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Rojas J, Hose J, Auguste Dutcher H, Place M, Wolters JF, Hittinger CT, Gasch AP. Comparative modeling reveals the molecular determinants of aneuploidy fitness cost in a wild yeast model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.09.588778. [PMID: 38645209 PMCID: PMC11030387 DOI: 10.1101/2024.04.09.588778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Although implicated as deleterious in many organisms, aneuploidy can underlie rapid phenotypic evolution. However, aneuploidy will only be maintained if the benefit outweighs the cost, which remains incompletely understood. To quantify this cost and the molecular determinants behind it, we generated a panel of chromosome duplications in Saccharomyces cerevisiae and applied comparative modeling and molecular validation to understand aneuploidy toxicity. We show that 74-94% of the variance in aneuploid strains' growth rates is explained by the additive cost of genes on each chromosome, measured for single-gene duplications using a genomic library, along with the deleterious contribution of snoRNAs and beneficial effects of tRNAs. Machine learning to identify properties of detrimental gene duplicates provided no support for the balance hypothesis of aneuploidy toxicity and instead identified gene length as the best predictor of toxicity. Our results present a generalized framework for the cost of aneuploidy with implications for disease biology and evolution.
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Affiliation(s)
- Julie Rojas
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - James Hose
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - H Auguste Dutcher
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Michael Place
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - John F Wolters
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Chris Todd Hittinger
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
- J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Audrey P Gasch
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
- J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, 53706, USA
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2
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Ángeles-Argáiz RE, Aguirre-Beltrán LFL, Hernández-Oaxaca D, Quintero-Corrales C, Trujillo-Roldán MA, Castillo-Ramírez S, Garibay-Orijel R. Assembly collapsing versus heterozygosity oversizing: detection of homokaryotic and heterokaryotic Laccaria trichodermophora strains by hybrid genome assembly. Microb Genom 2024; 10:001218. [PMID: 38529901 PMCID: PMC10995626 DOI: 10.1099/mgen.0.001218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 03/01/2024] [Indexed: 03/27/2024] Open
Abstract
Genome assembly and annotation using short-paired reads is challenging for eukaryotic organisms due to their large size, variable ploidy and large number of repetitive elements. However, the use of single-molecule long reads improves assembly quality (completeness and contiguity), but haplotype duplications still pose assembly challenges. To address the effect of read length on genome assembly quality, gene prediction and annotation, we compared genome assemblers and sequencing technologies with four strains of the ectomycorrhizal fungus Laccaria trichodermophora. By analysing the predicted repertoire of carbohydrate enzymes, we investigated the effects of assembly quality on functional inferences. Libraries were generated using three different sequencing platforms (Illumina Next-Seq, Mi-Seq and PacBio Sequel), and genomes were assembled using single and hybrid assemblies/libraries. Long reads or hybrid assemby resolved the collapsing of repeated regions, but the nuclear heterozygous versions remained unresolved. In dikaryotic fungi, each cell includes two nuclei and each nucleus has differences not only in allelic gene version but also in gene composition and synteny. These heterokaryotic cells produce fragmentation and size overestimation of the genome assembly of each nucleus. Hybrid assembly revealed a wider functional diversity of genomes. Here, several predicted oxidizing activities on glycosyl residues of oligosaccharides and several chitooligosaccharide acetylase activities would have passed unnoticed in short-read assemblies. Also, the size and fragmentation of the genome assembly, in combination with heterozygosity analysis, allowed us to distinguish homokaryotic and heterokaryotic strains isolated from L. trichodermophora fruit bodies.
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Affiliation(s)
- Rodolfo Enrique Ángeles-Argáiz
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Circuito de los Posgrados s/n, Ciudad Universitaria, Delegación Coyoacán, Ciudad de México, México, C.P. 04510, Mexico
- Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito s/n, Ciudad Universitaria, Delegación Coyoacán, Ciudad de México, México, C.P. 04510, Mexico
- Red de Manejo Biotecnológico de Recursos, Instituto de Ecología A. C. Carretera antigua a Coatepec 351, Col. El Haya, Xalapa, Veracruz, México, C.P. 91612, Mexico
| | - Luis Fernando Lozano Aguirre-Beltrán
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México, C.P. 62210, Mexico
| | - Diana Hernández-Oaxaca
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México, C.P. 62210, Mexico
- Red de Biodiversidad y Sistemática, Instituto de Ecología A. C. Carretera antigua a Coatepec 351, Col. El Haya, Xalapa, Veracruz, México, C.P. 91073, Mexico
| | - Christian Quintero-Corrales
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Circuito de los Posgrados s/n, Ciudad Universitaria, Delegación Coyoacán, Ciudad de México, México, C.P. 04510, Mexico
- Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito s/n, Ciudad Universitaria, Delegación Coyoacán, Ciudad de México, México, C.P. 04510, Mexico
| | - Mauricio A. Trujillo-Roldán
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer Circuito s/n, Ciudad Universitaria, Delegación Coyoacán, Ciudad de México, México, C.P. 04510, Mexico
- Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Km 107 carretera Tijuana-Ensenada, Ensenada, Baja California, Mexico, C.P. 22860, Mexico
| | - Santiago Castillo-Ramírez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México, C.P. 62210, Mexico
| | - Roberto Garibay-Orijel
- Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito s/n, Ciudad Universitaria, Delegación Coyoacán, Ciudad de México, México, C.P. 04510, Mexico
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3
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Ward CM, Onetto CA, Van Den Heuvel S, Cuijvers KM, Hale LJ, Borneman AR. Recombination, admixture and genome instability shape the genomic landscape of Saccharomyces cerevisiae derived from spontaneous grape ferments. PLoS Genet 2024; 20:e1011223. [PMID: 38517929 PMCID: PMC10990190 DOI: 10.1371/journal.pgen.1011223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 04/03/2024] [Accepted: 03/12/2024] [Indexed: 03/24/2024] Open
Abstract
Cultural exchange of fermentation techniques has driven the spread of Saccharomyces cerevisiae across the globe, establishing natural populations in many countries. Despite this, Oceania is thought to lack native populations of S. cerevisiae, only being introduced after colonisation. Here we investigate the genomic landscape of 411 S. cerevisiae isolated from spontaneous grape fermentations in Australia across multiple locations, years, and grape cultivars. Spontaneous fermentations contained highly recombined mosaic strains that exhibited high levels of genome instability. Assigning genomic windows to putative ancestral origin revealed that few closely related starter lineages have come to dominate the genetic landscape, contributing most of the genetic variation. Fine-scale phylogenetic analysis of loci not observed in strains of commercial wine origin identified widespread admixture with European derived beer yeast along with three independent admixture events from potentially endemic Oceanic lineages that was associated with genome instability. Finally, we investigated Australian ecological niches for basal isolates, identifying phylogenetically distinct S. cerevisiae of non-European, non-domesticated origin associated with admixture loci. Our results illustrate the effect commercial use of microbes may have on local microorganism genetic diversity and demonstrates the presence of non-domesticated, potentially endemic lineages of S. cerevisiae in Australian niches that are actively admixing.
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Affiliation(s)
- Chris M. Ward
- Australian Wine Research Institute, Urrbrae, South Australia, Australia
| | - Cristobal A. Onetto
- Australian Wine Research Institute, Urrbrae, South Australia, Australia
- University of Adelaide, Adelaide, South Australia, Australia
| | | | | | - Laura J. Hale
- Australian Wine Research Institute, Urrbrae, South Australia, Australia
| | - Anthony R. Borneman
- Australian Wine Research Institute, Urrbrae, South Australia, Australia
- University of Adelaide, Adelaide, South Australia, Australia
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4
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Cuamatzi-Flores J, Colón-González M, Requena-Romo F, Quiñones-Galeana S, Cervantes-Chávez JA, Morales L. Enhanced oxidative stress resistance in Ustilago maydis and its implications on the virulence. Int Microbiol 2024:10.1007/s10123-024-00489-8. [PMID: 38401003 DOI: 10.1007/s10123-024-00489-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/12/2024] [Accepted: 02/07/2024] [Indexed: 02/26/2024]
Abstract
The phytopathogenic fungus Ustilago maydis causes corn smut by suppressing host plant defenses, including the oxidative burst response. While many studies have investigated how U. maydis responds to oxidative stress during infection, the consequences of heightened resistance to oxidative stress on virulence remain understudied. This study aimed to identify the effects on virulence in U. maydis strains exhibiting enhanced resistance to hydrogen peroxide (H2O2).To achieve this, we exposed U. maydis SG200 to 20 escalating H2O2 shocks, resulting in an adapted strain resistant to concentrations as high as 60 mM of H2O2, a lethal dose for the initial strain. Genetic analysis of the adapted strain revealed five nucleotide substitutions, two minor copy number variants, and a large amplification event on chromosome nine (1-149 kb) encompassing the sole catalase gene. Overexpressing catalase increased resistance to H2O2; however, this resistance was lower than that observed in the adapted strain. Additionally, virulence was reduced in both strains with enhanced H2O2 resistance.In summary, enhanced H2O2 resistance, achieved through either continuous exposure to the oxidative agent or through catalase overexpression, decreased virulence. This suggests that the response to the oxidative stress burst in U. maydis is optimal and that increasing the resistance to H2O2 does not translate into increased virulence. These findings illuminate the intricate relationship between oxidative stress resistance and virulence in U. maydis, offering insights into its infection mechanisms.
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Affiliation(s)
- Jorge Cuamatzi-Flores
- Unit for Basic and Applied Microbiology, Faculty of Natural Sciences, Autonomous University of Queretaro, 76230, Querétaro, México.
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, 76230, Querétaro, México.
| | - Maritrini Colón-González
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, 76230, Querétaro, México
| | - Fernanda Requena-Romo
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, 76230, Querétaro, México
- Escuela Nacional de Estudios Superiores Unidad Juriquilla, Universidad Nacional Autónoma de México, 76230, Querétaro, México
| | - Samuel Quiñones-Galeana
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, 76230, Querétaro, México
- Escuela Nacional de Estudios Superiores Unidad Juriquilla, Universidad Nacional Autónoma de México, 76230, Querétaro, México
| | - José Antonio Cervantes-Chávez
- Unit for Basic and Applied Microbiology, Faculty of Natural Sciences, Autonomous University of Queretaro, 76230, Querétaro, México.
| | - Lucia Morales
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, 76230, Querétaro, México.
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5
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Kerruish DWM, Cormican P, Kenny EM, Kearns J, Colgan E, Boulton CA, Stelma SNE. The origins of the Guinness stout yeast. Commun Biol 2024; 7:68. [PMID: 38216745 PMCID: PMC10786833 DOI: 10.1038/s42003-023-05587-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 11/14/2023] [Indexed: 01/14/2024] Open
Abstract
Beer is made via the fermentation of an aqueous extract predominantly composed of malted barley flavoured with hops. The transforming microorganism is typically a single strain of Saccharomyces cerevisiae, and for the majority of major beer brands the yeast strain is a unique component. The present yeast used to make Guinness stout brewed in Dublin, Ireland, can be traced back to 1903, but its origins are unknown. To that end, we used Illumina and Nanopore sequencing to generate whole-genome sequencing data for a total of 22 S. cerevisiae yeast strains: 16 from the Guinness collection and 6 other historical Irish brewing. The origins of the Guinness yeast were determined with a SNP-based analysis, demonstrating that the Guinness strains occupy a distinct group separate from other historical Irish brewing yeasts. Assessment of chromosome number, copy number variation and phenotypic evaluation of key brewing attributes established Guinness yeast-specific SNPs but no specific chromosomal amplifications. Our analysis also demonstrated the effects of yeast storage on phylogeny. Altogether, our results suggest that the Guinness yeast used today is related to the first deposited Guinness yeast; the 1903 Watling Laboratory Guinness yeast.
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Affiliation(s)
| | | | | | - Jessica Kearns
- Diageo Ireland, St James's Gate, The Liberties, Dublin, Ireland
| | - Eibhlin Colgan
- Diageo Ireland, St James's Gate, The Liberties, Dublin, Ireland
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6
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Avecilla G, Spealman P, Matthews J, Caudal E, Schacherer J, Gresham D. Copy number variation alters local and global mutational tolerance. Genome Res 2023; 33:1340-1353. [PMID: 37652668 PMCID: PMC10547251 DOI: 10.1101/gr.277625.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 07/07/2023] [Indexed: 09/02/2023]
Abstract
Copy number variants (CNVs), duplications and deletions of genomic sequences, contribute to evolutionary adaptation but can also confer deleterious effects and cause disease. Whereas the effects of amplifying individual genes or whole chromosomes (i.e., aneuploidy) have been studied extensively, much less is known about the genetic and functional effects of CNVs of differing sizes and structures. Here, we investigated Saccharomyces cerevisiae (yeast) strains that acquired adaptive CNVs of variable structures and copy numbers following experimental evolution in glutamine-limited chemostats. Although beneficial in the selective environment, CNVs result in decreased fitness compared with the euploid ancestor in rich media. We used transposon mutagenesis to investigate mutational tolerance and genome-wide genetic interactions in CNV strains. We find that CNVs increase mutational target size, confer increased mutational tolerance in amplified essential genes, and result in novel genetic interactions with unlinked genes. We validated a novel genetic interaction between different CNVs and BMH1 that was common to multiple strains. We also analyzed global gene expression and found that transcriptional dosage compensation does not affect most genes amplified by CNVs, although gene-specific transcriptional dosage compensation does occur for ∼12% of amplified genes. Furthermore, we find that CNV strains do not show previously described transcriptional signatures of aneuploidy. Our study reveals the extent to which local and global mutational tolerance is modified by CNVs with implications for genome evolution and CNV-associated diseases, such as cancer.
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Affiliation(s)
- Grace Avecilla
- Department of Biology, New York University, New York, New York 10003, USA
- Center for Genomics and Systems Biology, New York University, New York, New York 10003, USA
| | - Pieter Spealman
- Department of Biology, New York University, New York, New York 10003, USA
- Center for Genomics and Systems Biology, New York University, New York, New York 10003, USA
| | - Julia Matthews
- Department of Biology, New York University, New York, New York 10003, USA
- Center for Genomics and Systems Biology, New York University, New York, New York 10003, USA
| | - Elodie Caudal
- Université de Strasbourg, CNRS, GMGM UMR, 7156 Strasbourg, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR, 7156 Strasbourg, France
- Institut Universitaire de France (IUF), 75231 Paris Cedex 05, France
| | - David Gresham
- Department of Biology, New York University, New York, New York 10003, USA;
- Center for Genomics and Systems Biology, New York University, New York, New York 10003, USA
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7
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Keller A, Gao LL, Witten D, Dunham MJ. Condition-dependent fitness effects of large synthetic chromosome amplifications. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.08.544269. [PMID: 37333112 PMCID: PMC10274924 DOI: 10.1101/2023.06.08.544269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Whole-chromosome aneuploidy and large segmental amplifications can have devastating effects in multicellular organisms, from developmental disorders and miscarriage to cancer. Aneuploidy in single-celled organisms such as yeast also results in proliferative defects and reduced viability. Yet, paradoxically, CNVs are routinely observed in laboratory evolution experiments with microbes grown in stressful conditions. The defects associated with aneuploidy are often attributed to the imbalance of many differentially expressed genes on the affected chromosomes, with many genes each contributing incremental effects. An alternate hypothesis is that a small number of individual genes are large effect 'drivers' of these fitness changes when present in an altered copy number. To test these two views, we have employed a collection of strains bearing large chromosomal amplifications that we previously assayed in nutrient-limited chemostat competitions. In this study, we focus on conditions known to be poorly tolerated by aneuploid yeast-high temperature, treatment with the Hsp90 inhibitor radicicol, and growth in extended stationary phase. To identify potential genes with a large impact on fitness, we fit a piecewise constant model to fitness data across chromosome arms, filtering breakpoints in this model by magnitude to focus on regions with a large impact on fitness in each condition. While fitness generally decreased as the length of the amplification increased, we were able to identify 91 candidate regions that disproportionately impacted fitness when amplified. Consistent with our previous work with this strain collection, nearly all candidate regions were condition specific, with only five regions impacting fitness in multiple conditions.
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Affiliation(s)
- Abigail Keller
- Molecular Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
- Genome Sciences Department, University of Washington, Seattle, WA 98195, USA
| | - Lucy L. Gao
- Statistics Department and Biostatistics Department, University of Washington, Seattle, WA 98195, USA
| | - Daniela Witten
- Statistics Department and Biostatistics Department, University of Washington, Seattle, WA 98195, USA
| | - Maitreya J. Dunham
- Genome Sciences Department, University of Washington, Seattle, WA 98195, USA
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8
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van Leeuwen J, Pons C, Tan G, Wang JZ, Hou J, Weile J, Gebbia M, Liang W, Shuteriqi E, Li Z, Lopes M, Ušaj M, Dos Santos Lopes A, van Lieshout N, Myers CL, Roth FP, Aloy P, Andrews BJ, Boone C. Systematic analysis of bypass suppression of essential genes. Mol Syst Biol 2021; 16:e9828. [PMID: 32939983 PMCID: PMC7507402 DOI: 10.15252/msb.20209828] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/11/2020] [Accepted: 08/13/2020] [Indexed: 12/15/2022] Open
Abstract
Essential genes tend to be highly conserved across eukaryotes, but, in some cases, their critical roles can be bypassed through genetic rewiring. From a systematic analysis of 728 different essential yeast genes, we discovered that 124 (17%) were dispensable essential genes. Through whole-genome sequencing and detailed genetic analysis, we investigated the genetic interactions and genome alterations underlying bypass suppression. Dispensable essential genes often had paralogs, were enriched for genes encoding membrane-associated proteins, and were depleted for members of protein complexes. Functionally related genes frequently drove the bypass suppression interactions. These gene properties were predictive of essential gene dispensability and of specific suppressors among hundreds of genes on aneuploid chromosomes. Our findings identify yeast's core essential gene set and reveal that the properties of dispensable essential genes are conserved from yeast to human cells, correlating with human genes that display cell line-specific essentiality in the Cancer Dependency Map (DepMap) project.
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Affiliation(s)
- Jolanda van Leeuwen
- Center for Integrative Genomics, Bâtiment Génopode, University of Lausanne, Lausanne, Switzerland.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Carles Pons
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology, Barcelona, Spain
| | - Guihong Tan
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Jason Zi Wang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Jing Hou
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Jochen Weile
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Marinella Gebbia
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Wendy Liang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Ermira Shuteriqi
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Zhijian Li
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Maykel Lopes
- Center for Integrative Genomics, Bâtiment Génopode, University of Lausanne, Lausanne, Switzerland
| | - Matej Ušaj
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Andreia Dos Santos Lopes
- Center for Integrative Genomics, Bâtiment Génopode, University of Lausanne, Lausanne, Switzerland
| | - Natascha van Lieshout
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Frederick P Roth
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada.,Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Patrick Aloy
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Brenda J Andrews
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Charles Boone
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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9
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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: 11] [Impact Index Per Article: 3.7] [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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10
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Zhang Z, Bendixsen DP, Janzen T, Nolte AW, Greig D, Stelkens R. Recombining Your Way Out of Trouble: The Genetic Architecture of Hybrid Fitness under Environmental Stress. Mol Biol Evol 2020; 37:167-182. [PMID: 31518427 PMCID: PMC6984367 DOI: 10.1093/molbev/msz211] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Hybridization between species can either promote or impede adaptation. But we know very little about the genetic basis of hybrid fitness, especially in nondomesticated organisms, and when populations are facing environmental stress. We made genetically variable F2 hybrid populations from two divergent Saccharomyces yeast species. We exposed populations to ten toxins and sequenced the most resilient hybrids on low coverage using ddRADseq to investigate four aspects of their genomes: 1) hybridity, 2) interspecific heterozygosity, 3) epistasis (positive or negative associations between nonhomologous chromosomes), and 4) ploidy. We used linear mixed-effect models and simulations to measure to which extent hybrid genome composition was contingent on the environment. Genomes grown in different environments varied in every aspect of hybridness measured, revealing strong genotype–environment interactions. We also found selection against heterozygosity or directional selection for one of the parental alleles, with larger fitness of genomes carrying more homozygous allelic combinations in an otherwise hybrid genomic background. In addition, individual chromosomes and chromosomal interactions showed significant species biases and pervasive aneuploidies. Against our expectations, we observed multiple beneficial, opposite-species chromosome associations, confirmed by epistasis- and selection-free computer simulations, which is surprising given the large divergence of parental genomes (∼15%). Together, these results suggest that successful, stress-resilient hybrid genomes can be assembled from the best features of both parents without paying high costs of negative epistasis. This illustrates the importance of measuring genetic trait architecture in an environmental context when determining the evolutionary potential of genetically diverse hybrid populations.
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Affiliation(s)
- Zebin Zhang
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Devin P Bendixsen
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Thijs Janzen
- Max Planck Institute for Evolutionary Biology, Plön, Germany.,Institute of Biology and Environmental Sciences, University of Oldenburg, Oldenburg, Germany
| | - Arne W Nolte
- Max Planck Institute for Evolutionary Biology, Plön, Germany.,Institute of Biology and Environmental Sciences, University of Oldenburg, Oldenburg, Germany
| | - Duncan Greig
- Max Planck Institute for Evolutionary Biology, Plön, Germany.,Centre for Life's Origins and Evolution (CLOE), Department of Genetics, Evolution, and Environment, University College London, London, United Kingdom
| | - Rike Stelkens
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden.,Max Planck Institute for Evolutionary Biology, Plön, Germany
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11
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Molecular signatures of aneuploidy-driven adaptive evolution. Nat Commun 2020; 11:588. [PMID: 32001709 PMCID: PMC6992709 DOI: 10.1038/s41467-019-13669-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 11/15/2019] [Indexed: 02/06/2023] Open
Abstract
Alteration of normal ploidy (aneuploidy) can have a number of opposing effects, such as unbalancing protein abundances and inhibiting cell growth but also accelerating genetic diversification and rapid adaptation. The interplay of these detrimental and beneficial effects remains puzzling. Here, to understand how cells develop tolerance to aneuploidy, we subject disomic (i.e. with an extra chromosome copy) strains of yeast to long-term experimental evolution under strong selection, by forcing disomy maintenance and daily population dilution. We characterize mutations, karyotype alterations and gene expression changes, and dissect the associated molecular strategies. Cells with different extra chromosomes accumulated mutations at distinct rates and displayed diverse adaptive events. They tended to evolve towards normal ploidy through chromosomal DNA loss and gene expression changes. We identify genes with recurrent mutations and altered expression in multiple lines, revealing a variant that improves growth under genotoxic stresses. These findings support rapid evolvability of disomic strains that can be used to characterize fitness effects of mutations under different stress conditions. Aneuploidy (abnormal chromosome number) can enable rapid adaptation to stress conditions, but it also entails fitness costs from gene imbalance. Here, the authors experimentally evolve yeast while forcing maintenance of aneuploidy to identify the mechanisms that promote tolerance of aneuploidy.
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12
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Gilchrist C, Stelkens R. Aneuploidy in yeast: Segregation error or adaptation mechanism? Yeast 2019; 36:525-539. [PMID: 31199875 PMCID: PMC6772139 DOI: 10.1002/yea.3427] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/30/2019] [Accepted: 06/04/2019] [Indexed: 01/24/2023] Open
Abstract
Aneuploidy is the loss or gain of chromosomes within a genome. It is often detrimental and has been associated with cell death and genetic disorders. However, aneuploidy can also be beneficial and provide a quick solution through changes in gene dosage when cells face environmental stress. Here, we review the prevalence of aneuploidy in Saccharomyces, Candida, and Cryptococcus yeasts (and their hybrid offspring) and analyse associations with chromosome size and specific stressors. We discuss how aneuploidy, a segregation error, may in fact provide a natural route for the diversification of microbes and enable important evolutionary innovations given the right ecological circumstances, such as the colonisation of new environments or the transition from commensal to pathogenic lifestyle. We also draw attention to a largely unstudied cross link between hybridisation and aneuploidy. Hybrid meiosis, involving two divergent genomes, can lead to drastically increased rates of aneuploidy in the offspring due to antirecombination and chromosomal missegregation. Because hybridisation and aneuploidy have both been shown to increase with environmental stress, we believe it important and timely to start exploring the evolutionary significance of their co-occurrence.
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Affiliation(s)
- Ciaran Gilchrist
- Division of Population Genetics, Department of ZoologyStockholm UniversityStockholmSweden
| | - Rike Stelkens
- Division of Population Genetics, Department of ZoologyStockholm UniversityStockholmSweden
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13
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Zhang K, Zheng DQ, Sui Y, Qi L, Petes T. Genome-wide analysis of genomic alterations induced by oxidative DNA damage in yeast. Nucleic Acids Res 2019; 47:3521-3535. [PMID: 30668788 PMCID: PMC6468167 DOI: 10.1093/nar/gkz027] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 12/11/2018] [Accepted: 01/15/2019] [Indexed: 12/16/2022] Open
Abstract
Oxidative DNA damage is a threat to genome stability. Using a genetic system in yeast that allows detection of mitotic recombination, we found that the frequency of crossovers is greatly elevated when cells are treated with hydrogen peroxide (H2O2). Using a combination of microarray analysis and genomic sequencing, we mapped the breakpoints of mitotic recombination events and other chromosome rearrangements at a resolution of about 1 kb. Gene conversions and crossovers were the two most common types of events, but we also observed deletions, duplications, and chromosome aneuploidy. In addition, H2O2-treated cells had elevated rates of point mutations (particularly A to T/T to A and C to G/G to C transversions) and small insertions/deletions (in/dels). In cells that underwent multiple rounds of H2O2 treatments, we identified a genetic alteration that resulted in improved H2O2 tolerance by amplification of the CTT1 gene that encodes cytosolic catalase T. Lastly, we showed that cells grown in the absence of oxygen have reduced levels of recombination. This study provided multiple novel insights into how oxidative stress affects genomic instability and phenotypic evolution in aerobic cells.
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Affiliation(s)
- Ke Zhang
- College of Life Science, Zhejiang University, Hangzhou 310058, China
| | - Dao-Qiong Zheng
- Ocean College, Zhejiang University, Zhoushan 316021, China
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Yang Sui
- Ocean College, Zhejiang University, Zhoushan 316021, China
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Lei Qi
- Ocean College, Zhejiang University, Zhoushan 316021, China
| | - Thomas D Petes
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
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