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Gay EJ, Jacques N, Lapalu N, Cruaud C, Laval V, Balesdent MH, Rouxel T. Location and timing govern tripartite interactions of fungal phytopathogens and host in the stem canker species complex. BMC Biol 2023; 21:247. [PMID: 37936151 PMCID: PMC10631019 DOI: 10.1186/s12915-023-01726-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 10/05/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUND Leptosphaeria maculans "brassicae" (Lmb) and Leptosphaeria biglobosa "brassicae" (Lbb) make up a species complex involved in the stem canker (blackleg) disease of rapeseed (Brassica napus). They coinfect rapeseed together, from the early stage of infection on leaves to the final necrotic stage at the stem base, and both perform sexual crossings on plant residues. L. biglobosa is suggested to be a potential biocontrol agent against Lmb, but there has been no mechanistic investigation of the different types of interactions that may occur between the plant and the two fungal species. RESULTS We investigated the bi- or tripartite interaction mechanisms by (i) confronting Lmb and Lbb in culture conditions or during cotyledon infection, with different timing and/or spore concentration regimes, (ii) performing RNA-Seq experiments in vitro or on the kinetics of infection of cotyledons infected by Lmb and/or Lbb to evaluate the transcriptomic activity and the plant response when both fungal species are inoculated together. Lbb infection of B. napus cotyledons was typical of a necrotrophic behavior, with a very early setup of one pathogenicity program and very limited colonization of tissues. This contrasted with the complex succession of pathogenicity programs of the hemibiotroph Lmb. During simultaneous co-infection by both species, Lmb was strongly impacted in its growth and transcriptomic dynamics both in vitro and in planta, while Lbb was unaffected by the presence of Lmb. However, the drastic inhibition of Lmb growth by Lbb was ineffective in the case of delayed inoculation with Lbb or a lower amount of spores of Lbb compared to Lmb. CONCLUSIONS Our data suggest that Lmb growth inhibition by Lbb is the result of a combination of factors that may include competition for trophic resources, the generation by Lbb of an environment unsuitable for the lifecycle of Lmb or/and the effect on Lmb of plant defense responses induced by Lbb. It indicates that growth inhibition occurs in very specific conditions (i.e., co-inoculation at the same place of an equal amount of inoculum) that are unlikely to occur in the field where their coexistence does not prevent any species from completing their life cycle.
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Affiliation(s)
- Elise J Gay
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Noémie Jacques
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Nicolas Lapalu
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Corinne Cruaud
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Valerie Laval
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | | | - Thierry Rouxel
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France.
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Tinsley CR, Jacques N, Lucas M, Grondin C, Legras JL, Casaregola S. Molecular Genetic Analysis with Microsatellite-like Loci Reveals Specific Dairy-Associated and Environmental Populations of the Yeast Geotrichum candidum. Microorganisms 2022; 10:103. [PMID: 35056553 PMCID: PMC8780849 DOI: 10.3390/microorganisms10010103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/23/2021] [Accepted: 12/27/2021] [Indexed: 02/01/2023] Open
Abstract
Geotrichum candidum is an environmental yeast, also found as part of the cheese surface microbiota, where it is important in the ripening of many traditional cheeses, such as Camembert. We have previously developed a Multi Locus Sequence Typing (MLST) scheme, which differentiated five clades, of which one contained only environmental isolates, two were composed almost entirely of dairy isolates, and two others contained a mixture of dairy, environmental, and miscellaneous food isolates. In order to provide a simple method to uniquely type G. candidum strains, and in addition to permit investigation of the population structure at a fine level, we describe here a molecular analysis using a set of twelve highly discriminating microsatellite-like markers. The present study consolidates the previously suggested division between dairy and environmental strains, and in addition distinguishes a specifically European group of environmental strains. This analysis permitted the discrimination of 72 genotypes from the collection of 80 isolates, while retaining the underlying meaningful phylogenetic relation between groups of strains.
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Affiliation(s)
- Colin R. Tinsley
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (C.R.T.); (N.J.); (M.L.); (C.G.); (S.C.)
- Unité Microbiologie et Génétique Moléculaire, Department des Sciences de la Vie et Santé, AgroParisTech, 16 Rue Claude Bernard, 75005 Paris, France
| | - Noémie Jacques
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (C.R.T.); (N.J.); (M.L.); (C.G.); (S.C.)
| | - Marine Lucas
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (C.R.T.); (N.J.); (M.L.); (C.G.); (S.C.)
| | - Cécile Grondin
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (C.R.T.); (N.J.); (M.L.); (C.G.); (S.C.)
- SPO, Université de Montpellier, INRAE, Institut Agro, 34000 Montpellier, France
| | - Jean-Luc Legras
- SPO, Université de Montpellier, INRAE, Institut Agro, 34000 Montpellier, France
| | - Serge Casaregola
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (C.R.T.); (N.J.); (M.L.); (C.G.); (S.C.)
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Devillers H, Sarilar V, Grondin C, Sterck L, Segond D, Jacques N, Sicard D, Casaregola S, Tinsley C. OUP accepted manuscript. Genome Biol Evol 2022; 14:6519748. [PMID: 35106561 PMCID: PMC8825440 DOI: 10.1093/gbe/evac007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2022] [Indexed: 11/23/2022] Open
Abstract
Recent studies have suggested that species of the Kazachstania genus may be interesting models of yeast domestication. Among these, Kazachstania barnettii has been isolated from various microbially transformed foodstuffs such as sourdough bread and kefir. In the present work, we sequence, assemble, and annotate the complete genomes of two K. barnettii strains: CLIB 433, being one of the two reference strains for K. barnettii that was isolated as a spoilage organism in soft drink, and CLIB 1767, recently isolated from artisan bread-making sourdough. Both assemblies are of high quality with N50 statistics greater than 1.3 Mb and BUSCO score greater than 99%. An extensive comparison of the two obtained genomes revealed very few differences between the two K. barnettii strains, considering both genome structure and gene content. The proposed genome assemblies will constitute valuable references for future comparative genomic, population genomic, or transcriptomic studies of the K. barnettii species.
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Affiliation(s)
- Hugo Devillers
- SPO, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
- Corresponding author: E-mail:
| | - Véronique Sarilar
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
- French Armed Forces Biomedical Research Institute (IRBA), Department of Platforms and Technology Research, Molecular Biology Unit, Brétigny-sur-Orge, France
| | - Cécile Grondin
- SPO, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Lieven Sterck
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Diego Segond
- SPO, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
| | - Noémie Jacques
- Université Paris-Saclay, INRAE, UMR BIOGER, Thiverval-Grignon, France
| | - Delphine Sicard
- SPO, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
| | - Serge Casaregola
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Colin Tinsley
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
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Sakpuntoon V, Angchuan J, Boonmak C, Khunnamwong P, Jacques N, Grondin C, Casaregola S, Srisuk N. Savitreea pentosicarens gen. nov., sp. nov., a yeast species in the family Saccharomycetaceae isolated from a grease trap. Int J Syst Evol Microbiol 2020; 70:5665-5670. [PMID: 32924919 DOI: 10.1099/ijsem.0.004457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains (DMKU-GTCP10-8 and CLIB 1740) representing a novel anamorphic yeast species were isolated from a grease sample collected from a grease trap in Thailand and from an unidentified fungus collected in French Guiana, respectively. On the basis of phylogenetic analysis based on the combined D1/D2 domain of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region, Lachancea fermentati CBS 707T was the closely related species with 12.8 % sequence divergence (70 nucleotide substitutions and three gaps in 571 nucleotides) and 28.1 % sequence divergence (93 nucleotide substitutions and 90 gaps in 651 nucleotides) in the D1/D2 domain of the LSU rRNA gene and the ITS region, respectively. Phylogenetic analysis based on the concatenated sequences of the five genes including the small subunit rRNA gene, the D1/D2 domain of the LSU rRNA gene, the ITS region, translation elongation factor-1 alpha (TEF1) and RNA polymerase II subunit 2 (RPB2) genes confirmed that the two strains (DMKU-GTCP10-8 and CLIB 1740) were well-separated from other described yeast genera in Saccharomycetaceae. Hence, Savitreea pentosicarens gen. nov., sp. nov. is proposed to accommodate these two strains as members of the family Saccharomycetaceae. The holotype is S. pentosicarens DMKU-GTCP10-8T (ex-type strain TBRC 12159=PYCC 8490; MycoBank number 835044).
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Affiliation(s)
- Varunya Sakpuntoon
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Jirameth Angchuan
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Chanita Boonmak
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Pannida Khunnamwong
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Noémie Jacques
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Cécile Grondin
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, CIRM-Levures, 78350, Jouy-en-Josas, France
| | - Serge Casaregola
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, CIRM-Levures, 78350, Jouy-en-Josas, France
| | - Nantana Srisuk
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
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Allonneau A, Mercier S, Menguy-Fleuriot A, Luu S, Louyot C, Nicolas A, Jost D, Jacques N, Bignand M. Étude de l’exposition aux fumées d’incendie des sapeurs-pompiers affectés en structure de feu contrôlé. ARCH MAL PROF ENVIRO 2019. [DOI: 10.1016/j.admp.2019.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Lopes MR, Santos ARO, Moreira JD, Santa-Brígida R, Martins MB, Pinto FO, Valente P, Morais PB, Jacques N, Grondin C, Casaregola S, Lachance MA, Rosa CA. Kurtzmaniella hittingeri f.a., sp. nov., isolated from rotting wood and fruits, and transfer of three Candida species to the genus Kurtzmaniella as new combinations. Int J Syst Evol Microbiol 2019; 69:1504-1508. [DOI: 10.1099/ijsem.0.003337] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Mariana R. Lopes
- 1Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Ana Raquel O. Santos
- 1Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Juliana D. Moreira
- 1Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | | | | | - Fernanda O. Pinto
- 3Departamento de Microbiologia, Imunologia e Parasitologia, ICBS, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 90050-170, Brazil
| | - Patrícia Valente
- 3Departamento de Microbiologia, Imunologia e Parasitologia, ICBS, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 90050-170, Brazil
| | - Paula B. Morais
- 4Laboratório de Microbiologia Ambiental e Biotecnologia, Universidade Federal do Tocantins, Palmas, TO, 77020-220, Brazil
| | - Noémie Jacques
- 5Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Universite Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Cécile Grondin
- 5Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Universite Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Serge Casaregola
- 5Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Universite Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Marc-André Lachance
- 6Department of Biology, University of Western Ontario, N6A 5B7, London, Ontario, Canada
| | - Carlos A. Rosa
- 1Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
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Jacques N, Casaregola S. Large biodiversity of yeasts in French Guiana and the description of Suhomyces coccinellae f.a. sp. nov. and Suhomyces faveliae f.a. sp. nov. Int J Syst Evol Microbiol 2019; 69:1634-1649. [PMID: 31033433 DOI: 10.1099/ijsem.0.003369] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The extent of the diversity of yeasts in tropical rain forest and different environments from French Guiana was investigated. A total of 365 samples were collected from various substrates, such as plants, fruits and insects, at 13 locations, yielding 276 pure yeast isolates. Sequence analysis of the D1/D2 domains of the large subunit rRNA gene indicated that 210 isolates out of 276 belonged to 82 described species (67 Saccharomycotina, 14 Basidiomycota and 1 Pezizomycotina). In addition to these, a total of 54 Saccharomycotina isolates could not be assigned to a known species. These belonged to 14 genera and should be studied further from a taxonomic point of view. In addition, among the 43 Basidiomycotina isolates found, 12 could not be assigned to a known species. This report shows an unexpected biodiversity and indicates that oversea territories, such as French Guiana, constitute a largely unexplored reservoir for yeast diversity. Two Saccharomycotina strains, CLIB 1706 and CLIB 1725, isolated from an insect and from a fern respectively, were characterized further and were shown to belong to the Suhomyces clade on the basis of the rDNA sequence comparison. CLIB 1706TrDNA sequences showed nine substitutions and three indels out of 556 bp (D1/D2 domains) and 32 substitutions and 12 indels out of 380 bp [internal transcribed spacer (ITS)] with that of the most closely related species Suhomyces guaymorum CBS 9823T. CLIB 1725T rDNA sequences presented 18 substitutions and one indel out of 549 bp (D1/D2 domains) and 48 substitutions and 11 indels out of 398 bp (ITS) with that of its closest relative Suhomyces vadensis CBS 9454T. Two novel species of the genus Suhomyces were described to accommodate these two strains: Suhomyces coccinellae f.a. sp. nov. (CLIB 1706T=CBS 14298T) and Suhomyces faveliae f.a. sp. nov. (CLIB 1725T=CBS 14299T).
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Affiliation(s)
- Noémie Jacques
- CIRM-Levures, INRA, Micalis Institute, Jouy-en-Josas, France.,†Present address: Bioger, INRA, Thiverval-Grignon, France
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Lachance MA, Vale HMM, Sperandio EM, Carvalho AOS, Santos ARO, Grondin C, Jacques N, Casaregola S, Rosa CA. Wickerhamiella dianesei f.a., sp. nov. and Wickerhamiella kurtzmanii f.a., sp. nov., two yeast species isolated from plants and insects. Int J Syst Evol Microbiol 2018; 68:3351-3355. [DOI: 10.1099/ijsem.0.003000] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Marc-André Lachance
- 1Department of Biology, University of Western Ontario, London Ontario N6A 5B7, Canada
| | - Helson M. M. Vale
- 2Departamento de Fitopatologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília Distrito Federal 70910-900, Brazil
| | - Eugenio M. Sperandio
- 2Departamento de Fitopatologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília Distrito Federal 70910-900, Brazil
| | - Andréa O. S. Carvalho
- 3Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte MG 31270-901, Brazil
| | - Ana R. O. Santos
- 3Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte MG 31270-901, Brazil
| | - Cécile Grondin
- 4Micalis Institute, INRA, CIRM-Levures, Université Paris-Saclay, Jouy-en-Josas 78352, France
| | - Noémie Jacques
- 4Micalis Institute, INRA, CIRM-Levures, Université Paris-Saclay, Jouy-en-Josas 78352, France
| | - Serge Casaregola
- 4Micalis Institute, INRA, CIRM-Levures, Université Paris-Saclay, Jouy-en-Josas 78352, France
| | - Carlos A. Rosa
- 3Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte MG 31270-901, Brazil
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Amoikon TLS, Grondin C, Djéni TN, Jacques N, Casaregola S. Starmerella reginensis f.a., sp. nov. and Starmerella kourouensis f.a., sp. nov., isolated from flowers in French Guiana. Int J Syst Evol Microbiol 2018; 68:2299-2305. [DOI: 10.1099/ijsem.0.002829] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Tiemele Laurent Simon Amoikon
- Laboratoire de Biotechnologie et Microbiologie des Aliments, Unité de Formation et de Recherche en Sciences et Technologie des Aliments (UFR-STA), Université Nangui-Abrogoua, 02 BP 801, Abidjan, 02, Côte d'Ivoire
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Cécile Grondin
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Théodore N'Dédé Djéni
- Laboratoire de Biotechnologie et Microbiologie des Aliments, Unité de Formation et de Recherche en Sciences et Technologie des Aliments (UFR-STA), Université Nangui-Abrogoua, 02 BP 801, Abidjan, 02, Côte d'Ivoire
| | - Noémie Jacques
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Serge Casaregola
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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Into P, Pontes A, Jacques N, Casaregola S, Limtong S, Sampaio JP. Papiliotrema plantarum sp. nov., a novel tremellaceous sexual yeast species. Int J Syst Evol Microbiol 2018; 68:1937-1941. [PMID: 29676729 DOI: 10.1099/ijsem.0.002771] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
During a survey of the yeast community associated with the phylloplane of corn in Thailand, a basidiomycetous yeast strain belonging to the genus Papiliotrema was isolated. Analyses of the D1/D2 domains of the 26S (LSU) rRNA gene and complete ITS region supported the recognition of a novel species, for which the name Papiliotrema plantarum sp. nov. is proposed (type strain DMKU-CP801T=CBS 15220T=PYCC 7257T). Another strain of P. plantarum sp. nov., isolated in French Guiana, was found to be sexually compatible with the Thai isolate and mycelium with clamp connections, basidia and basidiospores were observed in culture. The basidial morphology of P. plantarum combined features previously observed for Papiliotrema bandonii and Papiliotrema fuscus, which represent the only sexual species hitherto known in the genus, i.e. transversely septate basidia, with sexual structures of the Tremella type.
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Affiliation(s)
- Parichat Into
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, Thailand.,UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Ana Pontes
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Noémie Jacques
- CIRM-Levures, Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.,Present address: Bioger, Inra, AgroParisTech, Thiverval-Grignon, France
| | - Serge Casaregola
- CIRM-Levures, Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Savitree Limtong
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Academy of Science, The Royal Society of Thailand, Thailand
| | - José Paulo Sampaio
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
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Sarilar V, Sterck L, Matsumoto S, Jacques N, Neuvéglise C, Tinsley CR, Sicard D, Casaregola S. Genome sequence of the type strain CLIB 1764 T (= CBS 14374 T) of the yeast species Kazachstania saulgeensis isolated from French organic sourdough. Genom Data 2017; 13:41-43. [PMID: 28725555 PMCID: PMC5501885 DOI: 10.1016/j.gdata.2017.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 06/23/2017] [Accepted: 07/04/2017] [Indexed: 12/21/2022]
Abstract
Kazachstania saulgeensis is a recently described species isolated from French organic sourdough. Here, we report the high quality genome sequence of a monosporic segregant of the type strain of this species, CLIB 1764T (= CBS 14374T). The genome has a total length of 12.9 Mb and contains 5326 putative protein-coding genes, excluding pseudogenes and transposons. The nucleotide sequences were deposited into the European Nucleotide Archive under the genome assembly accession numbers FXLY01000001–FXLY01000017.
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Affiliation(s)
- Véronique Sarilar
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Lieven Sterck
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 927, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Saki Matsumoto
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Noémie Jacques
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Cécile Neuvéglise
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Colin R. Tinsley
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Delphine Sicard
- Sciences pour l'œnologie, INRA, Supagro, Université de Montpellier, 34060 Montpellier, France
| | - Serge Casaregola
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350 Jouy-en-Josas, France
- Corresponding author.
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Ribeiro LR, Santos ARO, Groenewald M, Smith MTH, Lara CA, Góes-Neto A, Jacques N, Grondin C, Casaregola S, Lachance MA, Rosa CA. Description of Hyphopichia buzzinii f.a., sp. nov. and Hyphopichia homilentoma comb. nov., the teleomorph of Candida homilentoma. Antonie van Leeuwenhoek 2017; 110:985-994. [DOI: 10.1007/s10482-017-0870-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 03/30/2017] [Indexed: 10/19/2022]
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Jacques N, Mallet S, Laaghouiti F, Tinsley CR, Casaregola S. Specific populations of the yeastGeotrichum candidumrevealed by molecular typing. Yeast 2016; 34:165-178. [DOI: 10.1002/yea.3223] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 11/14/2016] [Accepted: 11/14/2016] [Indexed: 12/20/2022] Open
Affiliation(s)
- Noémie Jacques
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures; Université Paris-Saclay; 78350 Jouy-en-Josas France
| | - Sandrine Mallet
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures; Université Paris-Saclay; 78350 Jouy-en-Josas France
| | - Fatima Laaghouiti
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures; Université Paris-Saclay; 78350 Jouy-en-Josas France
| | - Colin R. Tinsley
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures; Université Paris-Saclay; 78350 Jouy-en-Josas France
| | - Serge Casaregola
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures; Université Paris-Saclay; 78350 Jouy-en-Josas France
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Jacques N, Sarilar V, Urien C, Lopes MR, Morais CG, Uetanabaro APT, Tinsley CR, Rosa CA, Sicard D, Casaregola S. Three novel ascomycetous yeast species of the Kazachstania clade, Kazachstania saulgeensis sp. nov., Kazachstania
serrabonitensis sp. nov. and Kazachstania australis sp. nov. Reassignment of Candida humilis to Kazachstania humilis f.a. comb. nov. and Candida pseudohumilis to Kazachstania pseudohumilis f.a. comb. nov. Int J Syst Evol Microbiol 2016; 66:5192-5200. [DOI: 10.1099/ijsem.0.001495] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Noémie Jacques
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Véronique Sarilar
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Charlotte Urien
- Génétique Quantitative et Evolution-Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Mariana R. Lopes
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Camila G. Morais
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Ana Paula T. Uetanabaro
- Departamento de Ciências Biológicas e Agroindústria, Universidade Estadual Santa Cruz, Ilhéus, BA 45662-900, Brazil
| | - Colin R. Tinsley
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Carlos A. Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Delphine Sicard
- Sciences pour l’œnologie, INRA, Supagro, 34060 Montpellier, France
| | - Serge Casaregola
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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Burgaud G, Coton M, Jacques N, Debaets S, Maciel NOP, Rosa CA, Gadanho M, Sampaio JP, Casaregola S. Yamadazyma barbieri f.a. sp. nov., an ascomycetous anamorphic yeast isolated from a Mid-Atlantic Ridge hydrothermal site (−2300 m) and marine coastal waters. Int J Syst Evol Microbiol 2016; 66:3600-3606. [DOI: 10.1099/ijsem.0.001239] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Gaëtan Burgaud
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, ESIAB, Technopôle de Brest Iroise, 29280 Plouzané, France
| | - Monika Coton
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, ESIAB, Technopôle de Brest Iroise, 29280 Plouzané, France
| | - Noémie Jacques
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Stella Debaets
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, ESIAB, Technopôle de Brest Iroise, 29280 Plouzané, France
| | - Natália O. P. Maciel
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Carlos A. Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Mário Gadanho
- Biosystems and Integrative Sciences Institute (BioISI), Edifício TecLabs, Campus da FCUL, Campo Grande, 1749-016 Lisboa, Portugal
| | - José Paulo Sampaio
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Serge Casaregola
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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Morel G, Sterck L, Swennen D, Marcet-Houben M, Onesime D, Levasseur A, Jacques N, Mallet S, Couloux A, Labadie K, Amselem J, Beckerich JM, Henrissat B, Van de Peer Y, Wincker P, Souciet JL, Gabaldón T, Tinsley CR, Casaregola S. Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts. Sci Rep 2015; 5:11571. [PMID: 26108467 PMCID: PMC4479816 DOI: 10.1038/srep11571] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 05/29/2015] [Indexed: 12/13/2022] Open
Abstract
The evolutionary history of the characters underlying the adaptation of microorganisms to food and biotechnological uses is poorly understood. We undertook comparative genomics to investigate evolutionary relationships of the dairy yeast Geotrichum candidum within Saccharomycotina. Surprisingly, a remarkable proportion of genes showed discordant phylogenies, clustering with the filamentous fungus subphylum (Pezizomycotina), rather than the yeast subphylum (Saccharomycotina), of the Ascomycota. These genes appear not to be the result of Horizontal Gene Transfer (HGT), but to have been specifically retained by G. candidum after the filamentous fungi-yeasts split concomitant with the yeasts' genome contraction. We refer to these genes as SRAGs (Specifically Retained Ancestral Genes), having been lost by all or nearly all other yeasts, and thus contributing to the phenotypic specificity of lineages. SRAG functions include lipases consistent with a role in cheese making and novel endoglucanases associated with degradation of plant material. Similar gene retention was observed in three other distantly related yeasts representative of this ecologically diverse subphylum. The phenomenon thus appears to be widespread in the Saccharomycotina and argues that, alongside neo-functionalization following gene duplication and HGT, specific gene retention must be recognized as an important mechanism for generation of biodiversity and adaptation in yeasts.
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Affiliation(s)
- Guillaume Morel
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
| | - Lieven Sterck
- Department of Plant Systems Biology VIB, Technologiepark 927, 9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium
| | - Dominique Swennen
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
| | - Marina Marcet-Houben
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Djamila Onesime
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
| | - Anthony Levasseur
- INRA UMR1163, Biotechnologie des Champignons Filamenteux, Aix-Marseille Université, Polytech Marseille, 163 avenue de Luminy, CP 925, 13288 Marseille Cedex 09, France
| | - Noémie Jacques
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
| | - Sandrine Mallet
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
| | - Arnaux Couloux
- CEA, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, Évry F-91000, France
| | - Karine Labadie
- CEA, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, Évry F-91000, France
| | - Joëlle Amselem
- INRA UR1164, Unité de Recherche Génomique – Info, 78000 Versailles, France
| | - Jean-Marie Beckerich
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
| | | | - Yves Van de Peer
- Department of Plant Systems Biology VIB, Technologiepark 927, 9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium
- Genomics Research Institute, University of Pretoria, Hatfield Campus, Pretoria 0028, South Africa
| | - Patrick Wincker
- CEA, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, Évry F-91000, France
- CNRS UMR 8030, 2 Rue Gaston Crémieux, Évry, 91000, France
- Université d’Evry, Bd François Mitterand, Evry,91025, France
| | - Jean-Luc Souciet
- Université de Strasbourg, CNRS UMR7156, Strasbourg, 67000, France
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Colin R. Tinsley
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
| | - Serge Casaregola
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
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Jacques N, Louis-Mondesir C, Coton M, Coton E, Casaregola S. Two novel Saccharomycopsis species isolated from black olive brines and a tropical plant. Description of Saccharomycopsis olivae f. a., sp. nov. and Saccharomycopsis guyanensis f. a., sp. nov. Reassignment of Candida amapae to Saccharomycopsis amapae f. a., comb. nov., Candida lassenensis to Saccharomycopsis lassenensis f. a., comb. nov. and Arthroascus babjevae to Saccharomycopsis babjevae f. a., comb. nov. Int J Syst Evol Microbiol 2014; 64:2169-2175. [DOI: 10.1099/ijs.0.060418-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three yeast strains related to members of the genus Saccharomycopsis were isolated. One strain (CLIB 1310) was isolated from olive brines of fermented black olives in France and two strains (CLIB 1454 and CLIB 1455) were isolated from a plant in French Guiana. Sequence analyses based on the D1/D2 domains of the nuclear large subunit rRNA gene, small-subunit rRNA gene and partial EF-1α gene revealed that the strains represented two novel taxa exhibiting extensive sequence divergence from the previously described species of the genus Saccharomycopsis. Two novel species are described to accommodate these newly isolated strains: Saccharomycopsis olivae sp. nov. (type strain CLIB 1310T = CBS 12701T) and Saccharomycopsis guyanensis sp. nov. (type strain CLIB 1455T = CBS 12914T and strain CLIB 1454). Both strains CLIB 1454 and CLIB 1455T displayed identical sequences but differed in their ability to metabolize sorbitol and in their morphology on agar medium. Candida amapae, Candida lassensensis and Arthroascus babjevae belonging to the Saccharomycopsis clade, are reassigned to Saccharomycopsis as novel combinations.
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Affiliation(s)
- Noémie Jacques
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
| | - Christelle Louis-Mondesir
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
| | - Monika Coton
- Université de Brest, EA3882, Laboratoire Universitaire de Biodiversité et d’Ecologie Microbienne, ESIAB, Technopôle Brest Iroise, 29280 - Plouzané, France
| | - Emmanuel Coton
- Université de Brest, EA3882, Laboratoire Universitaire de Biodiversité et d’Ecologie Microbienne, ESIAB, Technopôle Brest Iroise, 29280 - Plouzané, France
| | - Serge Casaregola
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
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Casaregola S, Jacques N, Louis-Mondesir C, Coton M, Coton E. Citeromyces nyonsensis sp. nov., a novel yeast species isolated from black olive brine. Int J Syst Evol Microbiol 2013; 63:3086-3090. [PMID: 23710049 DOI: 10.1099/ijs.0.049296-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A yeast strain was isolated from olive brines in a fermented black olive and olive oil manufacturing plant in the town of Nyons (France). On the basis of domains 1 and 2 (D1/D2) large subunit (LSU) rRNA gene and internal transcribed spacer (ITS) region sequence analyses, the strain CLIB 1303(T) was found to be closely related, but clearly distinct, from the three existing species of the genus Citeromyces: Citeromyces matritensis, Citeromyces siamensis and Citeromyces haiwaiiensis. Strain CLIB 1303(T) exhibited 6 bp, 7 bp and 12 bp divergences in the D1/D2 LSU rRNA gene with C. siamensis, C. matritensis and C. hawaiiensis, respectively. ITS region divergence amounted to more than 8 %, 4 % and 4.5 % with C. siamensis, C. matritensis and C. hawaiiensis, respectively, in addition to several indels. Like C. matritensis and C. siamensis strains, strain CLIB 1303(T) was shown to be halotolerant and osmotolerant. Phenotypically, strain CLIB 1303(T) can be distinguished from other species of the genus Citeromyces by its inability to assimilate trehalose. The strain CLIB 1303(T) (= CBS 12700(T)) was assigned to a novel species, Citeromyces nyonsensis sp. nov.
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Affiliation(s)
- Serge Casaregola
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France.,INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
| | - Noémie Jacques
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France.,INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
| | - Christelle Louis-Mondesir
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France.,INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
| | - Monika Coton
- Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne (EA3882), Université de Brest, UEB, ESIAB, Technopôle Brest Iroise, 29280-Plouzané, France
| | - Emmanuel Coton
- Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne (EA3882), Université de Brest, UEB, ESIAB, Technopôle Brest Iroise, 29280-Plouzané, France
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Mallet S, Weiss S, Jacques N, Leh-Louis V, Sacerdot C, Casaregola S. Insights into the life cycle of yeasts from the CTG clade revealed by the analysis of the Millerozyma (Pichia) farinosa species complex. PLoS One 2012; 7:e35842. [PMID: 22574125 PMCID: PMC3344839 DOI: 10.1371/journal.pone.0035842] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2011] [Accepted: 03/23/2012] [Indexed: 11/30/2022] Open
Abstract
Among ascomycetous yeasts, the CTG clade is so-called because its constituent species translate CTG as serine instead of leucine. Though the biology of certain pathogenic species such as Candida albicans has been much studied, little is known about the life cycles of non-pathogen species of the CTG clade. Taking advantage of the recently obtained sequence of the biotechnological Millerozyma (Pichiasorbitophila) farinosa strain CBS 7064, we used MLST to better define phylogenic relationships between most of the Millerozyma farinosa strains available in public collections. This led to the constitution of four phylogenetic clades diverging from 8% to 15% at the DNA level and possibly constituting a species complex (M. farinosa) and to the proposal of two new species:Millerozyma miso sp. nov. CBS 2004T ( = CLIB 1230T) and Candida pseudofarinosa sp. nov.NCYC 386T( = CLIB 1231T).Further analysis showed that M. farinosa isolates exist as haploid and inter-clade hybrids. Despite the sequence divergence between the clades, secondary contacts after reproductive isolation were evidenced, as revealed by both introgression and mitochondria transfer between clades. We also showed that the inter-clade hybrids do sporulate to generate mainly viable vegetative diploid spores that are not the result of meiosis, and very rarely aneuploid spores possibly through the loss of heterozygosity during sporulation. Taken together, these results show that in this part of the CTG clade, non-Mendelian genetic exchanges occur at high rates through hybridization between divergent strainsfrom distinct clades and subsequent massive loss of heterozygosity. This combination of mechanisms could constitute an alternative sexuality leading to an unsuspected biodiversity.
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Affiliation(s)
- Sandrine Mallet
- INRA UMR1319, Micalis Institute, CIRM-Levures, Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, Thiverval-Grignon, France
| | - Stéphanie Weiss
- INRA UMR1319, Micalis Institute, CIRM-Levures, Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, Thiverval-Grignon, France
| | - Noémie Jacques
- INRA UMR1319, Micalis Institute, CIRM-Levures, Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, Thiverval-Grignon, France
| | | | - Christine Sacerdot
- Institut Pasteur, Unité de Génétique Moléculaire des Levures, CNRS, UMR 3525, Université Pierre et Marie Curie-Paris 06, UFR 927, Paris, France
| | - Serge Casaregola
- INRA UMR1319, Micalis Institute, CIRM-Levures, Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, Thiverval-Grignon, France
- * E-mail:
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Malka D, Boige V, Jacques N, Vimond N, Adenis A, Boucher E, Pierga J, Conroy T, Chauffert B, François E, Guichard P, Galais M, Cvitkovic F, Ducreux M, Farace F. Clinical value of circulating endothelial cell levels in metastatic colorectal cancer patients treated with first-line chemotherapy and bevacizumab. Ann Oncol 2012; 23:919-27. [DOI: 10.1093/annonc/mdr365] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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Jacques N, Mercier S, Molinari A. On the influence of microscale inertia on dynamic ductile crack extension. EPJ Web of Conferences 2012. [DOI: 10.1051/epjconf/20122604021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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N'guessan KF, Brou K, Jacques N, Casaregola S, Dje KM. Identification of yeasts during alcoholic fermentation of tchapalo, a traditional sorghum beer from Côte d'Ivoire. Antonie Van Leeuwenhoek 2011; 99:855-64. [PMID: 21318423 DOI: 10.1007/s10482-011-9560-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Accepted: 01/29/2011] [Indexed: 11/29/2022]
Abstract
This study investigated the diversity and dynamics of yeasts involved in alcoholic fermentation of a traditional sorghum beer from Côte d'Ivoire, tchapalo. A total of 240 yeast strains were isolated from fermenting sorghum wort inoculated with dry yeast from two geographic regions of Côte d'Ivoire (Abidjan and Bondoukou). Initial molecular identification to the species level was carried out using RFLP of PCR-amplified internal transcribed spacers of rDNA (ITS1-5.8S-ITS2). Ten different profiles were obtained from the restriction of PCR products with the three endonucleases HaeIII, CfoI and HinfI. Sequence analysis of the D1/D2 domain of the 26S rDNA and the ACT1 gene allowed us to assign these groups to six different species: Saccharomyces cerevisiae-like, Candida tropicalis, Pichia kudriavzevii, Pichia kluyveri, Kodamaea ohmeri and Meyerozyma caribbica. The most frequent species associated with tchapalo fermentation was S. cerevisiae-like (87.36%), followed by C. tropicalis (5.45%) and M. caribbica (2.71%). S. cerevisiae-like strains were diploid heterozygotes and exhibited three to four nucleotides divergence from the type strain in the D1/D2 domain and several indels in the more discriminant sequence of the intron of the ACT1 gene. During the process, the yeast species isolated and their frequencies varied according to the geographic origin of the dry yeast. The occurrence of some species was sporadic and only two non-Saccharomyces species were found in the final product.
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Affiliation(s)
- Kouadio Florent N'guessan
- Laboratoire de Biotechnologie et Microbiologie des Aliments, Unité de Formation et de Recherche en Sciences et Technologie des Aliments, Université d'Abobo-Adjamé, 02 BP 801, Abidjan 02, Côte d'Ivoire.
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Safadi RA, Talarek N, Jacques N, Aigle M. Yeast prions: could they be exaptations? The URE2/[URE3] system in Kluyveromyces lactis. FEMS Yeast Res 2010; 11:151-3. [DOI: 10.1111/j.1567-1364.2010.00700.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Jacques N, Mallet S, Casaregola S. Delimitation of the species of the Debaryomyces hansenii complex by intron sequence analysis. Int J Syst Evol Microbiol 2009; 59:1242-51. [DOI: 10.1099/ijs.0.004325-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Mounier J, Monnet C, Jacques N, Antoinette A, Irlinger F. Assessment of the microbial diversity at the surface of Livarot cheese using culture-dependent and independent approaches. Int J Food Microbiol 2009; 133:31-7. [PMID: 19481828 DOI: 10.1016/j.ijfoodmicro.2009.04.020] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2008] [Revised: 02/09/2009] [Accepted: 04/14/2009] [Indexed: 10/20/2022]
Abstract
The microbial diversity of the surface of a commercial red-smear cheese, Livarot cheese, sold on the retail market was studied using culture-dependent and independent approaches. Forty yeasts and 40 bacteria from the cheese surface were collected, dereplicated using single-strand conformation polymorphism (SSCP) analysis and identified using rRNA gene sequencing for the culture-dependent approach. The culture-independent approach involved cloning and sequencing of the 16S rRNA gene and SSCP analysis from total DNA extracted from the cheese. The most dominant bacteria were Microbacterium gubbeenense, Leucobacter komagatae and Gram-negative bacteria from the Gamma-Proteobacteria class. Fluorescence in situ hybridization (FISH) analysis was also used to study the cheese microbial diversity with class-level and specific rRNA-targeted probes for bacteria and yeasts, respectively. FISH analysis confirmed that Gamma-Proteobacteria were important microorganisms in this cheese. Four specific FISH probes targeting the dominant yeasts present in the cheese, Candida catenulata, Candida intermedia, Geotrichum spp. and Yarrowia lipolytica, were also designed and evaluated. These probes allowed the detection of these yeasts directly in cheese. The use of the rRNA gene-based approach combined with FISH analysis was useful to investigate the diversity of a surface microbial consortium from cheese.
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Affiliation(s)
- J Mounier
- UMR Génie et Microbiologie des Procédés Alimentaires, INRA, AgroParisTech, Thiverval Grignon, France
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Abstract
Hemiascomycetous yeasts constitute a class of unicellular fungi often associated with the food and drink processing industries. A number of species including Kluveromyces lactis, Debaryomyces hansenii, Yarrowia lipolytica, play a key role in the cheese-making process by providing aroma, affecting texture and/or permitting the growth of other microorgansisms. The large majority of yeast infections are due to a few opportunistic species presently classified within the genus Candida, and occur in immunocompromised patients. Recent advances in taxonomy have provided evidence for the incorrect classification of a number of yeasts and suggest that their association with the genus Candida should be reconsidered. Indeed, none of the most common pathogenic Candida species are found in cheese. Improved techniques, combined with more advanced analytical methods have brought to light several emerging pathogens, some of which are involved in cheese-making, for example D. hansenii and Y. lipolytica. Other emerging pathogens may also be found as rare occurrences in cheese. Problems in designation of these isolates are due in part to the still limited range of specific methods of identification and are exacerbated by lack of consensus concerning yeast taxonomy. These organisms cause rare infections in immunocompromised and hospitalized patients, which are generally mild and either self-limiting or easily treated. From studies with Saccharomyces cerevisiae, it seems that it is more the exposure to high doses of yeast than the identity of the species or strain that is associated with infection. As such yeasts in cheese cannot be considered to constitute a risk for healthy individuals.
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Affiliation(s)
- Noémie Jacques
- CIRM-Levures, Laboratoire de Microbiologie et Génétique Moléculaire, INRA, CNRS, AgroParisTech, F-78850 Thiverval-Grignon, France
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Suleau A, Jacques N, Reitz-Ausseur J, Casaregola S. Intraspecific gene expression variability in the yeast revealed by micro-array analysis. FEMS Yeast Res 2005; 5:595-604. [PMID: 15780658 DOI: 10.1016/j.femsyr.2004.11.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2004] [Revised: 11/22/2004] [Accepted: 11/29/2004] [Indexed: 11/27/2022] Open
Abstract
Using the Genolevures sequencing data, we developed an expression micro-array for the yeast Kluyveromyces lactis consisting of 482 genes, mainly involved in central metabolism, compound transport facilitators and stress response. The array was validated using the LAC/GAL system. By comparing gene expression in the laboratory reference strain CBS2359 and in an industrial strain B1, we demonstrated the influence of two carbon sources, glucose and lactose, on the expression of genes involved in the respiratory and in the fermentative metabolic pathways. We also showed that the two strains, although both originating from dairies, display unexpected differences in gene expression on each type of carbon source.
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Affiliation(s)
- Audrey Suleau
- Laboratoire de Microbiologie et Génétique Moléculaire, INRA UMR1238, CNRS/INA-PG UMR 2585, 78850 Thiverval-Grignon, France
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Abstract
This review explains some of the basic techniques of molecular biology and their application to the study of oral streptococci. Examples of how these techniques have furthered the understanding of streptococcal colonization in health and disease are discussed along with approaches to controlling dental caries that have been made plausible by the knowledge gained using these techniques.
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Affiliation(s)
- N Jacques
- Institute of Dental Research, Sydney
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Jacques N, Wilton K, Townsend M. Cooperative learning and social acceptance of children with mild intellectual disability. J Intellect Disabil Res 1998; 42 ( Pt 1):29-36. [PMID: 9534112 DOI: 10.1046/j.1365-2788.1998.00098.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The effects of the participation of non-disabled children in a cooperative learning programme on their social acceptance of classmates with mild intellectual disability was examined. A sample of 24 children with mild intellectual disability in the 9-11-year-old age-range was identified from educational psychologists' case records. All of the children were receiving mainstreaming special education programmes at the time of the study. Twelve of the children had previously attended special education classes, while the remainder had always attended regular classes. Half of the children's regular classes were randomly assigned to either receive an experimental cooperative learning programme or to serve as control classrooms. The non-disabled children in the experimental classes showed significant increases in their social acceptance (sociometric ratings) of the children with mild intellectual disability, both immediately following the programme and 5 weeks later, but no such increases were evident in the children in the control classrooms. This pattern held for both the former special class pupils and the children with mild intellectual disability who had never attended special classes. The results confirm the usefulness of cooperative learning strategies for enhancing the social acceptance of children with mild intellectual disability in mainstreaming special educational programmes, regardless of the nature of their previous special educational provisions.
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Affiliation(s)
- N Jacques
- Department of Education, University of Auckland, New Zealand
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Abstract
We have constructed a collection of Escherichia coli strains which differ by point mutations in the ribosome binding site (RBS) that drives the translation of the lacZ gene. These mutations affect the Shine-Dalgarno sequence or the initiation codon, or create secondary structures that sequester these elements, and result in a 200-fold variation in beta-galactosidase expression. Surprisingly, these variations of expression are paralleled by nearly equivalent changes in the lacZ mRNA level. The ratio of the beta-galactosidase expression to the mRNA level reflects the average spacing between translating ribosomes: hence, paradoxically, mutations that affect translation initiation do not correspondingly change this spacing. Further analysis of the mRNA level variations shows that they originate from two independent mechanisms. When beta-galactosidase expression exceeds a threshold corresponding roughly to one translation event per transcript, the variations in the efficiency of translation initiation affect largely the chemical and functional lifetimes of the mRNA. We further show that the rate-limiting step in the chemical decay process is an RNase E-dependent cleavage, which is outcompeted by translation initiation. Below this expression threshold, the mRNA lifetime levels out and strain-to-strain variations in mRNA level arise solely from polarity effects. We suggest that, in this activity range, most mRNA molecules that escape polarity are crossed by a single ribosome, and hence are identical from the viewpoint of degradation. Altogether, the tight couplings between translation initiation on one hand, polarity and/or mRNA degradation on the other, result in translation initiation events being closely spaced in time even from inefficient RBS, at the expense of the mRNA level. Finally, we evocate the possible beneficial consequences of a coupling between translation, transcription and mRNA degradation, for the management of cellular resources.
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Affiliation(s)
- O Yarchuk
- Laboratoire de Génétique Moléculaire (CNRS D 1302), Ecole Normale Supérieure, Paris, France
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31
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Abstract
Our aim is to investigate whether changes in growth conditions can differentially affect the initiation of translation from individual Escherichia coli mRNAs that are not subjected to specific translational control. As a model system, we have constructed a series of point-mutated lacZ genes which differ in their Shine-Dalgarno (SD) sequence, their initiator codon, or the secondary structure around these elements. Alterations in growth conditions produced large (up to 8-fold) changes in the relative expression from these genes, which, we argue, stem from changes in their relative efficiencies of translation initiation. In particular, compared to genes bearing mutations outside the SD or initiator codon, genes mutated in these elements experience a significant decrease in their expression when cells are grown in minimal rather than rich medium; at 42 degrees C rather than 37 degrees C; or under amino acid starvation. We discuss the mechanisms underlying these effects, and evocate their possible generality.
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Affiliation(s)
- N Jacques
- Laboratoire de Génétique Moléculaire (CNRS D1302), Ecole Normale Supérieure, Paris, France
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Chevrier-Miller M, Jacques N, Raibaud O, Dreyfus M. Transcription of single-copy hybrid lacZ genes by T7 RNA polymerase in Escherichia coli: mRNA synthesis and degradation can be uncoupled from translation. Nucleic Acids Res 1990; 18:5787-92. [PMID: 2216770 PMCID: PMC332315 DOI: 10.1093/nar/18.19.5787] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In Escherichia coli transcription of individual genes generally requires concomitant translation, and thus the decay of mRNAs cannot be studied without the complication of translation. Here we have used T7 RNA polymerase to transcribe in vivo lacZ genes carrying ribosome binding sites of variable efficiency. We show that neither cell viability nor growth rate is affected by the T7-driven transcription of these genes, provided that they are present as single chromosomal copy. Furthermore, transcription is now completely uncoupled from translation, allowing large amounts of even completely untranslated mRNAs to be synthesized. Taking advantage of these features, we discuss the influence of the frequency of translation upon the processing and degradation of the lac message.
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Affiliation(s)
- M Chevrier-Miller
- Laboratoire de Génétique Moléculaire (CNRS D 1302), ENS, Paris, France
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Abstract
We discuss the features of Escherichia coli mRNAs which determine where and how efficiently translation is initiated. We have shown that DNA fragments comprising 60-80 nucleotides that bracket the initiation codon of real genes generally promote translation when inserted within a foreign mRNA, while those not corresponding to an authentic gene start do not do so even if they include a Shine-Dalgarno-like element followed by AUG or GUG. Therefore, the information that pinpoints the correct start sites, while extending beyond the mere presence of these elements, remains essentially local. The possible nature of this information is discussed. Next, we point out that, in order to remain accessible, translational starts must escape long-range base-pairing within large mRNAs, and we argue that the tight coupling between translation and transcription plays an important role in achieving this. Finally, we discuss two intriguing situations in which the initiation frequency should be dependent upon the rate of translation elongation.
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Affiliation(s)
- N Jacques
- Laboratoire de Génétique Moléculaire (CNRS D 1302), Ecole Normale Supérieure, Paris, France
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