC, Plaza de Murillo 2, 28014 Madrid, Spain
| | - Sandy-Lynn Steenhuisen
- Department of Biological Sciences, University of Cape Town, P/Bag, Rondebosch 7701, South Africa
| | - Steven D Johnson
- School of Life Sciences, University of KwaZulu-Natal, P/ Bag X01, Scottsville, Pietermaritzburg 3209, South Africa
| | - Carlos M Herrera
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avenida de Américo Vespucio s/n, 41092 Sevilla, Spain
| | - Marc-André Lachance
- Department of Biology, University of Western Ontario, London, ON N6A 5B7, Canada
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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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Santos ARO, Leon MP, Barros KO, Freitas LFD, Hughes AFS, Morais PB, Lachance MA, Rosa CA. Starmerella camargoi f.a., sp. nov., Starmerella ilheusensis f.a., sp. nov., Starmerella litoralis f.a., sp. nov., Starmerella opuntiae f.a., sp. nov., Starmerella roubikii f.a., sp. nov. and Starmerella vitae f.a., sp. nov., isolated from flowers and bees, and transfer of related Candida species to the genus Starmerella as new combinations. Int J Syst Evol Microbiol 2018; 68:1333-1343. [DOI: 10.1099/ijsem.0.002675] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ana Raquel O. Santos
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Marina P. Leon
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Katharina O. Barros
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Larissa F. D. Freitas
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Alice F. S. Hughes
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Paula B. Morais
- Laboratorio de Microbiologia Ambiental e Biotecnologia, Universidade Federal do Tocantins, Palmas, TO 77020-220, Brazil
| | - Marc-André Lachance
- Department of Biology, University of Western Ontario, London, Ontario, N6A 5B7, Canada
| | - Carlos A. Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
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Opulente DA, Rollinson EJ, Bernick-Roehr C, Hulfachor AB, Rokas A, Kurtzman CP, Hittinger CT. Factors driving metabolic diversity in the budding yeast subphylum. BMC Biol 2018; 16:26. [PMID: 29499717 PMCID: PMC5833115 DOI: 10.1186/s12915-018-0498-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 02/13/2018] [Indexed: 12/02/2022] Open
Abstract
Background Associations between traits are prevalent in nature, occurring across a diverse range of taxa and traits. Individual traits may co-evolve with one other, and these correlations can be driven by factors intrinsic or extrinsic to an organism. However, few studies, especially in microbes, have simultaneously investigated both across a broad taxonomic range. Here we quantify pairwise associations among 48 traits across 784 diverse yeast species of the ancient budding yeast subphylum Saccharomycotina, assessing the effects of phylogenetic history, genetics, and ecology. Results We find extensive negative (traits that tend to not occur together) and positive (traits that tend to co-occur) pairwise associations among traits, as well as between traits and environments. These associations can largely be explained by the biological properties of the traits, such as overlapping biochemical pathways. The isolation environments of the yeasts explain a minor but significant component of the variance, while phylogeny (the retention of ancestral traits in descendant species) plays an even more limited role. Positive correlations are pervasive among carbon utilization traits and track with chemical structures (e.g., glucosides and sugar alcohols) and metabolic pathways, suggesting a molecular basis for the presence of suites of traits. In several cases, characterized genes from model organisms suggest that enzyme promiscuity and overlapping biochemical pathways are likely mechanisms to explain these macroevolutionary trends. Interestingly, fermentation traits are negatively correlated with the utilization of pentose sugars, which are major components of the plant biomass degraded by fungi and present major bottlenecks to the production of cellulosic biofuels. Finally, we show that mammalian pathogenic and commensal yeasts have a suite of traits that includes growth at high temperature and, surprisingly, the utilization of a narrowed panel of carbon sources. Conclusions These results demonstrate how both intrinsic physiological factors and extrinsic ecological factors drive the distribution of traits present in diverse organisms across macroevolutionary timescales. Electronic supplementary material The online version of this article (10.1186/s12915-018-0498-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dana A Opulente
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, 53706, USA.,DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Emily J Rollinson
- Applied Biomathematics, Setauket, NY, 11733, USA.,Department of Biological Sciences, East Stroudsburg University of Pennsylvania, East Stroudsburg, PA, 18301, USA
| | - Cleome Bernick-Roehr
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Amanda Beth Hulfachor
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, 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
| | - Chris Todd Hittinger
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, 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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The Genomes of Four Meyerozyma caribbica Isolates and Novel Insights into the Meyerozyma guilliermondii Species Complex. G3-GENES GENOMES GENETICS 2018; 8:755-759. [PMID: 29311113 PMCID: PMC5844296 DOI: 10.1534/g3.117.300316] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Yeasts of the Meyerozyma guilliermondii species complex are widespread in nature and can be isolated from a variety of sources, from the environment to arthropods to hospital patients. To date, the species complex comprises the thoroughly studied and versatile M. guilliermondii, the hard to distinguish M. caribbica, and Candida carpophila. Here we report the whole genome sequencing and de novo assembly of four M. caribbica isolates, identified with the most recent molecular techniques, derived from four Diptera species. The four novel assemblies present reduced fragmentation and comparable metrics (genome size, gene content) to the available genomes belonging to the species complex. We performed a phylogenomic analysis comprising all known members of the species complex, to investigate evolutionary relationships within this clade. Our results show a compact phylogenetic structure for the complex and indicate the presence of a sizable core set of genes. Furthermore, M. caribbica, despite a broad literature on the difficulties of discerning it from M. guilliermondii, seems to be more closely related to C. carpophila. Finally, we believe that there is evidence for considering these four genomes to be the first published for the species M. caribbica. Raw reads and assembled contigs have been made public to further the study of these organisms.
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Evolutionary Conservation of the Components in the TOR Signaling Pathways. Biomolecules 2017; 7:biom7040077. [PMID: 29104218 PMCID: PMC5745459 DOI: 10.3390/biom7040077] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 10/26/2017] [Accepted: 10/27/2017] [Indexed: 01/08/2023] Open
Abstract
Target of rapamycin (TOR) is an evolutionarily conserved protein kinase that controls multiple cellular processes upon various intracellular and extracellular stimuli. Since its first discovery, extensive studies have been conducted both in yeast and animal species including humans. Those studies have revealed that TOR forms two structurally and physiologically distinct protein complexes; TOR complex 1 (TORC1) is ubiquitous among eukaryotes including animals, yeast, protozoa, and plants, while TOR complex 2 (TORC2) is conserved in diverse eukaryotic species other than plants. The studies have also identified two crucial regulators of mammalian TORC1 (mTORC1), Ras homolog enriched in brain (RHEB) and RAG GTPases. Of these, RAG regulates TORC1 in yeast as well and is conserved among eukaryotes with the green algae and land plants as apparent exceptions. RHEB is present in various eukaryotes but sporadically missing in multiple taxa. RHEB, in the budding yeast Saccharomyces cerevisiae, appears to be extremely divergent with concomitant loss of its function as a TORC1 regulator. In this review, we summarize the evolutionarily conserved functions of the key regulatory subunits of TORC1 and TORC2, namely RAPTOR, RICTOR, and SIN1. We also delve into the evolutionary conservation of RHEB and RAG and discuss the conserved roles of these GTPases in regulating TORC1.
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48
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Morais CG, Batista TM, Kominek J, Borelli BM, Furtado C, Moreira RG, Franco GR, Rosa LH, Fonseca C, Hittinger CT, Lachance MA, Rosa CA. Spathaspora boniae sp. nov., a D-xylose-fermenting species in the Candida albicans/Lodderomyces clade. Int J Syst Evol Microbiol 2017; 67:3798-3805. [DOI: 10.1099/ijsem.0.002186] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Camila G. Morais
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Thiago M. Batista
- Departamento de Bioquímica e Imunologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Jacek Kominek
- Laboratory of Genetics, Genome Center of Wisconsin, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Beatriz M. Borelli
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | | | - Rennan G. Moreira
- Laboratorio Multiusuário de Genômica, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Gloria R. Franco
- Departamento de Bioquímica e Imunologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Luiz H. Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - César Fonseca
- Section for Sustainable Biotechnology, Aalborg University Copenhagen, A. C. Meyers Vænge 15, 2450 Copenhagen SV, Denmark
| | - Chris T. Hittinger
- Laboratory of Genetics, Genome Center of Wisconsin, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Marc-André Lachance
- Department of Biology, University of Western Ontario, N6A 5B7, London, Ontario, Canada
| | - Carlos A. Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
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Ekanayaka AH, Ariyawansa HA, Hyde KD, Jones EBG, Daranagama DA, Phillips AJL, Hongsanan S, Jayasiri SC, Zhao Q. DISCOMYCETES: the apothecial representatives of the phylum Ascomycota. FUNGAL DIVERS 2017. [DOI: 10.1007/s13225-017-0389-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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50
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Gao WL, Liu TT, Zheng J, Hui FL. Kodamaea neixiangensis f.a., sp. nov. and Kodamaea jinghongensis f.a., sp. nov., two yeast species isolated from rotting wood. Int J Syst Evol Microbiol 2017; 67:3358-3362. [DOI: 10.1099/ijsem.0.002117] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Wan-Li Gao
- School of Agricultural Engineering, Nanyang Normal University, Nanyang 473061, PR China
| | - Tian-tian Liu
- School of Life Science and Technology, Nanyang Normal University, Nanyang 473061, PR China
| | - Jun Zheng
- 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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