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Berdan EL, Aubier TG, Cozzolino S, Faria R, Feder JL, Giménez MD, Joron M, Searle JB, Mérot C. Structural Variants and Speciation: Multiple Processes at Play. Cold Spring Harb Perspect Biol 2024; 16:a041446. [PMID: 38052499 PMCID: PMC10910405 DOI: 10.1101/cshperspect.a041446] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Research on the genomic architecture of speciation has increasingly revealed the importance of structural variants (SVs) that affect the presence, abundance, position, and/or direction of a nucleotide sequence. SVs include large chromosomal rearrangements such as fusion/fissions and inversions and translocations, as well as smaller variants such as duplications, insertions, and deletions (CNVs). Although we have ample evidence that SVs play a key role in speciation, the underlying mechanisms differ depending on the type and length of the SV, as well as the ecological, demographic, and historical context. We review predictions and empirical evidence for classic processes such as underdominance due to meiotic aberrations and the coupling effect of recombination suppression before exploring how recent sequencing methodologies illuminate the prevalence and diversity of SVs. We discuss specific properties of SVs and their impact throughout the genome, highlighting that multiple processes are at play, and possibly interacting, in the relationship between SVs and speciation.
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Affiliation(s)
- Emma L Berdan
- Department of Marine Sciences, Gothenburg University, Gothenburg 40530, Sweden
- Bioinformatics Core, Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Thomas G Aubier
- Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier Toulouse III, UMR 5174, CNRS/IRD, 31077 Toulouse, France
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Salvatore Cozzolino
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, 80126 Napoli, Italia
| | - Rui Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, 4485-661 Vairão, Portugal
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Mabel D Giménez
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Genética Humana de Misiones (IGeHM), Parque de la Salud de la Provincia de Misiones "Dr. Ramón Madariaga," N3300KAZ Posadas, Misiones, Argentina
- Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, N3300LQH Posadas, Misiones, Argentina
| | - Mathieu Joron
- Centre d'Ecologie Fonctionnelle et Evolutive, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853, USA
| | - Claire Mérot
- CNRS, UMR 6553 Ecobio, OSUR, Université de Rennes, 35000 Rennes, France
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2
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Chou JY, Hsu PC, Leu JY. Enforcement of Postzygotic Species Boundaries in the Fungal Kingdom. Microbiol Mol Biol Rev 2022; 86:e0009822. [PMID: 36098649 PMCID: PMC9769731 DOI: 10.1128/mmbr.00098-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Understanding the molecular basis of speciation is a primary goal in evolutionary biology. The formation of the postzygotic reproductive isolation that causes hybrid dysfunction, thereby reducing gene flow between diverging populations, is crucial for speciation. Using various advanced approaches, including chromosome replacement, hybrid introgression and transcriptomics, population genomics, and experimental evolution, scientists have revealed multiple mechanisms involved in postzygotic barriers in the fungal kingdom. These results illuminate both unique and general features of fungal speciation. Our review summarizes experiments on fungi exploring how Dobzhansky-Muller incompatibility, killer meiotic drive, chromosome rearrangements, and antirecombination contribute to postzygotic reproductive isolation. We also discuss possible evolutionary forces underlying different reproductive isolation mechanisms and the potential roles of the evolutionary arms race under the Red Queen hypothesis and epigenetic divergence in speciation.
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Affiliation(s)
- Jui-Yu Chou
- Department of Biology, National Changhua University of Education, Changhua, Taiwan
| | - Po-Chen Hsu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Jun-Yi Leu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
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3
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Gorkovskiy A, Verstrepen KJ. The Role of Structural Variation in Adaptation and Evolution of Yeast and Other Fungi. Genes (Basel) 2021; 12:699. [PMID: 34066718 PMCID: PMC8150848 DOI: 10.3390/genes12050699] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 01/12/2023] Open
Abstract
Mutations in DNA can be limited to one or a few nucleotides, or encompass larger deletions, insertions, duplications, inversions and translocations that span long stretches of DNA or even full chromosomes. These so-called structural variations (SVs) can alter the gene copy number, modify open reading frames, change regulatory sequences or chromatin structure and thus result in major phenotypic changes. As some of the best-known examples of SV are linked to severe genetic disorders, this type of mutation has traditionally been regarded as negative and of little importance for adaptive evolution. However, the advent of genomic technologies uncovered the ubiquity of SVs even in healthy organisms. Moreover, experimental evolution studies suggest that SV is an important driver of evolution and adaptation to new environments. Here, we provide an overview of the causes and consequences of SV and their role in adaptation, with specific emphasis on fungi since these have proven to be excellent models to study SV.
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Affiliation(s)
- Anton Gorkovskiy
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Gaston Geenslaan 1, 3001 Leuven, Belgium;
- Laboratory for Systems Biology, VIB—KU Leuven Center for Microbiology, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Kevin J. Verstrepen
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Gaston Geenslaan 1, 3001 Leuven, Belgium;
- Laboratory for Systems Biology, VIB—KU Leuven Center for Microbiology, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
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4
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Giannakou K, Cotterrell M, Delneri D. Genomic Adaptation of Saccharomyces Species to Industrial Environments. Front Genet 2020; 11:916. [PMID: 33193572 PMCID: PMC7481385 DOI: 10.3389/fgene.2020.00916] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/23/2020] [Indexed: 01/07/2023] Open
Abstract
The budding yeast has been extensively studied for its physiological performance in fermentative environments and, due to its remarkable plasticity, is used in numerous industrial applications like in brewing, baking and wine fermentations. Furthermore, thanks to its small and relatively simple eukaryotic genome, the molecular mechanisms behind its evolution and domestication are more easily explored. Considerable work has been directed into examining the industrial adaptation processes that shaped the genotypes of species and hybrids belonging to the Saccharomyces group, specifically in relation to beverage fermentation performances. A variety of genetic mechanisms are responsible for the yeast response to stress conditions, such as genome duplication, chromosomal re-arrangements, hybridization and horizontal gene transfer, and these genetic alterations are also contributing to the diversity in the Saccharomyces industrial strains. Here, we review the recent genetic and evolutionary studies exploring domestication and biodiversity of yeast strains.
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Affiliation(s)
- Konstantina Giannakou
- Manchester Institute of Biotechnology, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom.,Cloudwater Brew Co., Manchester, United Kingdom
| | | | - Daniela Delneri
- Manchester Institute of Biotechnology, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
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5
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Fleiss A, O'Donnell S, Fournier T, Lu W, Agier N, Delmas S, Schacherer J, Fischer G. Reshuffling yeast chromosomes with CRISPR/Cas9. PLoS Genet 2019; 15:e1008332. [PMID: 31465441 PMCID: PMC6738639 DOI: 10.1371/journal.pgen.1008332] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 09/11/2019] [Accepted: 07/26/2019] [Indexed: 12/12/2022] Open
Abstract
Genome engineering is a powerful approach to study how chromosomal architecture impacts phenotypes. However, quantifying the fitness impact of translocations independently from the confounding effect of base substitutions has so far remained challenging. We report a novel application of the CRISPR/Cas9 technology allowing to generate with high efficiency both uniquely targeted and multiple concomitant reciprocal translocations in the yeast genome. Targeted translocations are constructed by inducing two double-strand breaks on different chromosomes and forcing the trans-chromosomal repair through homologous recombination by chimerical donor DNAs. Multiple translocations are generated from the induction of several DSBs in LTR repeated sequences and promoting repair using endogenous uncut LTR copies as template. All engineered translocations are markerless and scarless. Targeted translocations are produced at base pair resolution and can be sequentially generated one after the other. Multiple translocations result in a large diversity of karyotypes and are associated in many instances with the formation of unanticipated segmental duplications. To test the phenotypic impact of translocations, we first recapitulated in a lab strain the SSU1/ECM34 translocation providing increased sulphite resistance to wine isolates. Surprisingly, the same translocation in a laboratory strain resulted in decreased sulphite resistance. However, adding the repeated sequences that are present in the SSU1 promoter of the resistant wine strain induced sulphite resistance in the lab strain, yet to a lower level than that of the wine isolate, implying that additional polymorphisms also contribute to the phenotype. These findings illustrate the advantage brought by our technique to untangle the phenotypic impacts of structural variations from confounding effects of base substitutions. Secondly, we showed that strains with multiple translocations, even those devoid of unanticipated segmental duplications, display large phenotypic diversity in a wide range of environmental conditions, showing that simply reconfiguring chromosome architecture is sufficient to provide fitness advantages in stressful growth conditions. Chromosomes are highly dynamic objects that often undergo large structural variations such as reciprocal translocations. Such rearrangements can have dramatic functional consequences, as they can disrupt genes, change their regulation or create novel fusion genes at their breakpoints. For instance, 90–95% of patients diagnosed with chronic myeloid leukemia carry the Philadelphia chromosome characterized by a reciprocal translocation between chromosomes 9 and 22. In addition, translocations reorganize the genetic information along chromosomes, which in turn can modify the 3D architecture of the genome and potentially affect its functioning. Quantifying the fitness impact of translocations independently from the confounding effect of base substitutions has so far remained challenging. Here, we report a novel CRISPR/Cas9-based technology allowing to generate with high efficiency and at a base-pair precision either uniquely targeted or multiple reciprocal translocations in yeast, without leaving any marker or scar in the genome. Engineering targeted reciprocal translocations allowed us for the first time to untangle the phenotypic impacts of large chromosomal rearrangements from that of point mutations. In addition, the generation of multiple translocations led to a large reorganization of the genetic information along the chromosomes, often including unanticipated large segmental duplications. We showed that reshuffling the genome resulted in the emergence of fitness advantage in stressful environmental conditions, even in strains where no gene was disrupted or amplified by the translocations.
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Affiliation(s)
- Aubin Fleiss
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, Paris, France
| | - Samuel O'Donnell
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, Paris, France
| | - Téo Fournier
- Université de Strasbourg, CNRS, GMGM UMR7156, Strasbourg, France
| | - Wenqing Lu
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, Paris, France
| | - Nicolas Agier
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, Paris, France
| | - Stéphane Delmas
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, Paris, France
| | | | - Gilles Fischer
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, Paris, France
- * E-mail:
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6
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Abstract
The concept of the species ‘pan-genome’, the union of ‘core’ conserved genes and all ‘accessory’ non-conserved genes across all strains of a species, was first proposed in prokaryotes to account for intraspecific variability. Species pan-genomes have been extensively studied in prokaryotes, but evidence of species pan-genomes has also been demonstrated in eukaryotes such as plants and fungi. Using a previously published methodology based on sequence homology and conserved microsynteny, in addition to bespoke pipelines, we have investigated the pan-genomes of four model fungal species: Saccharomyces cerevisiae, Candida albicans, Cryptococcus neoformans var. grubii and Aspergillus fumigatus. Between 80 and 90 % of gene models per strain in each of these species are core genes that are highly conserved across all strains of that species, many of which are involved in housekeeping and conserved survival processes. In many of these species, the remaining ‘accessory’ gene models are clustered within subterminal regions and may be involved in pathogenesis and antimicrobial resistance. Analysis of the ancestry of species core and accessory genomes suggests that fungal pan-genomes evolve by strain-level innovations such as gene duplication as opposed to wide-scale horizontal gene transfer. Our findings lend further supporting evidence to the existence of species pan-genomes in eukaryote taxa.
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Affiliation(s)
- Charley G P McCarthy
- 1Genome Evolution Laboratory, Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland.,2Human Health Research Institute, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - David A Fitzpatrick
- 1Genome Evolution Laboratory, Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland.,2Human Health Research Institute, Maynooth University, Maynooth, Co. Kildare, Ireland
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7
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Whole Genome Sequencing, de Novo Assembly and Phenotypic Profiling for the New Budding Yeast Species Saccharomyces jurei. G3-GENES GENOMES GENETICS 2018; 8:2967-2977. [PMID: 30097472 PMCID: PMC6118302 DOI: 10.1534/g3.118.200476] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Saccharomyces sensu stricto complex consist of yeast species, which are not only important in the fermentation industry but are also model systems for genomic and ecological analysis. Here, we present the complete genome assemblies of Saccharomyces jurei, a newly discovered Saccharomyces sensu stricto species from high altitude oaks. Phylogenetic and phenotypic analysis revealed that S. jurei is more closely related to S. mikatae, than S. cerevisiae, and S. paradoxus. The karyotype of S. jurei presents two reciprocal chromosomal translocations between chromosome VI/VII and I/XIII when compared to the S. cerevisiae genome. Interestingly, while the rearrangement I/XIII is unique to S. jurei, the other is in common with S. mikatae strain IFO1815, suggesting shared evolutionary history of this species after the split between S. cerevisiae and S. mikatae. The number of Ty elements differed in the new species, with a higher number of Ty elements present in S. jurei than in S. cerevisiae. Phenotypically, the S. jurei strain NCYC 3962 has relatively higher fitness than the other strain NCYC 3947T under most of the environmental stress conditions tested and showed remarkably increased fitness in higher concentration of acetic acid compared to the other sensu stricto species. Both strains were found to be better adapted to lower temperatures compared to S. cerevisiae.
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8
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Fraczek MG, Naseeb S, Delneri D. History of genome editing in yeast. Yeast 2018; 35:361-368. [PMID: 29345746 PMCID: PMC5969250 DOI: 10.1002/yea.3308] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 12/12/2017] [Indexed: 12/27/2022] Open
Abstract
For thousands of years humans have used the budding yeast Saccharomyces cerevisiae for the production of bread and alcohol; however, in the last 30-40 years our understanding of the yeast biology has dramatically increased, enabling us to modify its genome. Although S. cerevisiae has been the main focus of many research groups, other non-conventional yeasts have also been studied and exploited for biotechnological purposes. Our experiments and knowledge have evolved from recombination to high-throughput PCR-based transformations to highly accurate CRISPR methods in order to alter yeast traits for either research or industrial purposes. Since the release of the genome sequence of S. cerevisiae in 1996, the precise and targeted genome editing has increased significantly. In this 'Budding topic' we discuss the significant developments of genome editing in yeast, mainly focusing on Cre-loxP mediated recombination, delitto perfetto and CRISPR/Cas.
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Affiliation(s)
- Marcin G. Fraczek
- The University of Manchester, Faculty of Biology, Medicine and HealthManchester Institute of BiotechnologyManchesterM1 7DNUK
| | - Samina Naseeb
- The University of Manchester, Faculty of Biology, Medicine and HealthManchester Institute of BiotechnologyManchesterM1 7DNUK
| | - Daniela Delneri
- The University of Manchester, Faculty of Biology, Medicine and HealthManchester Institute of BiotechnologyManchesterM1 7DNUK
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9
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Genome Characterization of Oleaginous Aspergillus oryzae BCC7051: A Potential Fungal-Based Platform for Lipid Production. Curr Microbiol 2017; 75:57-70. [DOI: 10.1007/s00284-017-1350-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 08/28/2017] [Indexed: 12/16/2022]
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10
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Guillamón JM, Barrio E. Genetic Polymorphism in Wine Yeasts: Mechanisms and Methods for Its Detection. Front Microbiol 2017; 8:806. [PMID: 28522998 PMCID: PMC5415627 DOI: 10.3389/fmicb.2017.00806] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 04/19/2017] [Indexed: 01/09/2023] Open
Abstract
The processes of yeast selection for using as wine fermentation starters have revealed a great phenotypic diversity both at interspecific and intraspecific level, which is explained by a corresponding genetic variation among different yeast isolates. Thus, the mechanisms involved in promoting these genetic changes are the main engine generating yeast biodiversity. Currently, an important task to understand biodiversity, population structure and evolutionary history of wine yeasts is the study of the molecular mechanisms involved in yeast adaptation to wine fermentation, and on remodeling the genomic features of wine yeast, unconsciously selected since the advent of winemaking. Moreover, the availability of rapid and simple molecular techniques that show genetic polymorphisms at species and strain levels have enabled the study of yeast diversity during wine fermentation. This review will summarize the mechanisms involved in generating genetic polymorphisms in yeasts, the molecular methods used to unveil genetic variation, and the utility of these polymorphisms to differentiate strains, populations, and species in order to infer the evolutionary history and the adaptive evolution of wine yeasts, and to identify their influence on their biotechnological and sensorial properties.
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Affiliation(s)
- José M Guillamón
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos - Consejo Superior de Investigaciones Científicas (CSIC)Valencia, Spain
| | - Eladio Barrio
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos - Consejo Superior de Investigaciones Científicas (CSIC)Valencia, Spain.,Departamento de Genética, Universidad de ValenciaValencia, Spain
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11
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Naseeb S, Carter Z, Minnis D, Donaldson I, Zeef L, Delneri D. Widespread Impact of Chromosomal Inversions on Gene Expression Uncovers Robustness via Phenotypic Buffering. Mol Biol Evol 2016; 33:1679-96. [PMID: 26929245 PMCID: PMC4915352 DOI: 10.1093/molbev/msw045] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The nonrandom gene organization in eukaryotes plays a significant role in genome evolution and function. Chromosomal structural changes impact meiotic fitness and, in several organisms, are associated with speciation and rapid adaptation to different environments. Small sized chromosomal inversions, encompassing few genes, are pervasive in Saccharomyces “sensu stricto” species, while larger inversions are less common in yeasts compared with higher eukaryotes. To explore the effect of gene order on phenotype, reproductive isolation, and gene expression, we engineered 16 Saccharomyces cerevisiae strains carrying all possible paracentric and pericentric inversions between Ty1 elements, a natural substrate for rearrangements. We found that 4 inversions were lethal, while the other 12 did not show any fitness advantage or disadvantage in rich and minimal media. At meiosis, only a weak negative correlation with fitness was seen with the size of the inverted region. However, significantly lower fertility was seen in heterozygote invertant strains carrying recombination hotspots within the breakpoints. Altered transcription was observed throughout the genome rather than being overrepresented within the inversions. In spite of the large difference in gene expression in the inverted strains, mitotic fitness was not impaired in the majority of the 94 conditions tested, indicating that the robustness of the expression network buffers the deleterious effects of structural changes in several environments. Overall, our results support the notion that transcriptional changes may compensate for Ty-mediated rearrangements resulting in the maintenance of a constant phenotype, and suggest that large inversions in yeast are unlikely to be a selectable trait during vegetative growth.
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Affiliation(s)
- Samina Naseeb
- Computational and Evolutionary Biology Research Theme, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Zorana Carter
- Computational and Evolutionary Biology Research Theme, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - David Minnis
- Computational and Evolutionary Biology Research Theme, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Ian Donaldson
- Computational and Evolutionary Biology Research Theme, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Leo Zeef
- Computational and Evolutionary Biology Research Theme, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Daniela Delneri
- Computational and Evolutionary Biology Research Theme, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
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12
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Aubrey W, Riley MC, Young M, King RD, Oliver SG, Clare A. A Tool for Multiple Targeted Genome Deletions that Is Precise, Scar-Free, and Suitable for Automation. PLoS One 2015; 10:e0142494. [PMID: 26630677 PMCID: PMC4668057 DOI: 10.1371/journal.pone.0142494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 10/22/2015] [Indexed: 11/29/2022] Open
Abstract
Many advances in synthetic biology require the removal of a large number of genomic elements from a genome. Most existing deletion methods leave behind markers, and as there are a limited number of markers, such methods can only be applied a fixed number of times. Deletion methods that recycle markers generally are either imprecise (remove untargeted sequences), or leave scar sequences which can cause genome instability and rearrangements. No existing marker recycling method is automation-friendly. We have developed a novel openly available deletion tool that consists of: 1) a method for deleting genomic elements that can be repeatedly used without limit, is precise, scar-free, and suitable for automation; and 2) software to design the method’s primers. Our tool is sequence agnostic and could be used to delete large numbers of coding sequences, promoter regions, transcription factor binding sites, terminators, etc in a single genome. We have validated our tool on the deletion of non-essential open reading frames (ORFs) from S. cerevisiae. The tool is applicable to arbitrary genomes, and we provide primer sequences for the deletion of: 90% of the ORFs from the S. cerevisiae genome, 88% of the ORFs from S. pombe genome, and 85% of the ORFs from the L. lactis genome.
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Affiliation(s)
- Wayne Aubrey
- Department of Computer Science, Aberystwyth University, Aberystwyth, SY23 3DB, United Kingdom
- * E-mail:
| | - Michael C. Riley
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DD, United Kingdom
| | - Michael Young
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DD, United Kingdom
| | - Ross D. King
- Manchester Institute of Biotechnology and School of Computer Science, University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Stephen G. Oliver
- Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Amanda Clare
- Department of Computer Science, Aberystwyth University, Aberystwyth, SY23 3DB, United Kingdom
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13
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Tosato V, Bruschi CV. Per aspera ad astra: When harmful chromosomal translocations become a plus value in genetic evolution. Lessons from Saccharomyces cerevisiae. ACTA ACUST UNITED AC 2015; 2:363-375. [PMID: 28357264 PMCID: PMC5354581 DOI: 10.15698/mic2015.10.230] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this review we will focus on chromosomal translocations (either spontaneous or induced) in budding yeast. Indeed, very few organisms tolerate so well aneuploidy like Saccharomyces, allowing in depth studies on chromosomal numerical aberrations. Many wild type strains naturally develop chromosomal rearrangements while adapting to different environmental conditions. Translocations, in particular, are valuable not only because they naturally drive species evolution, but because they might allow the artificial generation of new strains that can be optimized for industrial purposes. In this area, several methodologies to artificially trigger chromosomal translocations have been conceived in the past years, such as the chromosomal fragmentation vector (CFV) technique, the Cre-loxP procedure, the FLP/FRT recombination method and, recently, the bridge - induced translocation (BIT) system. An overview of the methodologies to generate chromosomal translocations in yeast will be presented and discussed considering advantages and drawbacks of each technology, focusing in particular on the recent BIT system. Translocants are important for clinical studies because translocated yeast cells resemble cancer cells from morphological and physiological points of view and because the translocation event ensues in a transcriptional de-regulation with a subsequent multi-factorial genetic adaptation to new, selective environmental conditions. The phenomenon of post-translocational adaptation (PTA) is discussed, providing some new unpublished data and proposing the hypothesis that translocations may drive evolution through adaptive genetic selection.
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Affiliation(s)
- Valentina Tosato
- Yeast Molecular Genetics Laboratory, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Carlo V Bruschi
- Yeast Molecular Genetics Laboratory, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
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14
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Ma J, Gao S, Stiller J, Jiang QT, Lan XJ, Liu YX, Pu ZE, Wang J, Wei Y, Zheng YL. Identification of genes bordering breakpoints of the pericentric inversions on 2B, 4B, and 5A in bread wheat (Triticum aestivum L.). Genome 2015; 58:385-90. [DOI: 10.1139/gen-2015-0060] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Chromosome translocation is an important driving force in shaping genomes during evolution. Detailed knowledge of chromosome translocations in a given species and its close relatives should increase the efficiency and precision of chromosome engineering in crop improvement. To identify genes flanking the breakpoints of translocations and inversions as a step toward identifying breakpoints in bread wheat, we systematically analysed genes in the Brachypodium genome against wheat survey sequences and bin-mapped ESTs (expressed sequence tags) derived from the hexaploid wheat genotype ‘Chinese Spring’. In addition to those well-known translocations between group 4, 5, and 7 chromosomes, this analysis identified genes flanking the three pericentric inversions on chromosomes 2B, 4B, and 5A. However, numerous chromosomal rearrangements reported in early studies could not be confirmed. The genes flanking the breakpoints reported in this study are valuable for isolating these breakpoints.
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Affiliation(s)
- Jian Ma
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Shang Gao
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Jiri Stiller
- CSIRO Agriculture Flagship, 306 Carmody Road, St Lucia, QLD 4067, Australia
| | - Qian-Tao Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Xiu-Jin Lan
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Ya-Xi Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Zhi-En Pu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Jirui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - You-Liang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
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15
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Ma J, Stiller J, Zheng Z, Wei Y, Zheng YL, Yan G, Doležel J, Liu C. Putative interchromosomal rearrangements in the hexaploid wheat (Triticum aestivum L.) genotype 'Chinese Spring' revealed by gene locations on homoeologous chromosomes. BMC Evol Biol 2015; 15:37. [PMID: 25880815 PMCID: PMC4364500 DOI: 10.1186/s12862-015-0313-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 02/20/2015] [Indexed: 01/26/2023] Open
Abstract
Background Chromosomal rearrangements are a major driving force in shaping genome during evolution. Previous studies show that translocated genes could undergo elevated rates of evolution and recombination frequencies around these genes can be altered. Based on the recently released genome sequences of Triticum urartu, Aegilops tauschii, Brachypodium distachyon and bread wheat, an analysis of interchromosomal translocations in the hexaploid wheat genotype ‘Chinese Spring’ (‘CS’) was conducted based on chromosome shotgun sequences from individual chromosome arms of this genotype. Results A total of 720 genes representing putative interchromosomal rearrangements was identified. They were distributed across the 42 chromosome arms. About 59% of these translocated genes were those involved in the well-characterized translocations involving chromosomes 4A, 5A and 7B. The other 41% of the genes represent a large numbers of putative interchromosomal rearrangements which have not yet been described. The number of the putative translocation events in the D subgenome was about half of those presented in either the A or B subgenomes, which agreed well with that the times of interaction between the A and B subgenomes almost doubled that between either of them and the D subgenome. Conclusions The possible existence of a large number of interchromosomal rearrangements detected in this study provide further evidence that caution should be taken when using synteny in ordering sequence contigs or in cloning genes in hexaploid wheat. The identification of these putative translocations in ‘CS’ also provide a base for a systematic evaluation of their presence or absence in the full spectrum of bread wheat and its close relatives, which could have significant implications in a wide array of fields ranging from studies of systematics and evolution to practical breeding. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0313-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jian Ma
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China. .,CSIRO Agriculture Flagship, 306 Carmody Road, St Lucia, QLD, 4067, Australia.
| | - Jiri Stiller
- CSIRO Agriculture Flagship, 306 Carmody Road, St Lucia, QLD, 4067, Australia.
| | - Zhi Zheng
- CSIRO Agriculture Flagship, 306 Carmody Road, St Lucia, QLD, 4067, Australia. .,School of Plant Biology, The University of Western Australia, Perth, WA, 6009, Australia.
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - You-Liang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Guijun Yan
- School of Plant Biology, The University of Western Australia, Perth, WA, 6009, Australia.
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, CZ-78371, Olomouc, Czech Republic.
| | - Chunji Liu
- CSIRO Agriculture Flagship, 306 Carmody Road, St Lucia, QLD, 4067, Australia. .,School of Plant Biology, The University of Western Australia, Perth, WA, 6009, Australia.
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16
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Heng HH, Bremer SW, Stevens JB, Horne SD, Liu G, Abdallah BY, Ye KJ, Ye CJ. Chromosomal instability (CIN): what it is and why it is crucial to cancer evolution. Cancer Metastasis Rev 2014; 32:325-40. [PMID: 23605440 DOI: 10.1007/s10555-013-9427-7] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Results of various cancer genome sequencing projects have "unexpectedly" challenged the framework of the current somatic gene mutation theory of cancer. The prevalence of diverse genetic heterogeneity observed in cancer questions the strategy of focusing on contributions of individual gene mutations. Much of the genetic heterogeneity in tumors is due to chromosomal instability (CIN), a predominant hallmark of cancer. Multiple molecular mechanisms have been attributed to CIN but unifying these often conflicting mechanisms into one general mechanism has been challenging. In this review, we discuss multiple aspects of CIN including its definitions, methods of measuring, and some common misconceptions. We then apply the genome-based evolutionary theory to propose a general mechanism for CIN to unify the diverse molecular causes. In this new evolutionary framework, CIN represents a system behavior of a stress response with adaptive advantages but also serves as a new potential cause of further destabilization of the genome. Following a brief review about the newly realized functions of chromosomes that defines system inheritance and creates new genomes, we discuss the ultimate importance of CIN in cancer evolution. Finally, a number of confusing issues regarding CIN are explained in light of the evolutionary function of CIN.
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Affiliation(s)
- Henry H Heng
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA,
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17
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Zanders SE, Eickbush MT, Yu JS, Kang JW, Fowler KR, Smith GR, Malik HS. Genome rearrangements and pervasive meiotic drive cause hybrid infertility in fission yeast. eLife 2014; 3:e02630. [PMID: 24963140 PMCID: PMC4066438 DOI: 10.7554/elife.02630] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Hybrid sterility is one of the earliest postzygotic isolating mechanisms to evolve between two recently diverged species. Here we identify causes underlying hybrid infertility of two recently diverged fission yeast species Schizosaccharomyces pombe and S. kambucha, which mate to form viable hybrid diploids that efficiently complete meiosis, but generate few viable gametes. We find that chromosomal rearrangements and related recombination defects are major but not sole causes of hybrid infertility. At least three distinct meiotic drive alleles, one on each S. kambucha chromosome, independently contribute to hybrid infertility by causing nonrandom spore death. Two of these driving loci are linked by a chromosomal translocation and thus constitute a novel type of paired meiotic drive complex. Our study reveals how quickly multiple barriers to fertility can arise. In addition, it provides further support for models in which genetic conflicts, such as those caused by meiotic drive alleles, can drive speciation. DOI:http://dx.doi.org/10.7554/eLife.02630.001 It is widely thought that all of the billions of species on Earth are descended from a common ancestor. New species are created via a process called speciation, and nature employs various ‘barriers’ to keep closely related species distinct from one another. One of these barriers is called hybrid sterility. Horses and donkeys, for example, can mate to produce hybrids called mules, but mules cannot produce offspring of their own because they are infertile. Hybrid sterility can occur for a number of reasons. Mules are infertile because they inherit 32 chromosomes from their horse parent, but only 31 chromosomes from their donkey parent—and so have an odd chromosome that they cannot pair-off when they make sperm or egg cells. However, even if a hybrid inherits the same number of chromosomes from each parent, if the chromosomes from the two parents have different structures, the hybrid may still be infertile. Zanders et al. have now looked at two species of fission yeast—S. pombe and S. kambucha—that share 99.5% of their DNA sequence. Although hybrids of these two species inherit three chromosomes from each parent, the majority of spores (the yeast equivalent of sperm) that these hybrids produce fail to develop into new yeast cells. Zanders et al. identified two causes of this infertility: one of these was chromosomal rearrangement; the other was due to three different sites in the DNA of S. kambucha that interfere with the development of the spores that inherit S. pombe chromosomes. Since these two yeast species are so closely related, the findings of Zanders et al. reveal how quickly multiple barriers to fertility can arise. In addition, these findings provide further support for models in which conflicts between different genes in genomes can drive the process of speciation. DOI:http://dx.doi.org/10.7554/eLife.02630.002
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Affiliation(s)
- Sarah E Zanders
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Michael T Eickbush
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Jonathan S Yu
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Ji-Won Kang
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States University of Washington, Seattle, United States
| | - Kyle R Fowler
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Gerald R Smith
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Harmit Singh Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, United States
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18
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Chromosome translocation may lead to PRK1-dependent anticancer drug resistance in yeast via endocytic actin network deregulation. Eur J Cell Biol 2014; 93:145-56. [DOI: 10.1016/j.ejcb.2014.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 02/24/2014] [Accepted: 03/31/2014] [Indexed: 11/21/2022] Open
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19
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Gladieux P, Ropars J, Badouin H, Branca A, Aguileta G, Vienne DM, Rodríguez de la Vega RC, Branco S, Giraud T. Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes. Mol Ecol 2014; 23:753-73. [DOI: 10.1111/mec.12631] [Citation(s) in RCA: 142] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 12/04/2013] [Indexed: 12/15/2022]
Affiliation(s)
- Pierre Gladieux
- Ecologie, Systématique et Evolution UMR8079 University of Paris‐Sud Orsay 91405 France
- Ecologie, Systématique et Evolution CNRS UMR8079 Orsay 91405 France
- Department of Plant and Microbial Biology University of California Berkeley CA 94720‐3102 USA
| | - Jeanne Ropars
- Ecologie, Systématique et Evolution UMR8079 University of Paris‐Sud Orsay 91405 France
- Ecologie, Systématique et Evolution CNRS UMR8079 Orsay 91405 France
| | - Hélène Badouin
- Ecologie, Systématique et Evolution UMR8079 University of Paris‐Sud Orsay 91405 France
- Ecologie, Systématique et Evolution CNRS UMR8079 Orsay 91405 France
| | - Antoine Branca
- Ecologie, Systématique et Evolution UMR8079 University of Paris‐Sud Orsay 91405 France
- Ecologie, Systématique et Evolution CNRS UMR8079 Orsay 91405 France
| | - Gabriela Aguileta
- Center for Genomic Regulation (CRG) Dr, Aiguader 88 Barcelona 08003 Spain
- Universitat Pompeu Fabra (UPF) Barcelona 08003 Spain
| | - Damien M. Vienne
- Center for Genomic Regulation (CRG) Dr, Aiguader 88 Barcelona 08003 Spain
- Universitat Pompeu Fabra (UPF) Barcelona 08003 Spain
- Laboratoire de Biométrie et Biologie Evolutive Université Lyon 1 CNRS UMR5558 Villeurbanne 69622 France
| | - Ricardo C. Rodríguez de la Vega
- Ecologie, Systématique et Evolution UMR8079 University of Paris‐Sud Orsay 91405 France
- Ecologie, Systématique et Evolution CNRS UMR8079 Orsay 91405 France
| | - Sara Branco
- Department of Plant and Microbial Biology University of California Berkeley CA 94720‐3102 USA
| | - Tatiana Giraud
- Ecologie, Systématique et Evolution UMR8079 University of Paris‐Sud Orsay 91405 France
- Ecologie, Systématique et Evolution CNRS UMR8079 Orsay 91405 France
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20
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Ma J, Stiller J, Berkman PJ, Wei Y, Rogers J, Feuillet C, Dolezel J, Mayer KF, Eversole K, Zheng YL, Liu C. Sequence-based analysis of translocations and inversions in bread wheat (Triticum aestivum L.). PLoS One 2013; 8:e79329. [PMID: 24260197 PMCID: PMC3829836 DOI: 10.1371/journal.pone.0079329] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 09/30/2013] [Indexed: 01/09/2023] Open
Abstract
Structural changes of chromosomes are a primary mechanism of genome rearrangement over the course of evolution and detailed knowledge of such changes in a given species and its close relatives should increase the efficiency and precision of chromosome engineering in crop improvement. We have identified sequences bordering each of the main translocation and inversion breakpoints on chromosomes 4A, 5A and 7B of the modern bread wheat genome. The locations of these breakpoints allow, for the first time, a detailed description of the evolutionary origins of these chromosomes at the gene level. Results from this study also demonstrate that, although the strategy of exploiting sorted chromosome arms has dramatically simplified the efforts of wheat genome sequencing, simultaneous analysis of sequences from homoeologous and non-homoeologous chromosomes is essential in understanding the origins of DNA sequences in polyploid species.
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Affiliation(s)
- Jian Ma
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, St Lucia, Brisbane, Queensland, Australia
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, China
| | - Jiri Stiller
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, St Lucia, Brisbane, Queensland, Australia
| | - Paul J. Berkman
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, St Lucia, Brisbane, Queensland, Australia
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, China
| | - Jan Rogers
- The Genome Analysis Centre and International Wheat Genome Sequencing Consortium, Norwich Research Park, Norwich, United Kingdom
| | - Catherine Feuillet
- Institute National de Researche Agronomieque (INRA) - University Blaise Pascal, Genetics, Diversity and Ecophysiology of Cereals, Domaine de Crouelle, Clermont Ferrand, France
| | - Jaroslav Dolezel
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc-Holice, Czech Republic
| | - Klaus F. Mayer
- Helmholtz Center Munich, German research Center for Environment and Health, Neuherberg, Germany
| | - Kellye Eversole
- International Wheat Genome Sequencing Consortium (IWGSC), Bethesda, Maryland, United States of America
| | - You-Liang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, China
| | - Chunji Liu
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, St Lucia, Brisbane, Queensland, Australia
- School of Plant Biology, The University of Western Australia, Perth, Australia
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21
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Teresa Avelar A, Perfeito L, Gordo I, Godinho Ferreira M. Genome architecture is a selectable trait that can be maintained by antagonistic pleiotropy. Nat Commun 2013; 4:2235. [DOI: 10.1038/ncomms3235] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 07/03/2013] [Indexed: 12/29/2022] Open
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22
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Structure, replication efficiency and fragility of yeast ARS elements. Res Microbiol 2012; 163:243-53. [DOI: 10.1016/j.resmic.2012.03.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Accepted: 01/21/2012] [Indexed: 11/16/2022]
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23
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Delneri D. Competition experiments coupled with high-throughput analyses for functional genomics studies in yeast. Methods Mol Biol 2011; 759:271-82. [PMID: 21863493 DOI: 10.1007/978-1-61779-173-4_16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Competition experiments are an effective way to provide a measurement of the fitness of yeast strains. The availability of the Saccharomyces cerevisiae yeast knock-out (YKO) deletion collection allows scientists to retrieve fitness data for the ~6,000 S. cerevisiae genes at the same time in a given environment. The molecular barcodes, characterizing each yeast mutant, serve as strain identifiers, which can be detected in a single microarray analysis. Competition experiments in continuous culture using chemically defined media allow a more specific discrimination of the strains based on their fitness profile. With this high-throughput approach, a series of genes that, when one allele is missing, result in either defective (haplo-insufficient) or favored (haplo-proficient) growth phenotype have been discovered, for each nutrient-limiting condition tested. While haplo-insufficient genes seemed to overlap largely across all the media used, the haplo-proficient ones seem to be more environment specific. For example, genes involved in the protein secretion pathway were highly haplo-insufficient in all the contexts, whereas most of the genes encoding for proteasome components showed a haplo-proficient phenotype specific to nitrogen-limiting conditions. In this chapter, the method used for implementation of competition experiments for high-throughput studies in yeast is presented.
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Affiliation(s)
- Daniela Delneri
- Faculty of Life Sciences, The University of Manchester, Manchester, UK.
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24
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Wóycicki R, Witkowicz J, Gawroński P, Dąbrowska J, Lomsadze A, Pawełkowicz M, Siedlecka E, Yagi K, Pląder W, Seroczyńska A, Śmiech M, Gutman W, Niemirowicz-Szczytt K, Bartoszewski G, Tagashira N, Hoshi Y, Borodovsky M, Karpiński S, Malepszy S, Przybecki Z. The genome sequence of the North-European cucumber (Cucumis sativus L.) unravels evolutionary adaptation mechanisms in plants. PLoS One 2011; 6:e22728. [PMID: 21829493 PMCID: PMC3145757 DOI: 10.1371/journal.pone.0022728] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Accepted: 07/05/2011] [Indexed: 01/01/2023] Open
Abstract
Cucumber (Cucumis sativus L.), a widely cultivated crop, has originated from Eastern Himalayas and secondary domestication regions includes highly divergent climate conditions e.g. temperate and subtropical. We wanted to uncover adaptive genome differences between the cucumber cultivars and what sort of evolutionary molecular mechanisms regulate genetic adaptation of plants to different ecosystems and organism biodiversity. Here we present the draft genome sequence of the Cucumis sativus genome of the North-European Borszczagowski cultivar (line B10) and comparative genomics studies with the known genomes of: C. sativus (Chinese cultivar – Chinese Long (line 9930)), Arabidopsis thaliana, Populus trichocarpa and Oryza sativa. Cucumber genomes show extensive chromosomal rearrangements, distinct differences in quantity of the particular genes (e.g. involved in photosynthesis, respiration, sugar metabolism, chlorophyll degradation, regulation of gene expression, photooxidative stress tolerance, higher non-optimal temperatures tolerance and ammonium ion assimilation) as well as in distributions of abscisic acid-, dehydration- and ethylene-responsive cis-regulatory elements (CREs) in promoters of orthologous group of genes, which lead to the specific adaptation features. Abscisic acid treatment of non-acclimated Arabidopsis and C. sativus seedlings induced moderate freezing tolerance in Arabidopsis but not in C. sativus. This experiment together with analysis of abscisic acid-specific CRE distributions give a clue why C. sativus is much more susceptible to moderate freezing stresses than A. thaliana. Comparative analysis of all the five genomes showed that, each species and/or cultivars has a specific profile of CRE content in promoters of orthologous genes. Our results constitute the substantial and original resource for the basic and applied research on environmental adaptations of plants, which could facilitate creation of new crops with improved growth and yield in divergent conditions.
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MESH Headings
- Adaptation, Physiological
- Chromosome Mapping
- Chromosomes, Artificial, Bacterial
- Chromosomes, Plant/genetics
- Cucumis sativus/genetics
- DNA, Plant/genetics
- Evolution, Molecular
- Gene Expression Regulation, Plant
- Genes, Plant
- Genome, Plant
- Polymerase Chain Reaction
- Promoter Regions, Genetic/genetics
- Regulatory Sequences, Nucleic Acid
- Sequence Analysis, DNA
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Affiliation(s)
- Rafał Wóycicki
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
- * E-mail: (ZP); (SK); (RW)
| | - Justyna Witkowicz
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Piotr Gawroński
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Joanna Dąbrowska
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Alexandre Lomsadze
- Center for Bioinformatics and Computational Genomics, Joint Wallace H. Coulter Georgia Tech and Emory Department of Biomedical Engineering, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Magdalena Pawełkowicz
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Ewa Siedlecka
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Kohei Yagi
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Wojciech Pląder
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Anna Seroczyńska
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Mieczysław Śmiech
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Wojciech Gutman
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Katarzyna Niemirowicz-Szczytt
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Grzegorz Bartoszewski
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Norikazu Tagashira
- Department of Living Design and Information Science, Faculty of Human Development, Hiroshima Jogakuin University, Higashi-ku, Japan
| | - Yoshikazu Hoshi
- Department of Plant Science, Tokai University, Minamiaso-mura, Kumamoto, Japan
| | - Mark Borodovsky
- Center for Bioinformatics and Computational Genomics, Joint Wallace H. Coulter Georgia Tech and Emory Department of Biomedical Engineering, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Stanisław Karpiński
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
- * E-mail: (ZP); (SK); (RW)
| | - Stefan Malepszy
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Zbigniew Przybecki
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
- * E-mail: (ZP); (SK); (RW)
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25
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Carter Z, Delneri D. New generation of loxP-mutated deletion cassettes for the genetic manipulation of yeast natural isolates. Yeast 2010; 27:765-75. [DOI: 10.1002/yea.1774] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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26
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Harewood L, Schütz F, Boyle S, Perry P, Delorenzi M, Bickmore WA, Reymond A. The effect of translocation-induced nuclear reorganization on gene expression. Genome Res 2010; 20:554-64. [PMID: 20212020 PMCID: PMC2860158 DOI: 10.1101/gr.103622.109] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2009] [Accepted: 03/04/2010] [Indexed: 01/27/2023]
Abstract
Translocations are known to affect the expression of genes at the breakpoints and, in the case of unbalanced translocations, alter the gene copy number. However, a comprehensive understanding of the functional impact of this class of variation is lacking. Here, we have studied the effect of balanced chromosomal rearrangements on gene expression by comparing the transcriptomes of cell lines from controls and individuals with the t(11;22)(q23;q11) translocation. The number of differentially expressed transcripts between translocation-carrying and control cohorts is significantly higher than that observed between control samples alone, suggesting that balanced rearrangements have a greater effect on gene expression than normal variation. Many of the affected genes are located along the length of the derived chromosome 11. We show that this chromosome is concomitantly altered in its spatial organization, occupying a more central position in the nucleus than its nonrearranged counterpart. Derivative 22-mapping chromosome 22 genes, on the other hand, remain in their usual environment. Our results are consistent with recent studies that experimentally altered nuclear organization, and indicated that nuclear position plays a functional role in regulating the expression of some genes in mammalian cells. Our study suggests that chromosomal translocations can result in hitherto unforeseen, large-scale changes in gene expression that are the consequence of alterations in normal chromosome territory positioning. This has consequences for the patterns of gene expression change seen during tumorigenesis-associated genome instability and during the karyotype changes that lead to speciation.
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MESH Headings
- Abnormalities, Multiple
- Cell Line, Tumor
- Chromosome Mapping
- Chromosomes, Artificial, Bacterial
- Chromosomes, Human, Pair 11/genetics
- Chromosomes, Human, Pair 22/genetics
- Gene Dosage
- Gene Expression
- Gene Expression Profiling
- Humans
- In Situ Hybridization, Fluorescence
- Syndrome
- Translocation, Genetic
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Affiliation(s)
- Louise Harewood
- Center for Integrative Genomics, University of Lausanne, Lausanne CH-1015, Switzerland
| | - Frédéric Schütz
- Center for Integrative Genomics, University of Lausanne, Lausanne CH-1015, Switzerland
- National Center of Competence in Research (NCCR) Molecular Oncology, Lausanne CH-1015, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
| | - Shelagh Boyle
- Medical Research Council, Human Genetics Unit, Institute of Genetics and Molecular, Medicine, Edinburgh EH4 2XU, United Kingdom
| | - Paul Perry
- Medical Research Council, Human Genetics Unit, Institute of Genetics and Molecular, Medicine, Edinburgh EH4 2XU, United Kingdom
| | - Mauro Delorenzi
- National Center of Competence in Research (NCCR) Molecular Oncology, Lausanne CH-1015, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
| | - Wendy A. Bickmore
- Medical Research Council, Human Genetics Unit, Institute of Genetics and Molecular, Medicine, Edinburgh EH4 2XU, United Kingdom
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne CH-1015, Switzerland
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27
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Abstract
Lateral gene transfer (LGT) and gene rearrangement are essential for shaping bacterial genomes during evolution. Separate attention has been focused on understanding the process of lateral gene transfer and the process of gene translocation. However, little is known about how gene translocation affects laterally transferred genes. Here we have examined gene translocations and lateral gene transfers in closely related genome pairs. The results reveal that translocated genes undergo elevated rates of evolution and gene translocation tends to take place preferentially in recently acquired genes. Translocated genes have a high probability to be truncated, suggesting that translocation followed by truncation/deletion might play an important role in the fast turnover of laterally transferred genes. Furthermore, more recently acquired genes have a higher proportion of genes on the leading strand, suggesting a strong strand bias of lateral gene transfer.
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29
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Cellular and molecular effects of nonreciprocal chromosome translocations in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2008; 105:9703-8. [PMID: 18599460 DOI: 10.1073/pnas.0800464105] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Saccharomyces cerevisiae strains harboring a nonreciprocal, bridge-induced translocation (BIT) between chromosomes VIII and XV exhibited an abnormal phenotype comprising elongated buds and multibudded, unevenly nucleated pseudohyphae. In these cells, we found evidence of molecular effects elicited by the translocation event and specific for its particular genomic location. Expression of genes flanking both translocation breakpoints increased up to five times, correlating with an increased RNA polymerase II binding to their promoters and with their histone acetylation pattern. Microarray data, CHEF, and quantitative PCR confirmed the data on the dosage of genes present on the chromosomal regions involved in the translocation, indicating that telomeric fragments were either duplicated or integrated mostly on chromosome XI. FACS analysis revealed that the majority of translocant cells were blocked in G(1) phase and a few of them in G(2). Some cells showed a posttranslational decrease of cyclin B1, in agreement with elongated buds diagnostic of a G(2)/M phase arrest. The actin1 protein was in some cases modified, possibly explaining the abnormal morphology of the cells. Together with the decrease in Rad53p and the lack of its phosphorylation, these results indicate that these cells have undergone adaptation after checkpoint-mediated G(2)/M arrest after chromosome translocation. These BIT translocants could serve as model systems to understand further the cellular and molecular effects of chromosome translocation and provide fundamental information on its etiology of neoplastic transformation in mammals.
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30
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Delneri D, Hoyle DC, Gkargkas K, Cross EJM, Rash B, Zeef L, Leong HS, Davey HM, Hayes A, Kell DB, Griffith GW, Oliver SG. Identification and characterization of high-flux-control genes of yeast through competition analyses in continuous cultures. Nat Genet 2008; 40:113-7. [PMID: 18157128 DOI: 10.1038/ng.2007.49] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2007] [Accepted: 10/18/2007] [Indexed: 11/09/2022]
Abstract
Using competition experiments in continuous cultures grown in different nutrient environments (glucose limited, ammonium limited, phosphate limited and white grape juice), we identified genes that show haploinsufficiency phenotypes (reduced growth rate when hemizygous) or haploproficiency phenotypes (increased growth rate when hemizygous). Haploproficient genes (815, 1,194, 733 and 654 in glucose-limited, ammonium-limited, phosphate-limited and white grape juice environments, respectively) frequently show that phenotype in a specific environmental context. For instance, genes encoding components of the ubiquitination pathway or the proteasome show haploproficiency in nitrogen-limited conditions where protein conservation may be beneficial. Haploinsufficiency is more likely to be observed in all environments, as is the case with genes determining polar growth of the cell. Haploproficient genes seem randomly distributed in the genome, whereas haploinsufficient genes (685, 765, 1,277 and 217 in glucose-limited, ammonium-limited, phosphate-limited and white grape juice environments, respectively) are over-represented on chromosome III. This chromosome determines a yeast's mating type, and the concentration of haploinsufficient genes there may be a mechanism to prevent its loss.
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Affiliation(s)
- Daniela Delneri
- Faculty of Life Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
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31
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Tai SL, Snoek I, Luttik MAH, Almering MJH, Walsh MC, Pronk JT, Daran JM. Correlation between transcript profiles and fitness of deletion mutants in anaerobic chemostat cultures of Saccharomyces cerevisiae. MICROBIOLOGY-SGM 2007; 153:877-886. [PMID: 17322208 PMCID: PMC2895221 DOI: 10.1099/mic.0.2006/002873-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The applicability of transcriptomics for functional genome analysis rests on the assumption that global information on gene function can be inferred from transcriptional regulation patterns. This study investigated whether Saccharomyces cerevisiae genes that show a consistently higher transcript level under anaerobic than aerobic conditions do indeed contribute to fitness in the absence of oxygen. Tagged deletion mutants were constructed in 27 S. cerevisiae genes that showed a strong and consistent transcriptional upregulation under anaerobic conditions, irrespective of the nature of the growth-limiting nutrient (glucose, ammonia, sulfate or phosphate). Competitive anaerobic chemostat cultivation showed that only five out of the 27 mutants (eug1Δ, izh2Δ, plb2Δ, ylr413wΔ and yor012wΔ) conferred a significant disadvantage relative to a tagged reference strain. The implications of this study are that: (i) transcriptome analysis has a very limited predictive value for the contribution of individual genes to fitness under specific environmental conditions, and (ii) competitive chemostat cultivation of tagged deletion strains offers an efficient approach to select relevant leads for functional analysis studies.
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Affiliation(s)
- Siew Leng Tai
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Ishtar Snoek
- Institute of Biology Leiden, Leiden University, Leiden, Wassenaarseweg 64, 2333 AL Leiden, The Netherlands
| | - Marijke A. H. Luttik
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Marinka J. H. Almering
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Michael C. Walsh
- Heineken Supply Chain, Research and Innovation, Burgemeester Smeetsweg 1, 2380 BB Zoeterwoude, The Netherlands
| | - Jack T. Pronk
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Jean-Marc Daran
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
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32
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Ranz JM, Maurin D, Chan YS, von Grotthuss M, Hillier LW, Roote J, Ashburner M, Bergman CM. Principles of genome evolution in the Drosophila melanogaster species group. PLoS Biol 2007; 5:e152. [PMID: 17550304 PMCID: PMC1885836 DOI: 10.1371/journal.pbio.0050152] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2006] [Accepted: 04/02/2007] [Indexed: 12/19/2022] Open
Abstract
That closely related species often differ by chromosomal inversions was discovered by Sturtevant and Plunkett in 1926. Our knowledge of how these inversions originate is still very limited, although a prevailing view is that they are facilitated by ectopic recombination events between inverted repetitive sequences. The availability of genome sequences of related species now allows us to study in detail the mechanisms that generate interspecific inversions. We have analyzed the breakpoint regions of the 29 inversions that differentiate the chromosomes of Drosophila melanogaster and two closely related species, D. simulans and D. yakuba, and reconstructed the molecular events that underlie their origin. Experimental and computational analysis revealed that the breakpoint regions of 59% of the inversions (17/29) are associated with inverted duplications of genes or other nonrepetitive sequences. In only two cases do we find evidence for inverted repetitive sequences in inversion breakpoints. We propose that the presence of inverted duplications associated with inversion breakpoint regions is the result of staggered breaks, either isochromatid or chromatid, and that this, rather than ectopic exchange between inverted repetitive sequences, is the prevalent mechanism for the generation of inversions in the melanogaster species group. Outgroup analysis also revealed evidence for widespread breakpoint recycling. Lastly, we have found that expression domains in D. melanogaster may be disrupted in D. yakuba, bringing into question their potential adaptive significance.
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Affiliation(s)
- José M Ranz
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom.
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33
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Holland S, Lodwig E, Sideri T, Reader T, Clarke I, Gkargkas K, Hoyle DC, Delneri D, Oliver SG, Avery SV. Application of the comprehensive set of heterozygous yeast deletion mutants to elucidate the molecular basis of cellular chromium toxicity. Genome Biol 2007; 8:R268. [PMID: 18088421 PMCID: PMC2246270 DOI: 10.1186/gb-2007-8-12-r268] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2007] [Revised: 12/18/2007] [Accepted: 12/18/2007] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The serious biological consequences of metal toxicity are well documented, but the key modes of action of most metals are unknown. To help unravel molecular mechanisms underlying the action of chromium, a metal of major toxicological importance, we grew over 6,000 heterozygous yeast mutants in competition in the presence of chromium. Microarray-based screens of these heterozygotes are truly genome-wide as they include both essential and non-essential genes. RESULTS The screening data indicated that proteasomal (protein degradation) activity is crucial for cellular chromium (Cr) resistance. Further investigations showed that Cr causes the accumulation of insoluble and toxic protein aggregates, which predominantly arise from proteins synthesised during Cr exposure. A protein-synthesis defect provoked by Cr was identified as mRNA mistranslation, which was oxygen-dependent. Moreover, Cr exhibited synergistic toxicity with a ribosome-targeting drug (paromomycin) that is known to act via mistranslation, while manipulation of translational accuracy modulated Cr toxicity. CONCLUSION The datasets from the heterozygote screen represent an important public resource that may be exploited to discover the toxic mechanisms of chromium. That potential was validated here with the demonstration that mRNA mistranslation is a primary cause of cellular Cr toxicity.
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Affiliation(s)
- Sara Holland
- School of Biology, Institute of Genetics, The University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Emma Lodwig
- School of Biology, Institute of Genetics, The University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Theodora Sideri
- School of Biology, Institute of Genetics, The University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Tom Reader
- School of Biology, Institute of Genetics, The University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Ian Clarke
- North West Institute for Bio-Health Informatics, The University of Manchester, ISBE, School of Medicine, Oxford Road, Manchester M13 9PT, UK
| | - Konstantinos Gkargkas
- Department of Biochemistry, University of Cambridge, Sanger Building, Tennis Court Road, Cambridge CB2 1GA, UK
| | - David C Hoyle
- North West Institute for Bio-Health Informatics, The University of Manchester, ISBE, School of Medicine, Oxford Road, Manchester M13 9PT, UK
| | - Daniela Delneri
- Faculty of Life Sciences, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Stephen G Oliver
- Department of Biochemistry, University of Cambridge, Sanger Building, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Simon V Avery
- School of Biology, Institute of Genetics, The University of Nottingham, University Park, Nottingham NG7 2RD, UK
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34
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Koszul R, Dujon B, Fischer G. Stability of large segmental duplications in the yeast genome. Genetics 2006; 172:2211-22. [PMID: 16489235 PMCID: PMC1456401 DOI: 10.1534/genetics.105.048058] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2005] [Accepted: 02/06/2006] [Indexed: 11/18/2022] Open
Abstract
The high level of gene redundancy that characterizes eukaryotic genomes results in part from segmental duplications. Spontaneous duplications of large chromosomal segments have been experimentally demonstrated in yeast. However, the dynamics of inheritance of such structures and their eventual fixation in populations remain largely unsolved. We analyzed the stability of a vast panel of large segmental duplications in Saccharomyces cerevisiae (from 41 kb for the smallest to 268 kb for the largest). We monitored the stability of three different types of interchromosomal duplications as well as that of three intrachromosomal direct tandem duplications. In the absence of any selective advantage associated with the presence of the duplication, we show that a duplicated segment internally translocated within a natural chromosome is stably inherited both mitotically and meiotically. By contrast, large duplications carried by a supernumerary chromosome are highly unstable. Duplications translocated into subtelomeric regions are lost at variable rates depending on the location of the insertion sites. Direct tandem duplications are lost by unequal crossing over, both mitotically and meiotically, at a frequency proportional to their sizes. These results show that most of the duplicated structures present an intrinsic level of instability. However, translocation within another chromosome significantly stabilizes a duplicated segment, increasing its chance to get fixed in a population even in the absence of any immediate selective advantage conferred by the duplicated genes.
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Affiliation(s)
- Romain Koszul
- Unité de Génétique Moléculaire des Levures (CNRS URA2171, UFR927 Université Pierre et Marie Curie), Département de Structure et Dynamique des Génomes, Institut Pasteur, Paris, 75724 Cedex 15, France
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35
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Abstract
Recent sequencing efforts and experiments have advanced our understanding of genome evolution in yeasts, particularly the Saccharomyces yeasts. The ancestral genome of the Saccharomyces sensu stricto complex has been subject to both whole-genome duplication, followed by massive sequence loss and divergence, and segmental duplication. In addition the subtelomeric regions are subject to further duplications and rearrangements via ectopic exchanges. Translocations and other gross chromosomal rearrangements that break down syntenic relationships occur; however, they do not appear to be a driving force of speciation. Analysis of single genomes has been fruitful for hypothesis generation such as the whole-genome duplication, but comparative genomics between close and more distant species has proven to be a powerful tool in testing these hypotheses as well as elucidating evolutionary processes acting on the genome. Future work on population genomics and experimental evolution will keep yeast at the forefront of studies in genome evolution.
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Affiliation(s)
- Gianni Liti
- Institute of Genetics, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, United Kingdom.
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Coghlan A, Eichler EE, Oliver SG, Paterson AH, Stein L. Chromosome evolution in eukaryotes: a multi-kingdom perspective. Trends Genet 2005; 21:673-82. [PMID: 16242204 DOI: 10.1016/j.tig.2005.09.009] [Citation(s) in RCA: 175] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2005] [Revised: 08/08/2005] [Accepted: 09/29/2005] [Indexed: 12/15/2022]
Abstract
In eukaryotes, chromosomal rearrangements, such as inversions, translocations and duplications, are common and range from part of a gene to hundreds of genes. Lineage-specific patterns are also seen: translocations are rare in dipteran flies, and angiosperm genomes seem prone to polyploidization. In most eukaryotes, there is a strong association between rearrangement breakpoints and repeat sequences. Current data suggest that some repeats promoted rearrangements via non-allelic homologous recombination, for others the association might not be causal but reflects the instability of particular genomic regions. Rearrangement polymorphisms in eukaryotes are correlated with phenotypic differences, so are thought to confer varying fitness in different habitats. Some seem to be under positive selection because they either trap favorable allele combinations together or alter the expression of nearby genes. There is little evidence that chromosomal rearrangements cause speciation, but they probably intensify reproductive isolation between species that have formed by another route.
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Affiliation(s)
- Avril Coghlan
- Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
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37
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Abstract
The objective of this review is to provide a synthesis of speciation theory, of what is known about mechanisms of speciation in fungi and from this, what is expected, and of ideas on how speciation can be elucidated in more fungal systems. The emphasis is on process rather than pattern. Phylogeographic studies in some groups, such as the agarics, demonstrate predominantly allopatric speciation, often through vicariance, as seen in many plants and animals. The variety of life history factors in fungi suggests, however, a diversity in speciation mechanisms that is borne out in comparison of some key examples. Life history features in fungi with a bearing on speciation include genetic mechanisms for intra- and interspecies interactions, haploidy as monokaryons, dikaryons, or coenocytes, distinctive types of propagules with distinctive modes of dispersal, as well as characteristic relationships to the substrate or host as specialized or generalist saprotrophs, parasites or mutualists with associated opportunities and selective pressures for hybridization. Approaches are proposed for both retrospective, phylogeographic determination of speciation mechanisms, and experimental studies with the potential for genomic applications, particularly in examining the relationship between adaptation and reproductive isolation.
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Affiliation(s)
- Linda M Kohn
- Department of Botany, University of Toronto, Mississauga, Ontario, Canada L5L 1C6.
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38
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Current awareness on yeast. Yeast 2004; 21:1233-40. [PMID: 15580707 DOI: 10.1002/yea.1096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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