1
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Villarreal P, Villarroel CA, O'Donnell S, Agier N, Quintero-Galvis JF, Peña TA, Nespolo RF, Fischer G, Varela C, Cubillos FA. Late Pleistocene-dated divergence between South Hemisphere populations of the non-conventional yeast L. cidri. Environ Microbiol 2022; 24:5615-5629. [PMID: 35769023 DOI: 10.1111/1462-2920.16103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/08/2022] [Accepted: 06/13/2022] [Indexed: 01/12/2023]
Abstract
Most organisms belonging to the Saccharomycotina subphylum have high genetic diversity and a vast repertoire of metabolisms and lifestyles. Lachancea cidri is an ideal yeast model for exploring the interplay between genetics, ecological function and evolution. Lachancea cidri diverged from the Saccharomyces lineage before the whole-genome duplication and is distributed across the South Hemisphere, displaying an important ecological success. We applied phylogenomics to investigate the genetic variation of L. cidri isolates obtained from Australia and South America. Our approach revealed the presence of two main lineages according to their geographic distribution (Aus and SoAm). Estimation of the divergence time suggests that SoAm and Aus lineages diverged near the last glacial maximum event during the Pleistocene (64-8 KYA). Interestingly, we found that the French reference strain is closely related to the Australian strains, with a recent divergence (405-51 YA), likely associated to human movements. Additionally, we identified different lineages within the South American population, revealing that Patagonia contains a similar genetic diversity comparable to that of other lineages in S. cerevisiae. These findings support the idea of a Pleistocene-dated divergence between South Hemisphere lineages, where the Nothofagus and Araucaria ecological niches likely favoured the extensive distribution of L. cidri in Patagonia.
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Affiliation(s)
- Pablo Villarreal
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Carlos A Villarroel
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile.,Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile.,Instituto de Investigación Interdisciplinaria (I3), Universidad de Talca, Talca, Chile
| | - Sam O'Donnell
- Laboratory of Computational and Quantitative Biology, CNRS, Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France
| | - Nicolas Agier
- Laboratory of Computational and Quantitative Biology, CNRS, Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France
| | - Julian F Quintero-Galvis
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile.,Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Tomas A Peña
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Roberto F Nespolo
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile.,Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile.,Center of Applied Ecology and Sustainability (CAPES), Facultad de Ciencias Biológicas, Universidad Católica de Chile, Santiago, Chile.,Millenium Nucleus of Patagonian Limit of Life (LiLi), Valdivia, Chile
| | - Gilles Fischer
- Laboratory of Computational and Quantitative Biology, CNRS, Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France
| | - Cristian Varela
- The Australian Wine Research Institute, Glen Osmond, Adelaide, South Australia, Australia.,Department of Wine and Food Science, University of Adelaide, Glen Osmond, Adelaide, South Australia, Australia
| | - Francisco A Cubillos
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile.,Millenium Nucleus of Patagonian Limit of Life (LiLi), Valdivia, Chile
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2
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Mozzachiodi S, Bai FY, Baldrian P, Bell G, Boundy-Mills K, Buzzini P, Čadež N, Riffo FC, Dashko S, Dimitrov R, Fisher KJ, Gibson BR, Gouliamova D, Greig D, Heistinger L, Hittinger CT, Jecmenica M, Koufopanou V, Landry CR, Mašínová T, Naumova ES, Opulente D, Peña JJ, Petrovič U, Tsai IJ, Turchetti B, Villarreal P, Yurkov A, Liti G, Boynton P. Yeasts from temperate forests. Yeast 2022; 39:4-24. [PMID: 35146791 DOI: 10.1002/yea.3699] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Yeasts are ubiquitous in temperate forests. While this broad habitat is well-defined, the yeasts inhabiting it and their life cycles, niches, and contributions to ecosystem functioning are less understood. Yeasts are present on nearly all sampled substrates in temperate forests worldwide. They associate with soils, macroorganisms, and other habitats, and no doubt contribute to broader ecosystem-wide processes. Researchers have gathered information leading to hypotheses about yeasts' niches and their life cycles based on physiological observations in the laboratory as well as genomic analyses, but the challenge remains to test these hypotheses in the forests themselves. Here we summarize the habitat and global patterns of yeast diversity, give some information on a handful of well-studied temperate forest yeast genera, discuss the various strategies to isolate forest yeasts, and explain temperate forest yeasts' contributions to biotechnology. We close with a summary of the many future directions and outstanding questions facing researchers in temperate forest yeast ecology. Yeasts present an exciting opportunity to better understand the hidden world of microbial ecology in this threatened and global habitat.
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Affiliation(s)
| | - Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha 4, Czech Republic
| | - Graham Bell
- Biology Department and Redpath Museum, McGill University, Québec, Canada
| | - Kyria Boundy-Mills
- Department of Food Science and Technology, University of California Davis, Davis, CA, USA
| | - Pietro Buzzini
- Department of Agriculture, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Italy
| | - Neža Čadež
- Biotechnical Faculty, Food Science and Technology Department, University of Ljubljana, Ljubljana, Slovenia
| | - Francisco Cubillos Riffo
- Universidad de Santiago de Chile, Facultad de Química y Biología, Departamento de Biología, Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Sofia Dashko
- DSM Food Specialties, Center for Food Innovation, AX, Delft, The Netherlands
| | - Roumen Dimitrov
- Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Kaitlin J Fisher
- Laboratory of Genetics, Wisconsin Energy Institute, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, USA
| | - Brian R Gibson
- Technische Universität Berlin, Institute of Food Technology and Food Chemistry, Chair of Brewing and Beverage Technology, Berlin, Germany
| | - Dilnora Gouliamova
- Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Duncan Greig
- Centre for Life's Origins and Evolution, University College London, London, UK
| | - Lina Heistinger
- ETH Zurich, Department of Biology, Institute of Biochemistry, Switzerland
| | - Chris Todd Hittinger
- Laboratory of Genetics, Wisconsin Energy Institute, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | - Christian R Landry
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Canada.,Institut de Biologie Intégrative et des Systèmes, Université Laval, Canada.,PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Canada.,Centre de Recherche sur les Données Massives, Université Laval, Canada.,Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Canada
| | - Tereza Mašínová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha 4, Czech Republic
| | - Elena S Naumova
- State Research Institute of Genetics and Selection of Industrial Microorganisms of National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Dana Opulente
- Department of Biology, Villanova University, Villanova, Pennsylvania, USA
| | | | - Uroš Petrovič
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Ljubljana, Slovenia.,Jožef Stefan Institute, Department of Molecular and Biomedical Sciences, Ljubljana, Slovenia
| | | | - Benedetta Turchetti
- Department of Agriculture, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Italy
| | - Pablo Villarreal
- Universidad de Santiago de Chile, Facultad de Química y Biología, Departamento de Biología, Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Andrey Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Gianni Liti
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
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3
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Chang CF, Liu YR, Naumov GI, Naumova ES, Lee CF. Taxonomy of the yeast genus Vanderwaltozyma and proposal of Vanderwaltozyma meishanica sp. nov., Vanderwaltozyma huisunica sp. nov., and Vanderwaltozyma molinica sp. nov. Antonie van Leeuwenhoek 2020; 113:663-676. [PMID: 31897851 DOI: 10.1007/s10482-019-01376-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 12/10/2019] [Indexed: 11/30/2022]
Abstract
Using electrophoretic karyotyping, RAPD fingerprinting and phylogenetic analysis of ribosomal RNA gene sequences, twenty-six Vanderwaltozyma strains were studied. Out of 19 strains isolated in mountainous areas of Taiwan, eighteen strains were isolated from soil and one strain was isolated from the fruiting body of mushroom, six were identified as V. polyspora and three as V. verrucispora. Based on the results of a multigene sequence analysis (D1/D2, ITS and mitochondrial COX II gene) and DNA-DNA reassociation, three new ascosporic members of the genus Vanderwaltozyma are formally described: V. huisunica sp. nov. (GA1S06T = CBS 12250T = BCRC 23260T), V. meishanica sp. nov. (EN4S02T = CBS 12249T = BCRC 23255T) and V. molinica sp. nov. (GJ8S05T = CBS 12251T = BCRC 23264T), and the holotypes of these novel species are assigned as BCRC 23260T, BCRC 23255T and BCRC 23264T, respectively.
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Affiliation(s)
- Chin-Feng Chang
- Department of Biological Science and Technology, China University of Science and Technology, Taipei, 11581, Taiwan
| | - Yi-Ru Liu
- Department of Applied Science, National Tsing Hua University, Nanda Campus, 521 Nanda Road, Hsinchu, 30014, Taiwan
| | - Gennadi I Naumov
- State Research Institute of Genetics and Selection of Industrial Microorganisms of National Research Centre, Kurchatov Institute, Moscow, Russia
| | - Elena S Naumova
- State Research Institute of Genetics and Selection of Industrial Microorganisms of National Research Centre, Kurchatov Institute, Moscow, Russia
| | - Ching-Fu Lee
- Department of Applied Science, National Tsing Hua University, Nanda Campus, 521 Nanda Road, Hsinchu, 30014, Taiwan.
- Institute of Analytical and Environmental Sciences, National Tsing Hua University, No. 101, Section 2, Kuang-Fu Road, Hsinchu, 30013, Taiwan.
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4
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Porter TJ, Divol B, Setati ME. Lachancea yeast species: Origin, biochemical characteristics and oenological significance. Food Res Int 2019; 119:378-389. [PMID: 30884668 DOI: 10.1016/j.foodres.2019.02.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 01/30/2019] [Accepted: 02/01/2019] [Indexed: 11/29/2022]
Abstract
The genus Lachancea, first proposed in 2003, currently comprises 12 valid species, all found to have eight chromosomes. Lachancea spp. occupy a myriad of natural and anthropic habitats, and their geographic as well as ecological origin have been identified as key drivers in the genetic variations amongst strains of several of the species. Lachancea thermotolerans is the type species of the genus and also the most widely explored, especially for its role in fermentation environments. Indeed, L. thermotolerans is desired for its ability to acidify beer and wine through the production of lactic acid, and to enhance aroma and flavor through increased production of various compounds. Similarly, L. fermentati has been characterized for its potential contribution to the chemical composition of these beverages, albeit to a lesser extent, while other species have received little attention. Overall, members of the genus Lachancea form part of the microbiomes in many fermentation ecosystems and contribute directly or indirectly to the modulation of aroma and flavor of different products. The current review provides an overview of this genus, including the latest reports on the genetic and biochemical characteristics of member species, as well as their biotechnological potential.
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Affiliation(s)
- Tristan Jade Porter
- Institute for Wine Biotechnology, Department of Viticulture and Oenology, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Benoit Divol
- Institute for Wine Biotechnology, Department of Viticulture and Oenology, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Mathabatha Evodia Setati
- Institute for Wine Biotechnology, Department of Viticulture and Oenology, Stellenbosch University, Stellenbosch 7600, South Africa.
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5
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Vakirlis N, Sarilar V, Drillon G, Fleiss A, Agier N, Meyniel JP, Blanpain L, Carbone A, Devillers H, Dubois K, Gillet-Markowska A, Graziani S, Huu-Vang N, Poirel M, Reisser C, Schott J, Schacherer J, Lafontaine I, Llorente B, Neuvéglise C, Fischer G. Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus. Genome Res 2016; 26:918-32. [PMID: 27247244 PMCID: PMC4937564 DOI: 10.1101/gr.204420.116] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 04/28/2016] [Indexed: 12/22/2022]
Abstract
Reconstructing genome history is complex but necessary to reveal quantitative principles governing genome evolution. Such reconstruction requires recapitulating into a single evolutionary framework the evolution of genome architecture and gene repertoire. Here, we reconstructed the genome history of the genus Lachancea that appeared to cover a continuous evolutionary range from closely related to more diverged yeast species. Our approach integrated the generation of a high-quality genome data set; the development of AnChro, a new algorithm for reconstructing ancestral genome architecture; and a comprehensive analysis of gene repertoire evolution. We found that the ancestral genome of the genus Lachancea contained eight chromosomes and about 5173 protein-coding genes. Moreover, we characterized 24 horizontal gene transfers and 159 putative gene creation events that punctuated species diversification. We retraced all chromosomal rearrangements, including gene losses, gene duplications, chromosomal inversions and translocations at single gene resolution. Gene duplications outnumbered losses and balanced rearrangements with 1503, 929, and 423 events, respectively. Gene content variations between extant species are mainly driven by differential gene losses, while gene duplications remained globally constant in all lineages. Remarkably, we discovered that balanced chromosomal rearrangements could be responsible for up to 14% of all gene losses by disrupting genes at their breakpoints. Finally, we found that nonsynonymous substitutions reached fixation at a coordinated pace with chromosomal inversions, translocations, and duplications, but not deletions. Overall, we provide a granular view of genome evolution within an entire eukaryotic genus, linking gene content, chromosome rearrangements, and protein divergence into a single evolutionary framework.
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Affiliation(s)
- Nikolaos Vakirlis
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005, Paris, France
| | - Véronique Sarilar
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Guénola Drillon
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005, Paris, France
| | - Aubin Fleiss
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005, Paris, France
| | - Nicolas Agier
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005, Paris, France
| | - Jean-Philippe Meyniel
- ISoft, Route de l'Orme, Parc "Les Algorithmes" Bâtiment Euclide, 91190 Saint-Aubin, France
| | - Lou Blanpain
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Alessandra Carbone
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005, Paris, France
| | - Hugo Devillers
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Kenny Dubois
- CRCM, CNRS, UMR7258, Inserm, U1068; Institut Paoli-Calmettes, Aix-Marseille Université, UM 105, F-13009, Marseille, France
| | - Alexandre Gillet-Markowska
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005, Paris, France
| | - Stéphane Graziani
- ISoft, Route de l'Orme, Parc "Les Algorithmes" Bâtiment Euclide, 91190 Saint-Aubin, France
| | - Nguyen Huu-Vang
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Marion Poirel
- ISoft, Route de l'Orme, Parc "Les Algorithmes" Bâtiment Euclide, 91190 Saint-Aubin, France
| | - Cyrielle Reisser
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS, UMR 7156, 67083 Strasbourg, France
| | - Jonathan Schott
- CRCM, CNRS, UMR7258, Inserm, U1068; Institut Paoli-Calmettes, Aix-Marseille Université, UM 105, F-13009, Marseille, France
| | - Joseph Schacherer
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS, UMR 7156, 67083 Strasbourg, France
| | - Ingrid Lafontaine
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005, Paris, France
| | - Bertrand Llorente
- CRCM, CNRS, UMR7258, Inserm, U1068; Institut Paoli-Calmettes, Aix-Marseille Université, UM 105, F-13009, Marseille, France
| | - Cécile Neuvéglise
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Gilles Fischer
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005, Paris, France
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6
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Freel KC, Charron G, Leducq JB, Landry CR, Schacherer J. Lachancea quebecensis sp. nov., a yeast species consistently isolated from tree bark in the Canadian province of Québec. Int J Syst Evol Microbiol 2016; 65:3392-3399. [PMID: 26297665 DOI: 10.1099/ijsem.0.000426] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
A thorough sampling of maple, oak, birch, and apple tree bark in North America yielded a set of isolates that represent a yeast species not yet formally described. The strains obtained were all isolated from the Canadian province of Québec. These four isolates have identical electrophoretic karyotypes, distinct from other species of the genus Lachancea, and are most closely related to the formally recognized species Lachancea thermotolerans according to the D1/D2 domain of the LSU rDNA gene and 5.8S–ITS region. Previous studies revealed the existence of a population of strains closely related to L. thermotolerans, with unique D1/D2 sequences and the ability to grow on melibiose, which is also true for these isolates. The sequences obtained here (for the D1/D2, and 5.8S–ITS region) are identical among the four strains, and in a phylogenetic analysis of the D1/D2 region, the strains form a distinct clade with the previously described population closely related to L. thermotolerans, composed of isolates from Japan, as well as from the provinces of Ontario and Québec in Canada. On the basis of select physiological and phylogenetic characteristics, a novel ascosporogenous yeast species, Lachancea quebecensis sp. nov., is proposed. The type strain LL11_022T ( = CBS 14138T = CLIB 1763T = UCDFST 15-106T) was isolated from maple tree bark in the Station Duchesnay, QC region of Québec, Canada. The MycoBank number is MB811749.
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Affiliation(s)
- Kelle C Freel
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS, UMR7156, Strasbourg, France
| | - Guillaume Charron
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, PROTEO Université Laval, Québec, Canada
| | - Jean-Baptiste Leducq
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, PROTEO Université Laval, Québec, Canada
| | - Christian R Landry
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, PROTEO Université Laval, Québec, Canada
| | - Joseph Schacherer
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS, UMR7156, Strasbourg, France
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7
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Cadete RM, Cheab MAM, Santos RO, Safar SVB, Zilli JE, Vital MJS, Basso LC, Lee CF, Kurtzman CP, Lachance MA, Rosa CA. Cyberlindnera xylosilytica sp. nov., a xylitol-producing yeast species isolated from lignocellulosic materials. Int J Syst Evol Microbiol 2015; 65:2968-2974. [PMID: 26025941 DOI: 10.1099/ijs.0.000363] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Independent surveys of yeasts associated with lignocellulosic-related materials led to the discovery of a novel yeast species belonging to the Cyberlindnera clade (Saccharomycotina, Ascomycota). Analysis of the sequences of the internal transcribed spacer (ITS) region and the D1/D2 domains of the large subunit rRNA gene showed that this species is related to C. japonica, C. maesa and C. easanensis. Six isolates were obtained from different sources, including rotting wood, tree bark and sugar cane filter cake in Brazil, frass from white oak in the USA and decayed leaf in Taiwan. A novel species is suggested to accommodate these isolates, for which the name C. xylosilytica sp. nov. is proposed. The type strain of C. xylosilytica sp. nov. is NRRL YB-2097(T) ( = CBS 13984(T) = UFMG-CM-Y347(T)) and the allotype is UFMG-CM-Y409 ( = CBS 14083). The novel species is heterothallic and complementary mating types are represented by the type and allotype strains. The MycoBank number is MB 811428.
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Affiliation(s)
- Raquel M Cadete
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Monaliza A M Cheab
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Renata O Santos
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Silvana V B Safar
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | | | - Marcos J S Vital
- Departamento de Biologia, Universidade Federal de Roraima, Campus do Paricarana, Boa Vista, Brazil
| | - Luiz C Basso
- Departamento de Ciências Biológicas, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Ching-Fu Lee
- Department of Applied Science, National Hsinchu University of Education, Hsinchu, 300 Taiwan, ROC
| | - Cletus P Kurtzman
- Bacterial Foodborne Pathogens and Mycology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, US Department of Agriculture, Peoria, IL, 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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8
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Hagler AN, Ribeiro JRA, Pinotti T, Brandão LR, Pimenta RS, Lins U, Lee CF, Hsieh CW, Lachance MA, Rosa CA. Wickerhamiella slavikovae sp. nov. and Wickerhamiella goesii sp. nov., two yeast species isolated from natural substrates. Int J Syst Evol Microbiol 2013; 63:3099-3103. [PMID: 23710055 DOI: 10.1099/ijs.0.051953-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two novel yeast species were isolated during three independent studies of yeasts associated with natural substrates in Brazil and Taiwan. Analysis of the sequences of the D1/D2 domains of the large subunit rRNA gene showed that these novel species belong to the Wickerhamiella clade. The first was isolated from freshwater and a leaf of sugar cane (Saccharum officinarum) in Brazil and from leaves of Wedelia biflora in Taiwan. Described here as Wickerhamiella slavikovae sp. nov., it differs by 56 nucleotide substitutions and 19 gaps in the D1/D2 region of the large subunit rRNA gene from Candida sorbophila, the least divergent species. The second species, named Wickerhamiella goesii sp. nov., was isolated from leaves and the rhizosphere of sugar cane collected in Rio de Janeiro, Brazil. The species differs by 54 nucleotide substitutions and nine gaps in the D1/D2 domains from Candida drosophilae, its least divergent relative. The type strains are Wickerhamiella slavikovae sp. nov. IMUFRJ 52096T ( = CBS 12417T = DBVPG 8032T) and Wickerhamiella goesii sp. nov. IMUFRJ 52102T ( = CBS 12419T = DBVPG 8034T).
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Affiliation(s)
- Allen N. Hagler
- Departamento de Microbiologia, Instituto de Microbiologia Prof. Paulo de Goes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - José R. A. Ribeiro
- Departamento de Microbiologia, Instituto de Microbiologia Prof. Paulo de Goes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - T. Pinotti
- Departamento de Microbiologia, Instituto de Microbiologia Prof. Paulo de Goes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luciana R. Brandão
- Departamento de Microbiologia, ICB, C. P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG 3120-901, Brazil
| | - Raphael S. Pimenta
- Laboratório de Microbiologia Ambiental e Biotecnologia, Campus Universitário de Palmas, Universidade Federal do Tocantins, 77020220 Palmas, TO, Brazil
| | - U. Lins
- Departamento de Microbiologia, Instituto de Microbiologia Prof. Paulo de Goes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ching-Fu Lee
- Department of Applied Science, National Hsinchu University of Education, 521 Nanda Road, Hsinchu 30014, Taiwan, ROC
| | - Chin-Wen Hsieh
- Department of Applied Science, National Hsinchu University of Education, 521 Nanda Road, Hsinchu 30014, Taiwan, ROC
| | - 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 3120-901, Brazil
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9
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Lachancea lanzarotensis sp. nov., an ascomycetous yeast isolated from grapes and wine fermentation in Lanzarote, Canary Islands. Int J Syst Evol Microbiol 2013; 63:358-363. [DOI: 10.1099/ijs.0.046029-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During the characterization of the microbiota biodiversity associated with grapes and wineries in different bioclimatic conditions of the Canary Islands (Spain), a novel yeast species was isolated from Lanzarote, the driest wine-producing region of the archipelago. Seven strains isolated from grapes, microvinifications and wineries are described. Sequence analysis of the D1/D2 domain of the LSU rDNA gene and 5.8S-ITS regions revealed that the isolates were phylogenetically a member of the genus Lachancea and are closely related to Lachancea meyersii NRRL Y-27269T and Lachancea nothofagi NRRL Y-48670T. On the basis of morphological, biochemical and physiological characterization and phylogenetic analysis, a novel ascosporogenous yeast species, Lachancea lanzarotensis sp. nov., is proposed. The type strain is L2C-15T ( = CBS 12615T = CECT 13066T) which was isolated from grape berries of Vitis vinifera L. cv. Listán Negro red grape variety in Tinajo, Lanzarote. The MycoBank no. is MB 801390.
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10
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Friedrich A, Jung PP, Hou J, Neuvéglise C, Schacherer J. Comparative mitochondrial genomics within and among yeast species of the Lachancea genus. PLoS One 2012; 7:e47834. [PMID: 23112855 PMCID: PMC3480396 DOI: 10.1371/journal.pone.0047834] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 09/21/2012] [Indexed: 12/18/2022] Open
Abstract
Yeasts are leading model organisms for mitochondrial genome studies. The explosion of complete sequence of yeast mitochondrial (mt) genomes revealed a wide diversity of organization and structure between species. Recently, genome-wide polymorphism survey on the mt genome of isolates of a single species, Lachancea kluyveri, was also performed. To compare the mitochondrial genome evolution at two hierarchical levels: within and among closely related species, we focused on five species of the Lachancea genus, which are close relatives of L. kluyveri. Hence, we sequenced the complete mt genome of L. dasiensis, L. nothofagi, L. mirantina, L. fantastica and L. meyersii. The phylogeny of the Lachancea genus was explored using these data. Analysis of intra- and interspecific variability across the whole Lachancea genus led to the same conclusions regarding the mitochondrial genome evolution. These genomes exhibit a similar architecture and are completely syntenic. Nevertheless, genome sizes vary considerably because of the variations of the intergenic regions and the intron content, contributing to mitochondrial genome plasticity. The high variability of the intergenic regions stands in contrast to the high level of similarity of protein sequences. Quantification of the selective constraints clearly revealed that most of the mitochondrial genes are under purifying selection in the whole genus.
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Affiliation(s)
- Anne Friedrich
- Department of Genetics, Genomics and Microbiology, University of Strasbourg, CNRS, UMR7156, Strasbourg, France
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11
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Naumov GI, Lee CF, Naumova ES. Molecular genetic diversity of the Saccharomyces yeasts in Taiwan: Saccharomyces arboricola, Saccharomyces cerevisiae and Saccharomyces kudriavzevii. Antonie van Leeuwenhoek 2012; 103:217-28. [PMID: 22941248 DOI: 10.1007/s10482-012-9803-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 08/20/2012] [Indexed: 10/27/2022]
Abstract
Genetic hybridization, sequence and karyotypic analyses of natural Saccharomyces yeasts isolated in different regions of Taiwan revealed three biological species: Saccharomyces arboricola, Saccharomyces cerevisiae and Saccharomyces kudriavzevii. Intraspecies variability of the D1/D2 and ITS1 rDNA sequences was detected among S. cerevisiae and S. kudriavzevii isolates. According to molecular and genetic analyses, the cosmopolitan species S. cerevisiae and S. kudriavzevii contain local divergent populations in Taiwan, Malaysia and Japan. Six of the seven known Saccharomyces species are documented in East Asia: S. arboricola, S. bayanus, S. cerevisiae, S. kudriavzevii, S. mikatae, and S. paradoxus.
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Affiliation(s)
- Gennadi I Naumov
- State Institute for Genetics and Selection of Industrial Microorganisms, 1-Dorozhnyi 1, Moscow, 117545, Russia.
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12
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Mestre MC, Ulloa JR, Rosa CA, Lachance MA, Fontenla S. Lachancea nothofagi sp. nov., a yeast associated with Nothofagus species in Patagonia, Argentina. Int J Syst Evol Microbiol 2010; 60:2247-2250. [DOI: 10.1099/ijs.0.018929-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Six strains of a novel yeast species were isolated from Nothofagus species trees in native forests in Patagonia, Argentina. The strains were isolated from bark, fluxes and the ectomycorrhizospheric soil fraction of Nothofagus antarctica, Nothofagus nervosa and Nothofagus pumilio. Analysis of the D1/D2 large-subunit rDNA sequences indicated that the novel species belonged to the genus Lachancea and is closely related to Lachancea meyersii. The name Lachancea nothofagi sp. nov. is proposed to accommodate these strains. The type strain is UWOPS 99-807.3T (=CBS 11611T=NRRL Y-48670T).
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Affiliation(s)
- M. C. Mestre
- Laboratorio de Microbiología Aplicada y Biotecnología, Centro Regional Universitario Bariloche (CRUB), INIBIOMA (Universidad Nacional del Comahue-CONICET), Quintral 1250, Bariloche 8400, Río Negro, Argentina
| | - J. R. Ulloa
- Laboratorio de Microbiología Aplicada y Biotecnología, Centro Regional Universitario Bariloche (CRUB), INIBIOMA (Universidad Nacional del Comahue-CONICET), Quintral 1250, Bariloche 8400, Río Negro, Argentina
| | - C. A. Rosa
- Departamento de Microbiologia – ICB, CP 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - M. A. Lachance
- Department of Biology, University of Western Ontario, London, ON N6A 5B7, Canada
| | - S. Fontenla
- Laboratorio de Microbiología Aplicada y Biotecnología, Centro Regional Universitario Bariloche (CRUB), INIBIOMA (Universidad Nacional del Comahue-CONICET), Quintral 1250, Bariloche 8400, Río Negro, Argentina
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13
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Canelhas MR, Barbosa AC, Medeiros AO, Lee CF, Huang LY, Lachance MA, Rosa CA. Saturnispora serradocipensis sp. nov. and Saturnispora gosingensis sp. nov., two ascomycetous yeasts from ephemeral habitats. Antonie van Leeuwenhoek 2010; 99:241-7. [DOI: 10.1007/s10482-010-9482-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Accepted: 06/25/2010] [Indexed: 11/24/2022]
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14
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Pereira LF, Costa CRL, Brasileiro BTRV, de Morais MA. Lachancea mirantina sp. nov., an ascomycetous yeast isolated from the cachaca fermentation process. Int J Syst Evol Microbiol 2010; 61:989-992. [PMID: 20435746 DOI: 10.1099/ijs.0.020008-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the present work, a novel ascomycete species, Lachancea mirantina sp. nov., isolated from the fermentation process that produces cachaça, a Brazilian spirit, is proposed. Nucleotide sequence analysis of the 26S D1/D2 rDNA locus showed that L. mirantina sp. nov. was genetically related to Lachancea cidri and Lachancea fermentati, although some physiological traits showed remarkable differences. Analysis of the D1/D2 large-subunit rDNA molecular marker showed a clear distinction among all three species, confirming that L. mirantina sp. nov. belongs to a separate taxonomic species in the Lachancea clade. The type strain of Lachancea mirantina sp. nov. is URM 5925(T) ( = CLIB 1160(T) = CBS 11717(T)).
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Affiliation(s)
- Luciana Filgueira Pereira
- Grupo Interdepartamental de Engenharia Metabólica, CCB, Universidade Federal de Pernambuco, Recife, PE 50760-901, Brazil
| | | | | | - Marcos Antonio de Morais
- Departamento de Genética, CCB, Universidade Federal de Pernambuco, Recife, PE 50760-901, Brazil
- Grupo Interdepartamental de Engenharia Metabólica, CCB, Universidade Federal de Pernambuco, Recife, PE 50760-901, Brazil
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15
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Chang CF, Yao CH, Young SS, Limtong S, Kaewwichian R, Srisuk N, Lee CF. Candida gosingica sp. nov., an anamorphic ascomycetous yeast closely related to Scheffersomyces spartinae. Int J Syst Evol Microbiol 2010; 61:690-694. [PMID: 20382788 DOI: 10.1099/ijs.0.020511-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During surveys on yeast diversity in forest soils from Taiwan and Thailand, ten yeast strains isolated from different samples were found to have similar molecular and physiological characteristics. Sequence analysis of small subunit (SSU) rDNA, the D1/D2 domain of large subunit (LSU) rDNA and internal transcribed spacer (ITS)-5.8S rDNA demonstrated that these strains were closely related to Scheffersomyces spartinae. The novel strains could be differentiated from S. spartinae by a 0.9 % sequence divergence (5 substitutions, 0 gaps) in the D1/D2 domain of LSU rDNA, a 1.5 % divergence (8 substitutions, 0 gaps) in the ITS-5.8S rDNA and a 0.7 % divergence (12 substitutions, 2 gaps) in the SSU rDNA. The novel strains also showed specific patterns of electrophoretic karyotypes that differed from that of S. spartinae. Therefore, a novel yeast species, Candida gosingica sp. nov., is proposed to accommodate these strains. The type strain SJ7S11(T) (=BCRC 23194(T)=CBS 11433(T)) was assigned and deposited in the Bioresource Collection and Research Center (BCRC), Food Industry Development and Research Institute, Hsinchu, Taiwan, and Centraalbureau voor Schimmelcultures (CBS), Utrecht, The Netherlands.
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Affiliation(s)
- Chin-Feng Chang
- Department of Applied Science, National Hsinchu University of Education, 521 Nanda Rd, Hsinchu 30014, Taiwan
| | - Cheng-Hsu Yao
- Department of Applied Science, National Hsinchu University of Education, 521 Nanda Rd, Hsinchu 30014, Taiwan
| | - Shuh-Sen Young
- Department of Applied Science, National Hsinchu University of Education, 521 Nanda Rd, Hsinchu 30014, Taiwan
| | - Savitree Limtong
- Department of Microbiology, Kasetsart University, Bangkok 10900, Thailand
| | | | - Nantana Srisuk
- Department of Microbiology, Kasetsart University, Bangkok 10900, Thailand
| | - Ching-Fu Lee
- Department of Applied Science, National Hsinchu University of Education, 521 Nanda Rd, Hsinchu 30014, Taiwan
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16
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Current awareness on yeast. Yeast 2010. [DOI: 10.1002/yea.1713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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17
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Lee CF, Yao CH, Liu YR, Young SS, Chang KS. Kazachstania wufongensis sp. nov., an ascosporogenous yeast isolated from soil in Taiwan. Antonie van Leeuwenhoek 2009; 95:335-41. [DOI: 10.1007/s10482-009-9319-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2008] [Accepted: 02/10/2009] [Indexed: 12/01/2022]
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