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Del Olmo V, Gabaldón T. Hybrids unleashed: exploring the emergence and genomic insights of pathogenic yeast hybrids. Curr Opin Microbiol 2024; 80:102491. [PMID: 38833792 DOI: 10.1016/j.mib.2024.102491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/04/2024] [Accepted: 05/09/2024] [Indexed: 06/06/2024]
Abstract
Hybridisation is the crossing of two divergent lineages that give rise to offspring carrying an admixture of both parental genomes. Genome sequencing has revealed that this process is common in the Saccharomycotina, where a growing number of hybrid strains or species, including many pathogenic ones, have been recently described. Hybrids can display unique traits that may drive adaptation to new niches, and some pathogenic hybrids have been shown to have higher prevalence over their parents in human and environmental niches, suggesting a higher fitness and potential to colonise humans. Here, we discuss how hybridisation and its genomic and phenotypic outcomes can shape the evolution of fungal species and may play a role in the emergence of new pathogens.
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Affiliation(s)
- Valentina Del Olmo
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034 Barcelona, Spain; Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Toni Gabaldón
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034 Barcelona, Spain; Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain; ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain; Centro de Investigación Biomédica En Red de Enfermedades Infecciosas, Barcelona, Spain.
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2
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Hénault M, Marsit S, Charron G, Landry CR. The genomic landscape of transposable elements in yeast hybrids is shaped by structural variation and genotype-specific modulation of transposition rate. eLife 2024; 12:RP89277. [PMID: 38411604 PMCID: PMC10911583 DOI: 10.7554/elife.89277] [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] [Indexed: 02/28/2024] Open
Abstract
Transposable elements (TEs) are major contributors to structural genomic variation by creating interspersed duplications of themselves. In return, structural variants (SVs) can affect the genomic distribution of TE copies and shape their load. One long-standing hypothesis states that hybridization could trigger TE mobilization and thus increase TE load in hybrids. We previously tested this hypothesis (Hénault et al., 2020) by performing a large-scale evolution experiment by mutation accumulation (MA) on multiple hybrid genotypes within and between wild populations of the yeasts Saccharomyces paradoxus and Saccharomyces cerevisiae. Using aggregate measures of TE load with short-read sequencing, we found no evidence for TE load increase in hybrid MA lines. Here, we resolve the genomes of the hybrid MA lines with long-read phasing and assembly to precisely characterize the role of SVs in shaping the TE landscape. Highly contiguous phased assemblies of 127 MA lines revealed that SV types like polyploidy, aneuploidy, and loss of heterozygosity have large impacts on the TE load. We characterized 18 de novo TE insertions, indicating that transposition only has a minor role in shaping the TE landscape in MA lines. Because the scarcity of TE mobilization in MA lines provided insufficient resolution to confidently dissect transposition rate variation in hybrids, we adapted an in vivo assay to measure transposition rates in various S. paradoxus hybrid backgrounds. We found that transposition rates are not increased by hybridization, but are modulated by many genotype-specific factors including initial TE load, TE sequence variants, and mitochondrial DNA inheritance. Our results show the multiple scales at which TE load is shaped in hybrid genomes, being highly impacted by SV dynamics and finely modulated by genotype-specific variation in transposition rates.
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Affiliation(s)
- Mathieu Hénault
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université LavalQuébecCanada
- Département de biochimie, microbiologie et bioinformatique, Université LavalQuébecCanada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université LavalQuébecCanada
- Université Laval Big Data Research Center (BDRC_UL)QuébecCanada
| | - Souhir Marsit
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université LavalQuébecCanada
- Département de biochimie, microbiologie et bioinformatique, Université LavalQuébecCanada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université LavalQuébecCanada
- Université Laval Big Data Research Center (BDRC_UL)QuébecCanada
- Département de biologie, Université LavalQuébecCanada
| | - Guillaume Charron
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université LavalQuébecCanada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université LavalQuébecCanada
- Université Laval Big Data Research Center (BDRC_UL)QuébecCanada
- Département de biologie, Université LavalQuébecCanada
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université LavalQuébecCanada
- Département de biochimie, microbiologie et bioinformatique, Université LavalQuébecCanada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université LavalQuébecCanada
- Université Laval Big Data Research Center (BDRC_UL)QuébecCanada
- Département de biologie, Université LavalQuébecCanada
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3
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Overton MS, Guy SE, Chen X, Martsul A, Carolino K, Akbari OS, Meyer JR, Kryazhimskiy S. Upper Bound on the Mutational Burden Imposed by a CRISPR-Cas9 Gene-Drive Element. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.28.569142. [PMID: 38076841 PMCID: PMC10705488 DOI: 10.1101/2023.11.28.569142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
CRISPR-Cas9 gene drives (CCGDs) are powerful tools for genetic control of wild populations, useful for eradication of disease vectors, conservation of endangered species and other applications. However, Cas9 alone and in a complex with gRNA can cause double-stranded DNA breaks at off-target sites, which could increase the mutational load and lead to loss of heterozygosity (LOH). These undesired effects raise potential concerns about the long-term evolutionary safety of CCGDs, but the magnitude of these effects is unknown. To estimate how the presence of a CCGD or a Cas9 alone in the genome affects the rates of LOH events and de novo mutations, we carried out a mutation accumulation experiment in yeast Saccharomyces cerevisiae. Despite its substantial statistical power, our experiment revealed no detectable effect of CCGD or Cas9 alone on the genome-wide rates of mutations or LOH events, suggesting that these rates are affected by less than 30%. Nevertheless, we found that Cas9 caused a slight but significant shift towards more interstitial and fewer terminal LOH events, and the CCGD caused a significant difference in the distribution of LOH events on Chromosome V. Taken together, our results show that these genetic elements impose a weak and likely localized additional mutational burden in the yeast model. Although the mutagenic effects of CCGDs need to be further evaluated in other systems, our results suggest that the effect of CCGDs on off-target mutation rates and genetic diversity may be acceptable.
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Affiliation(s)
- Michael S. Overton
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Sean E. Guy
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093
- Current address: Bionano Genomics, San Diego, CA 92121
| | - Xingsen Chen
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093
- Current address: Department of Entomology, University of Arizona, Tucson, Arizona, USA
| | - Alena Martsul
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093
- Current address: Illumina Inc., San Diego, CA 92122
| | - Krypton Carolino
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Omar S. Akbari
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Justin R. Meyer
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Sergey Kryazhimskiy
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093
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Li J, Stenberg S, Yue JX, Mikhalev E, Thompson D, Warringer J, Liti G. Genome instability footprint under rapamycin and hydroxyurea treatments. PLoS Genet 2023; 19:e1011012. [PMID: 37931001 PMCID: PMC10653606 DOI: 10.1371/journal.pgen.1011012] [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: 10/04/2023] [Revised: 11/16/2023] [Accepted: 10/10/2023] [Indexed: 11/08/2023] Open
Abstract
The mutational processes dictating the accumulation of mutations in genomes are shaped by genetic background, environment and their interactions. Accurate quantification of mutation rates and spectra under drugs has important implications in disease treatment. Here, we used whole-genome sequencing and time-resolved growth phenotyping of yeast mutation accumulation lines to give a detailed view of the mutagenic effects of rapamycin and hydroxyurea on the genome and cell growth. Mutation rates depended on the genetic backgrounds but were only marginally affected by rapamycin. As a remarkable exception, rapamycin treatment was associated with frequent chromosome XII amplifications, which compensated for rapamycin induced rDNA repeat contraction on this chromosome and served to maintain rDNA content homeostasis and fitness. In hydroxyurea, a wide range of mutation rates were elevated regardless of the genetic backgrounds, with a particularly high occurrence of aneuploidy that associated with dramatic fitness loss. Hydroxyurea also induced a high T-to-G and low C-to-A transversion rate that reversed the common G/C-to-A/T bias in yeast and gave rise to a broad range of structural variants, including mtDNA deletions. The hydroxyurea mutation footprint was consistent with the activation of error-prone DNA polymerase activities and non-homologues end joining repair pathways. Taken together, our study provides an in-depth view of mutation rates and signatures in rapamycin and hydroxyurea and their impact on cell fitness, which brings insights for assessing their chronic effects on genome integrity.
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Affiliation(s)
- Jing Li
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
- Université Côte d’Azur, CNRS, INSERM, IRCAN, Nice, France
| | - Simon Stenberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Jia-Xing Yue
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
- Université Côte d’Azur, CNRS, INSERM, IRCAN, Nice, France
| | | | - Dawn Thompson
- Ginkgo Bioworks, Boston, Massachusetts, United States of America
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Gianni Liti
- Université Côte d’Azur, CNRS, INSERM, IRCAN, Nice, France
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Crandall JG, Fisher KJ, Sato TK, Hittinger CT. Ploidy evolution in a wild yeast is linked to an interaction between cell type and metabolism. PLoS Biol 2023; 21:e3001909. [PMID: 37943740 PMCID: PMC10635434 DOI: 10.1371/journal.pbio.3001909] [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: 10/28/2022] [Accepted: 10/06/2023] [Indexed: 11/12/2023] Open
Abstract
Ploidy is an evolutionarily labile trait, and its variation across the tree of life has profound impacts on evolutionary trajectories and life histories. The immediate consequences and molecular causes of ploidy variation on organismal fitness are frequently less clear, although extreme mating type skews in some fungi hint at links between cell type and adaptive traits. Here, we report an unusual recurrent ploidy reduction in replicate populations of the budding yeast Saccharomyces eubayanus experimentally evolved for improvement of a key metabolic trait, the ability to use maltose as a carbon source. We find that haploids have a substantial, but conditional, fitness advantage in the absence of other genetic variation. Using engineered genotypes that decouple the effects of ploidy and cell type, we show that increased fitness is primarily due to the distinct transcriptional program deployed by haploid-like cell types, with a significant but smaller contribution from absolute ploidy. The link between cell-type specification and the carbon metabolism adaptation can be traced to the noncanonical regulation of a maltose transporter by a haploid-specific gene. This study provides novel mechanistic insight into the molecular basis of an environment-cell type fitness interaction and illustrates how selection on traits unexpectedly linked to ploidy states or cell types can drive karyotypic evolution in fungi.
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Affiliation(s)
- Johnathan G. Crandall
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kaitlin J. Fisher
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Trey K. Sato
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Chris Todd Hittinger
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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Del Olmo V, Mixão V, Fotedar R, Saus E, Al Malki A, Księżopolska E, Nunez-Rodriguez JC, Boekhout T, Gabaldón T. Origin of fungal hybrids with pathogenic potential from warm seawater environments. Nat Commun 2023; 14:6919. [PMID: 37903766 PMCID: PMC10616089 DOI: 10.1038/s41467-023-42679-4] [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: 05/30/2023] [Accepted: 10/17/2023] [Indexed: 11/01/2023] Open
Abstract
Hybridisation is a common event in yeasts often leading to genomic variability and adaptation. The yeast Candida orthopsilosis is a human-associated opportunistic pathogen belonging to the Candida parapsilosis species complex. Most C. orthopsilosis clinical isolates are hybrids resulting from at least four independent crosses between two parental lineages, of which only one has been identified. The rare presence or total absence of parentals amongst clinical isolates is hypothesised to be a consequence of a reduced pathogenicity with respect to their hybrids. Here, we sequence and analyse the genomes of environmental C. orthopsilosis strains isolated from warm marine ecosystems. We find that a majority of environmental isolates are hybrids, phylogenetically closely related to hybrid clinical isolates. Furthermore, we identify the missing parental lineage, thus providing a more complete overview of the genomic evolution of this species. Additionally, we discover phenotypic differences between the two parental lineages, as well as between parents and hybrids, under conditions relevant for pathogenesis. Our results suggest a marine origin of C. orthopsilosis hybrids, with intrinsic pathogenic potential, and pave the way to identify pre-existing environmental adaptations that rendered hybrids more prone than parental lineages to colonise and infect the mammalian host.
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Affiliation(s)
- Valentina Del Olmo
- Life Sciences Department. Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Verónica Mixão
- Life Sciences Department. Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Bioinformatics Unit, Infectious Diseases Department, National Institute of Health Dr. Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal
| | - Rashmi Fotedar
- Department of Genetic Engineering, Biotechnology Centre, Ministry of Municipality and Environment, P.O Box 20022, Doha, Qatar
| | - Ester Saus
- Life Sciences Department. Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Amina Al Malki
- Department of Genetic Engineering, Biotechnology Centre, Ministry of Municipality and Environment, P.O Box 20022, Doha, Qatar
| | - Ewa Księżopolska
- Life Sciences Department. Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Juan Carlos Nunez-Rodriguez
- Life Sciences Department. Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Teun Boekhout
- College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Toni Gabaldón
- Life Sciences Department. Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain.
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- ICREA, Pg. Lluis Companys 23, Barcelona, 08010, Spain.
- , Centro de Investigación Biomédica En Red de Enfermedades Infecciosas, Barcelona, Spain.
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Sharp NP, Smith DR, Driscoll G, Sun K, Vickerman CM, Martin SCT. Contribution of Spontaneous Mutations to Quantitative and Molecular Variation at the Highly Repetitive rDNA Locus in Yeast. Genome Biol Evol 2023; 15:evad179. [PMID: 37847861 PMCID: PMC10581546 DOI: 10.1093/gbe/evad179] [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] [Accepted: 09/26/2023] [Indexed: 10/19/2023] Open
Abstract
The ribosomal DNA array in Saccharomyces cerevisiae consists of many tandem repeats whose copy number is believed to be functionally important but highly labile. Regulatory mechanisms have evolved to maintain copy number by directed mutation, but how spontaneous variation at this locus is generated and selected has not been well characterized. We applied a mutation accumulation approach to quantify the impacts of mutation and selection on this unique genomic feature across hundreds of mutant strains. We find that mutational variance for this trait is relatively high, and that unselected mutations elsewhere in the genome can disrupt copy number maintenance. In consequence, copy number generally declines gradually, consistent with a previously proposed model of rDNA maintenance where a downward mutational bias is normally compensated by mechanisms that increase copy number when it is low. This pattern holds across ploidy levels and strains in the standard lab environment but differs under some stressful conditions. We identify several alleles, gene categories, and genomic features that likely affect copy number, including aneuploidy for chromosome XII. Copy number change is associated with reduced growth in diploids, consistent with stabilizing selection. Levels of standing variation in copy number are well predicted by a balance between mutation and stabilizing selection, suggesting this trait is not subject to strong diversifying selection in the wild. The rate and spectrum of point mutations within the rDNA locus itself are distinct from the rest of the genome and predictive of polymorphism locations. Our findings help differentiate the roles of mutation and selection and indicate that spontaneous mutation patterns shape several aspects of ribosomal DNA evolution.
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Affiliation(s)
- Nathaniel P Sharp
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Denise R Smith
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Gregory Driscoll
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kexin Sun
- Present address: Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, USA
| | | | - Sterling C T Martin
- Present address: Department of Biology, Washington University, St. Louis, Missouri, USA
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8
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Smukowski Heil C. Loss of Heterozygosity and Its Importance in Evolution. J Mol Evol 2023; 91:369-377. [PMID: 36752826 PMCID: PMC10276065 DOI: 10.1007/s00239-022-10088-8] [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: 09/14/2022] [Accepted: 12/23/2022] [Indexed: 02/09/2023]
Abstract
Loss of heterozygosity (LOH) is a mitotic recombination event that converts heterozygous loci to homozygous loci. This mutation event is widespread in organisms that have asexual reproduction like budding yeasts, and is also an important and frequent mutation event in tumorigenesis. Mutation accumulation studies have demonstrated that LOH occurs at a rate higher than the point mutation rate, and can impact large portions of the genome. Laboratory evolution experiments of heterozygous yeasts have revealed that LOH often unmasks beneficial recessive alleles that can confer large fitness advantages. Here, I highlight advances in understanding dominance, fitness, and phenotypes in laboratory evolved heterozygous yeast strains. I discuss best practices for detecting LOH in intraspecific and interspecific evolved clones and populations. Utilizing heterozygous strain backgrounds in laboratory evolution experiments offers an opportunity to advance our understanding of this important mutation type in shaping adaptation and genome evolution in wild, domesticated, and clinical populations.
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Affiliation(s)
- Caiti Smukowski Heil
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.
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9
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Martínez AA, Lang GI. Identifying Targets of Selection in Laboratory Evolution Experiments. J Mol Evol 2023; 91:345-355. [PMID: 36810618 PMCID: PMC11197053 DOI: 10.1007/s00239-023-10096-2] [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: 12/07/2022] [Accepted: 02/01/2023] [Indexed: 02/24/2023]
Abstract
Adaptive evolution navigates a balance between chance and determinism. The stochastic processes of mutation and drift generate phenotypic variation; however, once mutations reach an appreciable frequency in the population, their fate is governed by the deterministic action of selection, enriching for favorable genotypes and purging the less-favorable ones. The net result is that replicate populations will traverse similar-but not identical-pathways to higher fitness. This parallelism in evolutionary outcomes can be leveraged to identify the genes and pathways under selection. However, distinguishing between beneficial and neutral mutations is challenging because many beneficial mutations will be lost due to drift and clonal interference, and many neutral (and even deleterious) mutations will fix by hitchhiking. Here, we review the best practices that our laboratory uses to identify genetic targets of selection from next-generation sequencing data of evolved yeast populations. The general principles for identifying the mutations driving adaptation will apply more broadly.
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Affiliation(s)
| | - Gregory I Lang
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA.
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Yoosefzadeh Najafabadi M, Hesami M, Rajcan I. Unveiling the Mysteries of Non-Mendelian Heredity in Plant Breeding. PLANTS (BASEL, SWITZERLAND) 2023; 12:1956. [PMID: 37653871 PMCID: PMC10221147 DOI: 10.3390/plants12101956] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 07/30/2023]
Abstract
Mendelian heredity is the cornerstone of plant breeding and has been used to develop new varieties of plants since the 19th century. However, there are several breeding cases, such as cytoplasmic inheritance, methylation, epigenetics, hybrid vigor, and loss of heterozygosity (LOH), where Mendelian heredity is not applicable, known as non-Mendelian heredity. This type of inheritance can be influenced by several factors besides the genetic architecture of the plant and its breeding potential. Therefore, exploring various non-Mendelian heredity mechanisms, their prevalence in plants, and the implications for plant breeding is of paramount importance to accelerate the pace of crop improvement. In this review, we examine the current understanding of non-Mendelian heredity in plants, including the mechanisms, inheritance patterns, and applications in plant breeding, provide an overview of the various forms of non-Mendelian inheritance (including epigenetic inheritance, cytoplasmic inheritance, hybrid vigor, and LOH), explore insight into the implications of non-Mendelian heredity in plant breeding, and the potential it holds for future research.
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Affiliation(s)
| | | | - Istvan Rajcan
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (M.Y.N.); (M.H.)
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11
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Mixão V, Nunez-Rodriguez JC, Del Olmo V, Ksiezopolska E, Saus E, Boekhout T, Gacser A, Gabaldón T. Evolution of loss of heterozygosity patterns in hybrid genomes of Candida yeast pathogens. BMC Biol 2023; 21:105. [PMID: 37170256 PMCID: PMC10173528 DOI: 10.1186/s12915-023-01608-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 04/27/2023] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND Hybrids are chimeric organisms with highly plastic heterozygous genomes that may confer unique traits enabling the adaptation to new environments. However, most evolutionary theory frameworks predict that the high levels of genetic heterozygosity present in hybrids from divergent parents are likely to result in numerous deleterious epistatic interactions. Under this scenario, selection is expected to favor recombination events resulting in loss of heterozygosity (LOH) affecting genes involved in such negative interactions. Nevertheless, it is so far unknown whether this phenomenon actually drives genomic evolution in natural populations of hybrids. To determine the balance between selection and drift in the evolution of LOH patterns in natural yeast hybrids, we analyzed the genomic sequences from fifty-five hybrid strains of the pathogenic yeasts Candida orthopsilosis and Candida metapsilosis, which derived from at least six distinct natural hybridization events. RESULTS We found that, although LOH patterns in independent hybrid clades share some level of convergence that would not be expected from random occurrence, there is an apparent lack of strong functional selection. Moreover, while mitosis is associated with a limited number of inter-homeologous chromosome recombinations in these genomes, induced DNA breaks seem to increase the LOH rate. We also found that LOH does not accumulate linearly with time in these hybrids. Furthermore, some C. orthopsilosis hybrids present LOH patterns compatible with footprints of meiotic recombination. These meiotic-like patterns are at odds with a lack of evidence of sexual recombination and with our inability to experimentally induce sporulation in these hybrids. CONCLUSIONS Our results suggest that genetic drift is the prevailing force shaping LOH patterns in these hybrid genomes. Moreover, the observed LOH patterns suggest that these are likely not the result of continuous accumulation of sporadic events-as expected by mitotic repair of rare chromosomal breaks-but rather of acute episodes involving many LOH events in a short period of time.
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Affiliation(s)
- Verónica Mixão
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Present address: Genomics and Bioinformatics Unit, Infectious Diseases Department, National Institute of Health Dr. Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal
| | - Juan Carlos Nunez-Rodriguez
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Valentina Del Olmo
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ewa Ksiezopolska
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ester Saus
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Attila Gacser
- Department of Microbiology, University of Szeged, Szeged, Hungary
- MTA-SZTE "Lendület" Mycobiome Research Group, University of Szeged, Szeged, Hungary
| | - Toni Gabaldón
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain.
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- ICREA, Pg. Lluis Companys 23, 08010, Barcelona, Spain.
- Centro de Investigación Biomédica En Red de Enfermedades Infecciosas, Barcelona, Spain.
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12
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Purkanti R, Thattai M. Genome doubling enabled the expansion of yeast vesicle traffic pathways. Sci Rep 2022; 12:11213. [PMID: 35780185 PMCID: PMC9250509 DOI: 10.1038/s41598-022-15419-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/23/2022] [Indexed: 11/09/2022] Open
Abstract
Vesicle budding and fusion in eukaryotes depend on a suite of protein types, such as Arfs, Rabs, coats and SNAREs. Distinct paralogs of these proteins act at distinct intracellular locations, suggesting a link between gene duplication and the expansion of vesicle traffic pathways. Genome doubling, a common source of paralogous genes in fungi, provides an ideal setting in which to explore this link. Here we trace the fates of paralog doublets derived from the 100-Ma-old hybridization event that gave rise to the whole genome duplication clade of budding yeast. We find that paralog doublets involved in specific vesicle traffic functions and pathways are convergently retained across the entire clade. Vesicle coats and adaptors involved in secretory and early-endocytic pathways are retained as doublets, at rates several-fold higher than expected by chance. Proteins involved in later endocytic steps and intra-Golgi traffic, including the entire set of multi-subunit and coiled-coil tethers, have reverted to singletons. These patterns demonstrate that selection has acted to expand and diversify the yeast vesicle traffic apparatus, across species and time.
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Affiliation(s)
- Ramya Purkanti
- Center for Integrative Genomics, Université de Lausanne, Lausanne, Switzerland
| | - Mukund Thattai
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India.
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13
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Multiple Stochastic Parameters Influence Genome Dynamics in a Heterozygous Diploid Eukaryotic Model. J Fungi (Basel) 2022; 8:jof8070650. [PMID: 35887406 PMCID: PMC9323731 DOI: 10.3390/jof8070650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/10/2022] [Accepted: 06/14/2022] [Indexed: 12/10/2022] Open
Abstract
The heterozygous diploid genome of Candida albicans displays frequent genomic rearrangements, in particular loss-of-heterozygosity (LOH) events, which can be seen on all eight chromosomes and affect both laboratory and clinical strains. LOHs, which are often the consequence of DNA damage repair, can be observed upon stresses reminiscent of the host environment, and result in homozygous regions of various sizes depending on the molecular mechanisms at their origins. Recent studies have shed light on the biological importance of these frequent and ubiquitous LOH events in C. albicans. In diploid Saccharomyces cerevisiae, LOH facilitates the passage of recessive beneficial mutations through Haldane’s sieve, allowing rapid evolutionary adaptation. This also appears to be true in C. albicans, where the full potential of an adaptive mutation is often only observed upon LOH, as illustrated in the case of antifungal resistance and niche adaptation. To understand the genome-wide dynamics of LOH events in C. albicans, we constructed a collection of 15 strains, each one carrying a LOH reporter system on a different chromosome arm. This system involves the insertion of two fluorescent marker genes in a neutral genomic region on both homologs, allowing spontaneous LOH events to be detected by monitoring the loss of one of the fluorescent markers using flow cytometry. Using this collection, we observed significant LOH frequency differences between genomic loci in standard laboratory growth conditions; however, we further demonstrated that comparable heterogeneity was also observed for a given genomic locus between independent strains. Additionally, upon exposure to stress, three outcomes could be observed in C. albicans, where individual strains displayed increases, decreases, or no effect of stress in terms of LOH frequency. Our results argue against a general stress response triggering overall genome instability. Indeed, we showed that the heterogeneity of LOH frequency in C. albicans is present at various levels, inter-strain, intra-strain, and inter-chromosomes, suggesting that LOH events may occur stochastically within a cell, though the genetic background potentially impacts genome stability in terms of LOH throughout the genome in both basal and stress conditions. This heterogeneity in terms of genome stability may serve as an important adaptive strategy for the predominantly clonal human opportunistic pathogen C. albicans, by quickly generating a wide spectrum of genetic variation combinations potentially permitting subsistence in a rapidly evolving environment.
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14
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Baselga-Cervera B, Gettle N, Travisano M. Loss-of-heterozygosity facilitates a fitness valley crossing in experimentally evolved multicellular yeast. Proc Biol Sci 2022; 289:20212722. [PMID: 36547392 PMCID: PMC9185828 DOI: 10.1098/rspb.2021.2722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Determining how adaptive possibilities do or do not become evolutionary realities is central to understanding the tempo and mode of evolutionary change. Some of the simplest evolutionary landscapes arise from underdominance at a single locus where the fitness valley consists of only one less-fit genotype. Despite their potential for rapid evolutionary change, few such examples have been investigated. We capitalized on an experimental system in which a significant evolutionary shift, the transition from uni-to-multicellularity, was observed in asexual diploid populations of Saccharomyces cerevisiae experimentally selected for increased settling rates. The multicellular phenotype results from recessive single-locus mutations that undergo loss-of-heterozygosity (LOH) events. By reconstructing the necessary heterozygous intermediate steps, we found that the evolution of multicellularity involves a decrease in size during the first steps. Heterozygous genotypes are 20% smaller in size than genotypes with functional alleles. Nevertheless, populations of heterozygotes give rise to multicellular genotypes more readily than unicellular genotypes with two functional alleles, by rapid LOH events. LOH drives adaptation that may enable rapid evolution in diploid yeast. Together these results show discordance between the phenotypic and genotypic multicellular transition. The evolutionary path to multicellularity, and the adaptive benefits of increased size, requires initial size reductions.
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Affiliation(s)
- Beatriz Baselga-Cervera
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St Paul, MN 55108, USA,Minnesota Center for Philosophy of Science, University of Minnesota, Minneapolis, MN 55455, USA
| | - Noah Gettle
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Michael Travisano
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St Paul, MN 55108, USA,The BioTechnology Institute, University of Minnesota, St Paul, MN 55108, USA,Minnesota Center for Philosophy of Science, University of Minnesota, Minneapolis, MN 55455, USA
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15
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Harrouard J, Eberlein C, Ballestra P, Dols-Lafargue M, Masneuf-Pomarede I, Miot-Sertier C, Schacherer J, Albertin W. Brettanomyces bruxellensis: Overview of the genetic and phenotypic diversity of an anthropized yeast. Mol Ecol 2022; 32:2374-2395. [PMID: 35318747 DOI: 10.1111/mec.16439] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 03/08/2022] [Accepted: 03/16/2022] [Indexed: 12/24/2022]
Abstract
Human-associated microorganisms are ideal models to study the impact of environmental changes on species evolution and adaptation because of their small genome, short generation time, and their colonization of contrasting and ever-changing ecological niches. The yeast Brettanomyces bruxellensis is a good example of organism facing anthropogenic-driven selective pressures. It is associated with fermentation processes in which it can be considered either as a spoiler (e.g. winemaking, bioethanol production) or as a beneficial microorganism (e.g. production of specific beers, kombucha). Besides its industrial interests, noteworthy parallels and dichotomies with Saccharomyces cerevisiae propelled B. bruxellensis as a valuable complementary yeast model. In this review, we emphasize that the broad genetic and phenotypic diversity of this species is only beginning to be uncovered. Population genomic studies have revealed the co-existence of auto- and allotriploidization events with different evolutionary outcomes. The different diploid, autotriploid and allotriploid subpopulations are associated with specific fermented processes, suggesting independent adaptation events to anthropized environments. Phenotypically, B. bruxellensis is renowned for its ability to metabolize a wide variety of carbon and nitrogen sources, which may explain its ability to colonize already fermented environments showing low-nutrient contents. Several traits of interest could be related to adaptation to human activities (e.g. nitrate metabolization in bioethanol production, resistance to sulphite treatments in winemaking). However, phenotypic traits are insufficiently studied in view of the great genomic diversity of the species. Future work will have to take into account strains of varied substrates, geographical origins as well as displaying different ploidy levels to improve our understanding of an anthropized yeast's phenotypic landscape.
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Affiliation(s)
- Jules Harrouard
- UMR 1366 OENOLOGIE, Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, Institut des Sciences de la Vigne et du Vin, 33140, Villenave d'Ornon, France
| | - Chris Eberlein
- Université de Strasbourg, CNRS, GMGM, UMR 7156, Strasbourg, France
| | - Patricia Ballestra
- UMR 1366 OENOLOGIE, Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, Institut des Sciences de la Vigne et du Vin, 33140, Villenave d'Ornon, France
| | - Marguerite Dols-Lafargue
- UMR 1366 OENOLOGIE, Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, Institut des Sciences de la Vigne et du Vin, 33140, Villenave d'Ornon, France.,ENSCBP, Bordeaux INP, 33600, Pessac, France
| | - Isabelle Masneuf-Pomarede
- UMR 1366 OENOLOGIE, Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, Institut des Sciences de la Vigne et du Vin, 33140, Villenave d'Ornon, France.,BSA, 33170, Gradignan
| | - Cécile Miot-Sertier
- UMR 1366 OENOLOGIE, Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, Institut des Sciences de la Vigne et du Vin, 33140, Villenave d'Ornon, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM, UMR 7156, Strasbourg, France.,Institut Universitaire de France (IUF), Paris, France
| | - Warren Albertin
- UMR 1366 OENOLOGIE, Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, Institut des Sciences de la Vigne et du Vin, 33140, Villenave d'Ornon, France.,ENSCBP, Bordeaux INP, 33600, Pessac, France
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16
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Yeast Hybrids in Brewing. FERMENTATION 2022. [DOI: 10.3390/fermentation8020087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Microbiology has long been a keystone in fermentation, and innovative yeast molecular biotechnology continues to represent a fruitful frontier in brewing science. Consequently, modern understanding of brewer’s yeast has undergone significant refinement over the last few decades. This publication presents a condensed summation of Saccharomyces species dynamics with an emphasis on the relationship between; traditional Saccharomyces cerevisiae ale yeast, S. pastorianus interspecific hybrids used in lager production, and novel hybrid yeast progress. Moreover, introgression from other Saccharomyces species is briefly addressed. The unique history of Saccharomyces cerevisiae and Saccharomyces hybrids is exemplified by recent genomic sequencing studies aimed at categorizing brewing strains through phylogeny and redefining Saccharomyces species boundaries. Phylogenetic investigations highlight the genomic diversity of Saccharomyces cerevisiae ale strains long known to brewers for their fermentation characteristics and phenotypes. The discovery of genomic contributions from interspecific Saccharomyces species into the genome of S. cerevisiae strains is ever more apparent with increasing research investigating the hybrid nature of modern industrial and historical fermentation yeast.
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17
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Bai FY, Han DY, Duan SF, Wang QM. The Ecology and Evolution of the Baker’s Yeast Saccharomyces cerevisiae. Genes (Basel) 2022; 13:genes13020230. [PMID: 35205274 PMCID: PMC8871604 DOI: 10.3390/genes13020230] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 01/01/2023] Open
Abstract
The baker’s yeast Saccharomyces cerevisiae has become a powerful model in ecology and evolutionary biology. A global effort on field survey and population genetics and genomics of S. cerevisiae in past decades has shown that the yeast distributes ubiquitously in nature with clearly structured populations. The global genetic diversity of S. cerevisiae is mainly contributed by strains from Far East Asia, and the ancient basal lineages of the species have been found only in China, supporting an ‘out-of-China’ origin hypothesis. The wild and domesticated populations are clearly separated in phylogeny and exhibit hallmark differences in sexuality, heterozygosity, gene copy number variation (CNV), horizontal gene transfer (HGT) and introgression events, and maltose utilization ability. The domesticated strains from different niches generally form distinct lineages and harbor lineage-specific CNVs, HGTs and introgressions, which contribute to their adaptations to specific fermentation environments. However, whether the domesticated lineages originated from a single, or multiple domestication events is still hotly debated and the mechanism causing the diversification of the wild lineages remains to be illuminated. Further worldwide investigations on both wild and domesticated S. cerevisiae, especially in Africa and West Asia, will be helpful for a better understanding of the natural and domestication histories and evolution of S. cerevisiae.
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Affiliation(s)
- Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China; (D.-Y.H.); (S.-F.D.)
- College of Life Sciences, University of Chinese Academy of Sciences, Shijingshan District, Beijing 100049, China
- Correspondence: ; Tel.: +86-10-6480-7406
| | - Da-Yong Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China; (D.-Y.H.); (S.-F.D.)
| | - Shou-Fu Duan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China; (D.-Y.H.); (S.-F.D.)
| | - Qi-Ming Wang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China;
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18
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Bendixsen DP, Frazão JG, Stelkens R. Saccharomyces yeast hybrids on the rise. Yeast 2021; 39:40-54. [PMID: 34907582 DOI: 10.1002/yea.3684] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/19/2021] [Accepted: 12/08/2021] [Indexed: 12/23/2022] Open
Abstract
Saccharomyces hybrid yeasts are receiving increasing attention as a powerful model system to understand adaptation to environmental stress and speciation mechanisms, using experimental evolution and omics techniques. We compiled all genomic resources available from public repositories of the eight recognized Saccharomyces species and their interspecific hybrids. We present the newest numbers on genomes sequenced, assemblies, annotations, and sequencing runs, and an updated species phylogeny using orthogroup inference. While genomic resources are highly skewed towards Saccharomyces cerevisiae, there is a noticeable movement to use wild, recently discovered yeast species in recent years. To illustrate the degree and potential causes of reproductive isolation, we reanalyzed published data on hybrid spore viabilities across the entire genus and tested for the role of genetic, geographic, and ecological divergence within and between species (28 cross types and 371 independent crosses). Hybrid viability generally decreased with parental genetic distance likely due to antirecombination and negative epistasis, but notable exceptions emphasize the importance of strain-specific structural variation and ploidy differences. Surprisingly, the viability of crosses within species varied widely, from near reproductive isolation to near-perfect viability. Geographic and ecological origins of the parents predicted cross viability to an extent, but with certain caveats. Finally, we highlight publication trends in the field and point out areas of special interest, where hybrid yeasts are particularly promising for innovation through research and development, and experimental evolution and fermentation.
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Affiliation(s)
- Devin P Bendixsen
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - João G Frazão
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Rike Stelkens
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
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19
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Cheng Y, Miller MJ, Zhang D, Xiong Y, Hao Y, Jia C, Cai T, Li SH, Johansson US, Liu Y, Chang Y, Song G, Qu Y, Lei F. Parallel genomic responses to historical climate change and high elevation in East Asian songbirds. Proc Natl Acad Sci U S A 2021; 118:e2023918118. [PMID: 34873033 PMCID: PMC8685689 DOI: 10.1073/pnas.2023918118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2021] [Indexed: 12/01/2022] Open
Abstract
Parallel evolution can be expected among closely related taxa exposed to similar selective pressures. However, parallelism is typically stronger at the phenotypic level, while genetic solutions to achieve these phenotypic similarities may differ. For polygenic traits, the availability of standing genetic variation (i.e., heterozygosity) may influence such genetic nonparallelism. Here, we examine the extent to which high-elevation adaptation is parallel-and whether the level of parallelism is affected by heterozygosity-by analyzing genomes of 19 Paridae species distributed across East Asia with a dramatic east-west elevation gradient. We find that western highlands endemic parids have consistently lower levels of heterozygosity-likely the result of late-Pleistocene demographic contraction-than do parids found exclusively in eastern lowlands, which remained unglaciated during the late Pleistocene. Three widespread species (east to west) have high levels of heterozygosity similar to that observed in eastern species, although their western populations are less variable than eastern ones. Comparing genomic responses to extreme environments of the Qinghai-Tibet Plateau, we find that the most differentiated genomic regions between each high-elevation taxon and its low-elevation relative are significantly enriched for genes potentially related to the oxygen transport cascade and/or thermogenesis. Despite no parallelism at particular genes, high similarity in gene function is found among comparisons. Furthermore, parallelism is not higher in more heterozygous widespread parids than in highland endemics. Thus, in East Asian parids, parallel functional response to extreme elevation appears to rely on different genes, with differences in heterozygosity having no effect on the degree of genetic parallelism.
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Affiliation(s)
- Yalin Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Matthew J Miller
- Reneco International Wildlife Consultants, LLC, Abu Dhabi, UAE
- University of Alaska Museum, University of Alaska Fairbanks, AK
| | - Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ying Xiong
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Hao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenxi Jia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tianlong Cai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shou-Hsien Li
- Department of Life Sciences, National Taiwan Normal University, Taipei, 116, Taiwan, China
| | - Ulf S Johansson
- Department of Zoology, Swedish Museum of Natural History, SE-104 05 Stockholm, Sweden
| | - Yang Liu
- State Key Laboratory of Biocontrol, Department of Ecology/School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yongbin Chang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650201, China
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20
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Janko K, Bartoš O, Kočí J, Roslein J, Drdová EJ, Kotusz J, Eisner J, Mokrejš M, Štefková-Kašparová E. Genome Fractionation and Loss of Heterozygosity in Hybrids and Polyploids: Mechanisms, Consequences for Selection, and Link to Gene Function. Mol Biol Evol 2021; 38:5255-5274. [PMID: 34410426 PMCID: PMC8662595 DOI: 10.1093/molbev/msab249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Hybridization and genome duplication have played crucial roles in the evolution of many animal and plant taxa. The subgenomes of parental species undergo considerable changes in hybrids and polyploids, which often selectively eliminate segments of one subgenome. However, the mechanisms underlying these changes are not well understood, particularly when the hybridization is linked with asexual reproduction that opens up unexpected evolutionary pathways. To elucidate this problem, we compared published cytogenetic and RNAseq data with exome sequences of asexual diploid and polyploid hybrids between three fish species; Cobitis elongatoides, C. taenia, and C. tanaitica. Clonal genomes remained generally static at chromosome-scale levels but their heterozygosity gradually deteriorated at the level of individual genes owing to allelic deletions and conversions. Interestingly, the impact of both processes varies among animals and genomic regions depending on ploidy level and the properties of affected genes. Namely, polyploids were more tolerant to deletions than diploid asexuals where conversions prevailed, and genomic restructuring events accumulated preferentially in genes characterized by high transcription levels and GC-content, strong purifying selection and specific functions like interacting with intracellular membranes. Although hybrids were phenotypically more similar to C. taenia, we found that they preferentially retained C. elongatoides alleles. This demonstrates that favored subgenome is not necessarily the transcriptionally dominant one. This study demonstrated that subgenomes in asexual hybrids and polyploids evolve under a complex interplay of selection and several molecular mechanisms whose efficiency depends on the organism's ploidy level, as well as functional properties and parental ancestry of the genomic region.
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Affiliation(s)
- Karel Janko
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Oldřich Bartoš
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jan Kočí
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Jan Roslein
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Edita Janková Drdová
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jan Kotusz
- Museum of Natural History, University of Wroclaw, Wroclaw, Poland
| | - Jan Eisner
- Department of Mathematics, Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czech Republic
| | - Martin Mokrejš
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- IT4Innovations, VŠB—Technical University of Ostrava, Ostrava-Poruba, Czech Republic
| | - Eva Štefková-Kašparová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Genetics and Breeding, FAFNR, Czech University of Life Sciences Prague, Czech Republic
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21
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Abstract
AbstractYeasts, usually defined as unicellular fungi, occur in various fungal lineages. Hence, they are not a taxonomic unit, but rather represent a fungal lifestyle shared by several unrelated lineages. Although the discovery of new yeast species occurs at an increasing speed, at the current rate it will likely take hundreds of years, if ever, before they will all be documented. Many parts of the earth, including many threatened habitats, remain unsampled for yeasts and many others are only superficially studied. Cold habitats, such as glaciers, are home to a specific community of cold-adapted yeasts, and, hence, there is some urgency to study such environments at locations where they might disappear soon due to anthropogenic climate change. The same is true for yeast communities in various natural forests that are impacted by deforestation and forest conversion. Many countries of the so-called Global South have not been sampled for yeasts, despite their economic promise. However, extensive research activity in Asia, especially China, has yielded many taxonomic novelties. Comparative genomics studies have demonstrated the presence of yeast species with a hybrid origin, many of them isolated from clinical or industrial environments. DNA-metabarcoding studies have demonstrated the prevalence, and in some cases dominance, of yeast species in soils and marine waters worldwide, including some surprising distributions, such as the unexpected and likely common presence of Malassezia yeasts in marine habitats.
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22
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Eberlein C, Abou Saada O, Friedrich A, Albertin W, Schacherer J. Different trajectories of polyploidization shape the genomic landscape of the Brettanomyces bruxellensis yeast species. Genome Res 2021; 31:2316-2326. [PMID: 34815309 PMCID: PMC8647821 DOI: 10.1101/gr.275380.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 10/25/2021] [Indexed: 01/01/2023]
Abstract
Polyploidization events are observed across the tree of life and occur in many fungi, plant, and animal species. During evolution, polyploidy is thought to be an important source of speciation and tumorigenesis. However, the origin of polyploid populations is not always clear, and little is known about the precise nature and structure of their complex genome. Using a long-read sequencing strategy, we sequenced 71 strains from the Brettanomyces bruxellensis yeast species, which is found in anthropized environments (e.g., beer, contaminant of wine, kombucha, and ethanol production) and characterized by several polyploid subpopulations. To reconstruct the polyploid genomes, we phased them by using different strategies and found that each subpopulation had a unique polyploidization history with distinct trajectories. The polyploid genomes contain either genetically closely related (with a genetic divergence <1%) or diverged copies (>3%), indicating auto- as well as allopolyploidization events. These latest events have occurred independently with a specific and unique donor in each of the polyploid subpopulations and exclude the known Brettanomyces sister species as possible donors. Finally, loss of heterozygosity events has shaped the structure of these polyploid genomes and underline their dynamics. Overall, our study highlights the multiplicity of the trajectories leading to polyploid genomes within the same species.
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Affiliation(s)
- Chris Eberlein
- Université de Strasbourg, CNRS, GMGM UMR 7156, 67000 Strasbourg, France
| | - Omar Abou Saada
- Université de Strasbourg, CNRS, GMGM UMR 7156, 67000 Strasbourg, France
| | - Anne Friedrich
- Université de Strasbourg, CNRS, GMGM UMR 7156, 67000 Strasbourg, France
| | - Warren Albertin
- Université de Bordeaux, ISVV, Unité de Recherche Œnologie EA 4577, USC 1366 INRA, Bordeaux INP, F-33140 Villenave d'Ornon, France
- ENSCBP, Bordeaux INP, 33600 Pessac, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR 7156, 67000 Strasbourg, France
- Institut Universitaire de France (IUF), 75231 Paris, France
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23
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Mozzachiodi S, Tattini L, Llored A, Irizar A, Škofljanc N, D'Angiolo M, De Chiara M, Barré BP, Yue JX, Lutazi A, Loeillet S, Laureau R, Marsit S, Stenberg S, Albaud B, Persson K, Legras JL, Dequin S, Warringer J, Nicolas A, Liti G. Aborting meiosis allows recombination in sterile diploid yeast hybrids. Nat Commun 2021; 12:6564. [PMID: 34772931 PMCID: PMC8589840 DOI: 10.1038/s41467-021-26883-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 10/20/2021] [Indexed: 12/03/2022] Open
Abstract
Hybrids between diverged lineages contain novel genetic combinations but an impaired meiosis often makes them evolutionary dead ends. Here, we explore to what extent an aborted meiosis followed by a return-to-growth (RTG) promotes recombination across a panel of 20 Saccharomyces cerevisiae and S. paradoxus diploid hybrids with different genomic structures and levels of sterility. Genome analyses of 275 clones reveal that RTG promotes recombination and generates extensive regions of loss-of-heterozygosity in sterile hybrids with either a defective meiosis or a heavily rearranged karyotype, whereas RTG recombination is reduced by high sequence divergence between parental subgenomes. The RTG recombination preferentially arises in regions with low local heterozygosity and near meiotic recombination hotspots. The loss-of-heterozygosity has a profound impact on sexual and asexual fitness, and enables genetic mapping of phenotypic differences in sterile lineages where linkage analysis would fail. We propose that RTG gives sterile yeast hybrids access to a natural route for genome recombination and adaptation.
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Grants
- This work was supported by Agence Nationale de la Recherche (ANR-11-LABX-0028-01, ANR-13-BSV6-0006-01, ANR-15-IDEX-01, ANR-16-CE12-0019 and ANR-18-CE12-0004), Fondation pour la Recherche Médicale (FRM EQU202003010413), CEFIPRA, Cancéropôle PACA (AAP Equipment 2018), Meiogenix and the Swedish Research Council (2014-6547, 2014-4605 and 2018-03638). S.Mo. is funded by the convention CIFRE 2016/0582 between Meiogenix and ANRT. The Institut Curie NGS platform is supported by ANR-10-EQPX-03 (Equipex), ANR-10-INBS-09-08 (France Génomique Consortium), ITMO-CANCER and SiRIC INCA-DGOS (4654 program).
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Affiliation(s)
- Simone Mozzachiodi
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
- Meiogenix, 38, rue Servan, Paris, 75011, France
| | | | - Agnes Llored
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
| | | | - Neža Škofljanc
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
| | | | | | | | - Jia-Xing Yue
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Angela Lutazi
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
| | - Sophie Loeillet
- Institut Curie, Centre de Recherche, CNRS-UMR3244, PSL Research University, Paris, 75005, France
| | - Raphaelle Laureau
- Institut Curie, Centre de Recherche, CNRS-UMR3244, PSL Research University, Paris, 75005, France
- Department of Genetics and Development, Hammer Health Sciences Center, Columbia University Medical Center, New York, NY, USA
| | - Souhir Marsit
- Institut Curie, Centre de Recherche, CNRS-UMR3244, PSL Research University, Paris, 75005, France
- SPO, Université Montpellier, INRAE, Montpellier SupAgro, Montpellier, France
- Département de Biologie Chimie et Géographie, Université du Québec à Rimouski, Rimouski, Québec, Canada
| | - Simon Stenberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Benoit Albaud
- Institut Curie, ICGEX NGS Platform, Paris, 75005, France
| | - Karl Persson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Jean-Luc Legras
- SPO, Université Montpellier, INRAE, Montpellier SupAgro, Montpellier, France
| | - Sylvie Dequin
- SPO, Université Montpellier, INRAE, Montpellier SupAgro, Montpellier, France
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Alain Nicolas
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
- Meiogenix, 38, rue Servan, Paris, 75011, France
- Institut Curie, Centre de Recherche, CNRS-UMR3244, PSL Research University, Paris, 75005, France
| | - Gianni Liti
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France.
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24
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Bendixsen DP, Peris D, Stelkens R. Patterns of Genomic Instability in Interspecific Yeast Hybrids With Diverse Ancestries. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:742894. [PMID: 37744091 PMCID: PMC10512264 DOI: 10.3389/ffunb.2021.742894] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/06/2021] [Indexed: 09/26/2023]
Abstract
The genomes of hybrids often show substantial deviations from the features of the parent genomes, including genomic instabilities characterized by chromosomal rearrangements, gains, and losses. This plastic genomic architecture generates phenotypic diversity, potentially giving hybrids access to new ecological niches. It is however unclear if there are any generalizable patterns and predictability in the type and prevalence of genomic variation and instability across hybrids with different genetic and ecological backgrounds. Here, we analyzed the genomic architecture of 204 interspecific Saccharomyces yeast hybrids isolated from natural, industrial fermentation, clinical, and laboratory environments. Synchronous mapping to all eight putative parental species showed significant variation in read depth indicating frequent aneuploidy, affecting 44% of all hybrid genomes and particularly smaller chromosomes. Early generation hybrids with largely equal genomic content from both parent species were more likely to contain aneuploidies than introgressed genomes with an older hybridization history, which presumably stabilized the genome. Shared k-mer analysis showed that the degree of genomic diversity and variability varied among hybrids with different parent species. Interestingly, more genetically distant crosses produced more similar hybrid genomes, which may be a result of stronger negative epistasis at larger genomic divergence, putting constraints on hybridization outcomes. Mitochondrial genomes were typically inherited from the species also contributing the majority nuclear genome, but there were clear exceptions to this rule. Together, we find reliable genomic predictors of instability in hybrids, but also report interesting cross- and environment-specific idiosyncrasies. Our results are an important step in understanding the factors shaping divergent hybrid genomes and their role in adaptive evolution.
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Affiliation(s)
- Devin P. Bendixsen
- Population Genetics Division, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - David Peris
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
- Department of Health, Valencian International University, Valencia, Spain
| | - Rike Stelkens
- Population Genetics Division, Department of Zoology, Stockholm University, Stockholm, Sweden
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25
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Cosentino RO, Brink BG, Siegel TN. Allele-specific assembly of a eukaryotic genome corrects apparent frameshifts and reveals a lack of nonsense-mediated mRNA decay. NAR Genom Bioinform 2021; 3:lqab082. [PMID: 34541528 PMCID: PMC8445201 DOI: 10.1093/nargab/lqab082] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/25/2021] [Accepted: 09/06/2021] [Indexed: 11/14/2022] Open
Abstract
To date, most reference genomes represent a mosaic consensus sequence in which the homologous chromosomes are collapsed into one sequence. This approach produces sequence artefacts and impedes analyses of allele-specific mechanisms. Here, we report an allele-specific genome assembly of the diploid parasite Trypanosoma brucei and reveal allelic variants affecting gene expression. Using long-read sequencing and chromosome conformation capture data, we could assign 99.5% of all heterozygote variants to a specific homologous chromosome and build a 66 Mb long allele-specific genome assembly. The phasing of haplotypes allowed us to resolve hundreds of artefacts present in the previous mosaic consensus assembly. In addition, it revealed allelic recombination events, visible as regions of low allelic heterozygosity, enabling the lineage tracing of T. brucei isolates. Interestingly, analyses of transcriptome and translatome data of genes with allele-specific premature termination codons point to the absence of a nonsense-mediated decay mechanism in trypanosomes. Taken together, this study delivers a reference quality allele-specific genome assembly of T. brucei and demonstrates the importance of such assemblies for the study of gene expression control. We expect the new genome assembly will increase the awareness of allele-specific phenomena and provide a platform to investigate them.
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Affiliation(s)
- Raúl O Cosentino
- Division of Experimental Parasitology, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität in Munich, Lena-Christ-Str. 48, Planegg-Martinsried 82152, Germany
| | - Benedikt G Brink
- Division of Experimental Parasitology, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität in Munich, Lena-Christ-Str. 48, Planegg-Martinsried 82152, Germany
| | - T Nicolai Siegel
- Division of Experimental Parasitology, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität in Munich, Lena-Christ-Str. 48, Planegg-Martinsried 82152, Germany
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26
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Krogerus K, Magalhães F, Castillo S, Peddinti G, Vidgren V, De Chiara M, Yue JX, Liti G, Gibson B. Lager Yeast Design Through Meiotic Segregation of a Saccharomyces cerevisiae × Saccharomyces eubayanus Hybrid. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:733655. [PMID: 37744092 PMCID: PMC10512403 DOI: 10.3389/ffunb.2021.733655] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/20/2021] [Indexed: 09/26/2023]
Abstract
Yeasts in the lager brewing group are closely related and consequently do not exhibit significant genetic variability. Here, an artificial Saccharomyces cerevisiae × Saccharomyces eubayanus tetraploid interspecies hybrid was created by rare mating, and its ability to sporulate and produce viable gametes was exploited to generate phenotypic diversity. Four spore clones obtained from a single ascus were isolated, and their brewing-relevant phenotypes were assessed. These F1 spore clones were found to differ with respect to fermentation performance under lager brewing conditions (15°C, 15 °Plato), production of volatile aroma compounds, flocculation potential and temperature tolerance. One spore clone, selected for its rapid fermentation and acetate ester production was sporulated to produce an F2 generation, again comprised of four spore clones from a single ascus. Again, phenotypic diversity was introduced. In two of these F2 clones, the fermentation performance was maintained and acetate ester production was improved relative to the F1 parent and the original hybrid strain. Strains also performed well in comparison to a commercial lager yeast strain. Spore clones varied in ploidy and chromosome copy numbers, and faster wort fermentation was observed in strains with a higher ploidy. An F2 spore clone was also subjected to 10 consecutive wort fermentations, and single cells were isolated from the resulting yeast slurry. These isolates also exhibited variable fermentation performance and chromosome copy numbers, highlighting the instability of polyploid interspecific hybrids. These results demonstrate the value of this natural approach to increase the phenotypic diversity of lager brewing yeast strains.
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Affiliation(s)
- Kristoffer Krogerus
- VTT Technical Research Centre of Finland, Espoo, Finland
- Department of Biotechnology and Chemical Technology, Aalto University, School of Chemical Technology, Espoo, Finland
| | - Frederico Magalhães
- VTT Technical Research Centre of Finland, Espoo, Finland
- Department of Biotechnology and Chemical Technology, Aalto University, School of Chemical Technology, Espoo, Finland
| | | | - Gopal Peddinti
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - Virve Vidgren
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - Matteo De Chiara
- Institute for Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284, INSERM U1081, University of Nice Sophia Antipolis, Nice, France
| | - Jia-Xing Yue
- Institute for Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284, INSERM U1081, University of Nice Sophia Antipolis, Nice, France
| | - Gianni Liti
- Institute for Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284, INSERM U1081, University of Nice Sophia Antipolis, Nice, France
| | - Brian Gibson
- VTT Technical Research Centre of Finland, Espoo, Finland
- Brewing and Beverage Technology, Technische Universität Berlin, Berlin, Germany
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27
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Lairón-Peris M, Castiglioni GL, Routledge SJ, Alonso-Del-Real J, Linney JA, Pitt AR, Melcr J, Goddard AD, Barrio E, Querol A. Adaptive response to wine selective pressures shapes the genome of a Saccharomyces interspecies hybrid. Microb Genom 2021; 7. [PMID: 34448691 PMCID: PMC8549368 DOI: 10.1099/mgen.0.000628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
During industrial processes, yeasts are exposed to harsh conditions, which eventually lead to adaptation of the strains. In the laboratory, it is possible to use experimental evolution to link the evolutionary biology response to these adaptation pressures for the industrial improvement of a specific yeast strain. In this work, we aimed to study the adaptation of a wine industrial yeast in stress conditions of the high ethanol concentrations present in stopped fermentations and secondary fermentations in the processes of champagne production. We used a commercial Saccharomyces cerevisiae × S. uvarum hybrid and assessed its adaptation in a modified synthetic must (M-SM) containing high ethanol, which also contained metabisulfite, a preservative that is used during wine fermentation as it converts to sulfite. After the adaptation process under these selected stressful environmental conditions, the tolerance of the adapted strain (H14A7-etoh) to sulfite and ethanol was investigated, revealing that the adapted hybrid is more resistant to sulfite compared to the original H14A7 strain, whereas ethanol tolerance improvement was slight. However, a trade-off in the adapted hybrid was found, as it had a lower capacity to ferment glucose and fructose in comparison with H14A7. Hybrid genomes are almost always unstable, and different signals of adaptation on H14A7-etoh genome were detected. Each subgenome present in the adapted strain had adapted differently. Chromosome aneuploidies were present in S. cerevisiae chromosome III and in S. uvarum chromosome VII–XVI, which had been duplicated. Moreover, S. uvarum chromosome I was not present in H14A7-etoh and a loss of heterozygosity (LOH) event arose on S. cerevisiae chromosome I. RNA-sequencing analysis showed differential gene expression between H14A7-etoh and H14A7, which can be easily correlated with the signals of adaptation that were found on the H14A7-etoh genome. Finally, we report alterations in the lipid composition of the membrane, consistent with conserved tolerance mechanisms.
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Affiliation(s)
- María Lairón-Peris
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos, CSIC, Valencia, Spain
| | - Gabriel L Castiglioni
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos, CSIC, Valencia, Spain
| | - Sarah J Routledge
- College of Health and Life Sciences, Aston University, Birmingham, UK
| | - Javier Alonso-Del-Real
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos, CSIC, Valencia, Spain
| | - John A Linney
- College of Health and Life Sciences, Aston University, Birmingham, UK
| | - Andrew R Pitt
- College of Health and Life Sciences, Aston University, Birmingham, UK.,Manchester Institute of Biotechnology and Department of Chemistry, University of Manchester, Manchester, UK
| | - Josef Melcr
- Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Material, University of Groningen, Groningen, The Netherlands
| | - Alan D Goddard
- College of Health and Life Sciences, Aston University, Birmingham, UK
| | - Eladio Barrio
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos, CSIC, Valencia, Spain.,Departament de Genètica, Universitat de València, Valencia, Spain
| | - Amparo Querol
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos, CSIC, Valencia, Spain
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28
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Fisher KJ, Vignogna RC, Lang GI. Overdominant Mutations Restrict Adaptive Loss of Heterozygosity at Linked Loci. Genome Biol Evol 2021; 13:6345346. [PMID: 34363476 PMCID: PMC8382679 DOI: 10.1093/gbe/evab181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2021] [Indexed: 12/29/2022] Open
Abstract
Loss of heterozygosity is a common mode of adaptation in asexual diploid populations. Because mitotic recombination frequently extends the full length of a chromosome arm, the selective benefit of loss of heterozygosity may be constrained by linked heterozygous mutations. In a previous laboratory evolution experiment with diploid yeast, we frequently observed homozygous mutations in the WHI2 gene on the right arm of Chromosome XV. However, when heterozygous mutations arose in the STE4 gene, another common target on Chromosome XV, loss of heterozygosity at WHI2 was not observed. Here, we show that mutations at WHI2 are partially dominant and that mutations at STE4 are overdominant. We test whether beneficial heterozygous mutations at these two loci interfere with one another by measuring loss of heterozygosity at WHI2 over 1,000 generations for ∼300 populations that differed initially only at STE4 and WHI2. We show that the presence of an overdominant mutation in STE4 reduces, but does not eliminate, loss of heterozygosity at WHI2. By sequencing 40 evolved clones, we show that populations with linked overdominant and partially dominant mutations show less parallelism at the gene level, more varied evolutionary outcomes, and increased rates of aneuploidy. Our results show that the degree of dominance and the phasing of heterozygous beneficial mutations can constrain loss of heterozygosity along a chromosome arm, and that conflicts between partially dominant and overdominant mutations can affect evolutionary outcomes.
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Affiliation(s)
- Kaitlin J Fisher
- Department of Biological Sciences, Lehigh University, USA.,Laboratory of Genetics, University of Wisconsin-Madison, USA
| | | | - Gregory I Lang
- Department of Biological Sciences, Lehigh University, USA
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29
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Hanson SJ, Cinnéide EÓ, Salzberg LI, Wolfe KH, McGowan J, Fitzpatrick DA, Matlin K. Genomic diversity, chromosomal rearrangements, and interspecies hybridization in the Ogataea polymorpha species complex. G3 (BETHESDA, MD.) 2021; 11:jkab211. [PMID: 34849824 PMCID: PMC8496258 DOI: 10.1093/g3journal/jkab211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/11/2021] [Indexed: 11/13/2022]
Abstract
The methylotrophic yeast Ogataea polymorpha has long been a useful system for recombinant protein production, as well as a model system for methanol metabolism, peroxisome biogenesis, thermotolerance, and nitrate assimilation. It has more recently become an important model for the evolution of mating-type switching. Here, we present a population genomics analysis of 47 isolates within the O. polymorpha species complex, including representatives of the species O. polymorpha, Ogataea parapolymorpha, Ogataea haglerorum, and Ogataea angusta. We found low levels of nucleotide sequence diversity within the O. polymorpha species complex and identified chromosomal rearrangements both within and between species. In addition, we found that one isolate is an interspecies hybrid between O. polymorpha and O. parapolymorpha and present evidence for loss of heterozygosity following hybridization.
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Affiliation(s)
- Sara J Hanson
- Department of Molecular Biology, Colorado College, Colorado Springs, CO 80903, USA
| | - Eoin Ó Cinnéide
- School of Medicine, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Letal I Salzberg
- School of Medicine, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Kenneth H Wolfe
- School of Medicine, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Jamie McGowan
- Genome Evolution Laboratory, Department of Biology, Maynooth University, Maynooth, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Ireland
| | - David A Fitzpatrick
- Genome Evolution Laboratory, Department of Biology, Maynooth University, Maynooth, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Ireland
| | - Kate Matlin
- Department of Molecular Biology, Colorado College, Colorado Springs, CO 80903, USA
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30
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Interspecific hybridization as a driver of fungal evolution and adaptation. Nat Rev Microbiol 2021; 19:485-500. [PMID: 33767366 DOI: 10.1038/s41579-021-00537-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2021] [Indexed: 02/01/2023]
Abstract
Cross-species gene transfer is often associated with bacteria, which have evolved several mechanisms that facilitate horizontal DNA exchange. However, the increased availability of whole-genome sequences has revealed that fungal species also exchange DNA, leading to intertwined lineages, blurred species boundaries or even novel species. In contrast to prokaryotes, fungal DNA exchange originates from interspecific hybridization, where two genomes are merged into a single, often highly unstable, polyploid genome that evolves rapidly into stabler derivatives. The resulting hybrids can display novel combinations of genetic and phenotypic variation that enhance fitness and allow colonization of new niches. Interspecific hybridization led to the emergence of important pathogens of humans and plants (for example, various Candida and 'powdery mildew' species, respectively) and industrially important yeasts, such as Saccharomyces hybrids that are important in the production of cold-fermented lagers or cold-cellared Belgian ales. In this Review, we discuss the genetic processes and evolutionary implications of fungal interspecific hybridization and highlight some of the best-studied examples. In addition, we explain how hybrids can be used to study molecular mechanisms underlying evolution, adaptation and speciation, and serve as a route towards development of new variants for industrial applications.
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31
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Abstract
Hybridization is an important evolutionary mechanism that can enable organisms to adapt to environmental challenges. It has previously been shown that the fungal allodiploid species Verticillium longisporum, the causal agent of verticillium stem striping in rapeseed, originated from at least three independent hybridization events between two haploid Verticillium species. To reveal the impact of genome duplication as a consequence of hybridization, we studied the genome and transcriptome dynamics upon two independent V. longisporum hybridization events, represented by the hybrid lineages “A1/D1” and “A1/D3.” We show that V. longisporum genomes are characterized by extensive chromosomal rearrangements, including between parental chromosomal sets. V. longisporum hybrids display signs of evolutionary dynamics that are typically associated with the aftermath of allodiploidization, such as haploidization and more relaxed gene evolution. The expression patterns of the two subgenomes within the two hybrid lineages are more similar than those of the shared A1 parent between the two lineages, showing that the expression patterns of the parental genomes homogenized within a lineage. However, as genes that display differential parental expression in planta do not typically display the same pattern in vitro, we conclude that subgenome-specific responses occur in both lineages. Overall, our study uncovers genomic and transcriptomic plasticity during the evolution of the filamentous fungal hybrid V. longisporum and illustrates its adaptive potential.
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32
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Boekhout T, Aime MC, Begerow D, Gabaldón T, Heitman J, Kemler M, Khayhan K, Lachance MA, Louis EJ, Sun S, Vu D, Yurkov A. The evolving species concepts used for yeasts: from phenotypes and genomes to speciation networks. FUNGAL DIVERS 2021; 109:27-55. [PMID: 34720775 PMCID: PMC8550739 DOI: 10.1007/s13225-021-00475-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 05/31/2021] [Indexed: 12/12/2022]
Abstract
Here we review how evolving species concepts have been applied to understand yeast diversity. Initially, a phenotypic species concept was utilized taking into consideration morphological aspects of colonies and cells, and growth profiles. Later the biological species concept was added, which applied data from mating experiments. Biophysical measurements of DNA similarity between isolates were an early measure that became more broadly applied with the advent of sequencing technology, leading to a sequence-based species concept using comparisons of parts of the ribosomal DNA. At present phylogenetic species concepts that employ sequence data of rDNA and other genes are universally applied in fungal taxonomy, including yeasts, because various studies revealed a relatively good correlation between the biological species concept and sequence divergence. The application of genome information is becoming increasingly common, and we strongly recommend the use of complete, rather than draft genomes to improve our understanding of species and their genome and genetic dynamics. Complete genomes allow in-depth comparisons on the evolvability of genomes and, consequently, of the species to which they belong. Hybridization seems a relatively common phenomenon and has been observed in all major fungal lineages that contain yeasts. Note that hybrids may greatly differ in their post-hybridization development. Future in-depth studies, initially using some model species or complexes may shift the traditional species concept as isolated clusters of genetically compatible isolates to a cohesive speciation network in which such clusters are interconnected by genetic processes, such as hybridization.
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Affiliation(s)
- Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - M. Catherine Aime
- Dept Botany and Plant Pathology, College of Agriculture, Purdue University, West Lafayette, IN 47907 USA
| | - Dominik Begerow
- Evolution of Plants and Fungi, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BSC–CNS), Jordi Girona, 29, 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710 USA
| | - Martin Kemler
- Evolution of Plants and Fungi, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Kantarawee Khayhan
- Department of Microbiology and Parasitology, Faculty of Medical Sciences, University of Phayao, Phayao, 56000 Thailand
| | - Marc-André Lachance
- Department of Biology, University of Western Ontario, London, ON N6A 5B7 Canada
| | - Edward J. Louis
- Department of Genetics and Genome Biology, Genetic Architecture of Complex Traits, University of Leicester, Leicester, LE1 7RH UK
| | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710 USA
| | - Duong Vu
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Andrey Yurkov
- German Collection of Microorganisms and Cell Cultures, Leibniz Institute DSMZ, Brunswick, Germany
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33
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Dutta A, Dutreux F, Schacherer J. Loss of heterozygosity results in rapid but variable genome homogenization across yeast genetic backgrounds. eLife 2021; 10:70339. [PMID: 34159898 PMCID: PMC8245132 DOI: 10.7554/elife.70339] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 06/11/2021] [Indexed: 12/12/2022] Open
Abstract
The dynamics and diversity of the appearance of genetic variants play an essential role in the evolution of the genome and the shaping of biodiversity. Recent population-wide genome sequencing surveys have highlighted the importance of loss of heterozygosity (LOH) events and have shown that they are a neglected part of the genetic diversity landscape. To assess the extent, variability, and spectrum, we explored the accumulation of LOH events in 169 heterozygous diploid Saccharomyces cerevisiae mutation accumulation lines across nine genetic backgrounds. In total, we detected a large set of 22,828 LOH events across distinct genetic backgrounds with a heterozygous level ranging from 0.1% to 1%. LOH events are very frequent with a rate consistently much higher than the mutation rate, showing their importance for genome evolution. We observed that the interstitial LOH (I-LOH) events, resulting in internal short LOH tracts, were much frequent (n = 19,660) than the terminal LOH (T-LOH) events, that is, tracts extending to the end of the chromosome (n = 3168). However, the spectrum, the rate, and the fraction of the genome under LOH vary across genetic backgrounds. Interestingly, we observed that the more the ancestors were heterozygous, the more they accumulated T-LOH events. In addition, frequent short I-LOH tracts are a signature of the lines derived from hybrids with low spore fertility. Finally, we found lines showing almost complete homozygotization during vegetative progression. Overall, our results highlight that the variable dynamics of the LOH accumulation across distinct genetic backgrounds might lead to rapid differential genome evolution during vegetative growth.
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Affiliation(s)
- Abhishek Dutta
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Fabien Dutreux
- 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), Paris, France
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Solieri L. The revenge of Zygosaccharomyces yeasts in food biotechnology and applied microbiology. World J Microbiol Biotechnol 2021; 37:96. [PMID: 33969449 DOI: 10.1007/s11274-021-03066-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 04/28/2021] [Indexed: 12/01/2022]
Abstract
Non-conventional yeasts refer to a huge and still poorly explored group of species alternative to the well-known model organism Saccharomyces cerevisiae. Among them, Zygosaccharomyces rouxii and the sister species Zygosaccharomyces bailii are infamous for spoiling food and beverages even in presence of several food preservatives. On the other hand, their capability to cope with a wide range of process conditions makes these yeasts very attractive factories (the so-called "ZygoFactories") for bio-converting substrates poorly permissive for the growth of other species. In balsamic vinegar Z. rouxii is the main yeast responsible for converting highly concentrated sugars into ethanol, with a preference for fructose over glucose (a trait called fructophily). Z. rouxii has also attracted much attention for the ability to release important flavor compounds, such as fusel alcohols and the derivatives of 4-hydroxyfuranone, which markedly contribute to fragrant and smoky aroma in soy sauce. While Z. rouxii was successfully proposed in brewing for producing low ethanol beer, Z. bailii is promising for lactic acid and bioethanol production. Recently, several research efforts exploited omics tools to pinpoint the genetic bases of distinctive traits in "ZygoFactories", like fructophily, tolerance to high concentrations of sugars, lactic acid and salt. Here, I provided an overview of Zygosaccharomyces industrially relevant phenotypes and summarized the most recent findings in disclosing their genetic bases. I suggest that the increasing number of genomes available for Z. rouxii and other Zygosaccharomyces relatives, combined with recently developed genetic engineering toolkits, will boost the applications of these yeasts in biotechnology and applied microbiology.
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Affiliation(s)
- L Solieri
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122, Reggio Emilia, Italy.
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35
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Hao Y, Mabry ME, Edger PP, Freeling M, Zheng C, Jin L, VanBuren R, Colle M, An H, Abrahams RS, Washburn JD, Qi X, Barry K, Daum C, Shu S, Schmutz J, Sankoff D, Barker MS, Lyons E, Pires JC, Conant GC. The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible. Genome Res 2021; 31:799-810. [PMID: 33863805 PMCID: PMC8092008 DOI: 10.1101/gr.270033.120] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 03/05/2021] [Indexed: 01/08/2023]
Abstract
The members of the tribe Brassiceae share a whole-genome triplication (WGT), and one proposed model for its formation is a two-step pair of hybridizations producing hexaploid descendants. However, evidence for this model is incomplete, and the evolutionary and functional constraints that drove evolution after the hexaploidy are even less understood. Here, we report a new genome sequence of Crambe hispanica, a species sister to most sequenced Brassiceae. Using this new genome and three others that share the hexaploidy, we traced the history of gene loss after the WGT using the Polyploidy Orthology Inference Tool (POInT). We confirm the two-step formation model and infer that there was a significant temporal gap between those two allopolyploidizations, with about a third of the gene losses from the first two subgenomes occurring before the arrival of the third. We also, for the 90,000 individual genes in our study, make parental subgenome assignments, inferring, with measured uncertainty, from which of the progenitor genomes of the allohexaploidy each gene derives. We further show that each subgenome has a statistically distinguishable rate of homoeolog losses. There is little indication of functional distinction between the three subgenomes: the individual subgenomes show no patterns of functional enrichment, no excess of shared protein-protein or metabolic interactions between their members, and no biases in their likelihood of having experienced a recent selective sweep. We propose a "mix and match" model of allopolyploidy, in which subgenome origin drives homoeolog loss propensities but where genes from different subgenomes function together without difficulty.
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Affiliation(s)
- Yue Hao
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Makenzie E Mabry
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri 65211, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA
- Genetics and Genome Sciences, Michigan State University, East Lansing, Michigan 48824, USA
| | - Michael Freeling
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Chunfang Zheng
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Lingling Jin
- Department of Computer Science, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C9, Canada
| | - Robert VanBuren
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, Michigan 48824, USA
| | - Marivi Colle
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA
| | - Hong An
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri 65211, USA
| | - R Shawn Abrahams
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri 65211, USA
| | - Jacob D Washburn
- Plant Genetics Research Unit, USDA-ARS, Columbia, Missouri 65211, USA
| | - Xinshuai Qi
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Christopher Daum
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Shengqiang Shu
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - David Sankoff
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Eric Lyons
- School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
- BIO5 Institute, University of Arizona, Tucson, Arizona 85721, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri 65211, USA
- Informatics Institute, University of Missouri-Columbia, Columbia, Missouri 65211, USA
| | - Gavin C Conant
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27695, USA
- Program in Genetics, North Carolina State University, Raleigh, North Carolina 27695, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
- Division of Animal Sciences, University of Missouri-Columbia, Columbia, Missouri 65211, USA
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Calvelo J, D'Anatro A. Mitochondrial genome architecture and phylogenetic relationships of Odontesthes argentinensis within Atherinomorpha. Genetica 2021; 149:129-141. [PMID: 33817771 DOI: 10.1007/s10709-021-00116-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 03/15/2021] [Indexed: 12/30/2022]
Abstract
Silversides are a widely distributed group across South America, with several species occupying marine, freshwater and estuarine environments. Several authors suggest main transitions among these environments took place during Pleistocene, and were accompanied with rapid speciation events. This scenario produced very limited genetic and morphological differentiation among the species. However, most of these surveys have an incomplete coverage of the intraspecific genetic diversity of the taxa studied. In this work, we reconstructed six mitochondrial genomes of O. argentinensis using transcriptomic data, and used them-in combination with several nuclear markers retrieved from the same transcriptomes-to explore the effect of additional coverage of intraspecific diversity of this species in phylogenetic reconstructions. Unlike previous works, phylogenetic analyses failed to identify O. argentinensis as a monophyletic group in relation with closely related taxa. Our results suggest that several species of the genus, especially those related to O. argentinensis, need further taxonomic revision.
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Affiliation(s)
- Javier Calvelo
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, 11400, Montevideo, Uruguay
| | - Alejandro D'Anatro
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, 11400, Montevideo, Uruguay.
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Bautista C, Marsit S, Landry CR. Interspecific hybrids show a reduced adaptive potential under DNA damaging conditions. Evol Appl 2021; 14:758-769. [PMID: 33767750 PMCID: PMC7980265 DOI: 10.1111/eva.13155] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 10/12/2020] [Indexed: 12/15/2022] Open
Abstract
Hybridization may increase the probability of adaptation to extreme stresses. This advantage could be caused by an increased genome plasticity in hybrids, which could accelerate the search for adaptive mutations. High ultraviolet (UV) radiation is a particular challenge in terms of adaptation because it affects the viability of organisms by directly damaging DNA, while also challenging future generations by increasing mutation rate. Here we test whether hybridization accelerates adaptive evolution in response to DNA damage, using yeast as a model. We exposed 180 populations of hybrids between species (Saccharomyces cerevisiae and Saccharomyces paradoxus) and their parental strains to UV mimetic and control conditions for approximately 100 generations. Although we found that adaptation occurs in both hybrids and parents, hybrids achieved a lower rate of adaptation, contrary to our expectations. Adaptation to DNA damage conditions comes with a large and similar cost for parents and hybrids, suggesting that this cost is not responsible for the lower adaptability of hybrids. We suggest that the lower adaptive potential of hybrids in this condition may result from the interaction between DNA damage and the inherent genetic instability of hybrids.
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Affiliation(s)
- Carla Bautista
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
- Département de BiologieFaculté des Sciences et de GénieUniversité LavalQuébecQCCanada
- Regroupement québécois de recherche sur la fonction, la structure et l'ingénierie des protéines (PROTEO)Université LavalQuébecQCCanada
- Centre de Recherche en Données Massives (CRDM)Université LavalQuébecQCCanada
| | - Souhir Marsit
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
- Département de BiologieFaculté des Sciences et de GénieUniversité LavalQuébecQCCanada
- Regroupement québécois de recherche sur la fonction, la structure et l'ingénierie des protéines (PROTEO)Université LavalQuébecQCCanada
- Centre de Recherche en Données Massives (CRDM)Université LavalQuébecQCCanada
| | - Christian R. Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
- Département de BiologieFaculté des Sciences et de GénieUniversité LavalQuébecQCCanada
- Regroupement québécois de recherche sur la fonction, la structure et l'ingénierie des protéines (PROTEO)Université LavalQuébecQCCanada
- Centre de Recherche en Données Massives (CRDM)Université LavalQuébecQCCanada
- Département de Biochimie, de Microbiologie et de Bio‐informatiqueFaculté des Sciences et de GénieUniversité LavalQuébecQCCanada
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Smukowski Heil C, Patterson K, Hickey ASM, Alcantara E, Dunham MJ. Transposable Element Mobilization in Interspecific Yeast Hybrids. Genome Biol Evol 2021; 13:6141023. [PMID: 33595639 PMCID: PMC7952228 DOI: 10.1093/gbe/evab033] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2021] [Indexed: 12/13/2022] Open
Abstract
Barbara McClintock first hypothesized that interspecific hybridization could provide a “genomic shock” that leads to the mobilization of transposable elements (TEs). This hypothesis is based on the idea that regulation of TE movement is potentially disrupted in hybrids. However, the handful of studies testing this hypothesis have yielded mixed results. Here, we set out to identify if hybridization can increase transposition rate and facilitate colonization of TEs in Saccharomyces cerevisiae × Saccharomyces uvarum interspecific yeast hybrids. Saccharomyces cerevisiae have a small number of active long terminal repeat retrotransposons (Ty elements), whereas their distant relative S. uvarum have lost the Ty elements active in S. cerevisiae. Although the regulation system of Ty elements is known in S. cerevisiae, it is unclear how Ty elements are regulated in other Saccharomyces species, and what mechanisms contributed to the loss of most classes of Ty elements in S. uvarum. Therefore, we first assessed whether TEs could insert in the S. uvarum sub-genome of a S. cerevisiae × S. uvarum hybrid. We induced transposition to occur in these hybrids and developed a sequencing technique to show that Ty elements insert readily and nonrandomly in the S. uvarum genome. We then used an in vivo reporter construct to directly measure transposition rate in hybrids, demonstrating that hybridization itself does not alter rate of mobilization. However, we surprisingly show that species-specific mitochondrial inheritance can change transposition rate by an order of magnitude. Overall, our results provide evidence that hybridization can potentially facilitate the introduction of TEs across species boundaries and alter transposition via mitochondrial transmission, but that this does not lead to unrestrained proliferation of TEs suggested by the genomic shock theory.
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Affiliation(s)
- Caiti Smukowski Heil
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Kira Patterson
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | | | - Erica Alcantara
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Maitreya J Dunham
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
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39
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A yeast living ancestor reveals the origin of genomic introgressions. Nature 2020; 587:420-425. [PMID: 33177709 DOI: 10.1038/s41586-020-2889-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 08/11/2020] [Indexed: 11/08/2022]
Abstract
Genome introgressions drive evolution across the animal1, plant2 and fungal3 kingdoms. Introgressions initiate from archaic admixtures followed by repeated backcrossing to one parental species. However, how introgressions arise in reproductively isolated species, such as yeast4, has remained unclear. Here we identify a clonal descendant of the ancestral yeast hybrid that founded the extant Saccharomyces cerevisiae Alpechin lineage5, which carries abundant Saccharomyces paradoxus introgressions. We show that this clonal descendant, hereafter defined as a 'living ancestor', retained the ancestral genome structure of the first-generation hybrid with contiguous S. cerevisiae and S. paradoxus subgenomes. The ancestral first-generation hybrid underwent catastrophic genomic instability through more than a hundred mitotic recombination events, mainly manifesting as homozygous genome blocks generated by loss of heterozygosity. These homozygous sequence blocks rescue hybrid fertility by restoring meiotic recombination and are the direct origins of the introgressions present in the Alpechin lineage. We suggest a plausible route for introgression evolution through the reconstruction of extinct stages and propose that genome instability allows hybrids to overcome reproductive isolation and enables introgressions to emerge.
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40
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Lahue C, Madden AA, Dunn RR, Smukowski Heil C. History and Domestication of Saccharomyces cerevisiae in Bread Baking. Front Genet 2020; 11:584718. [PMID: 33262788 PMCID: PMC7686800 DOI: 10.3389/fgene.2020.584718] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/13/2020] [Indexed: 11/30/2022] Open
Abstract
The yeast Saccharomyces cerevisiae has been instrumental in the fermentation of foods and beverages for millennia. In addition to fermentations like wine, beer, cider, sake, and bread, S. cerevisiae has been isolated from environments ranging from soil and trees, to human clinical isolates. Each of these environments has unique selection pressures that S. cerevisiae must adapt to. Bread dough, for example, requires S. cerevisiae to efficiently utilize the complex sugar maltose; tolerate osmotic stress due to the semi-solid state of dough, high salt, and high sugar content of some doughs; withstand various processing conditions, including freezing and drying; and produce desirable aromas and flavors. In this review, we explore the history of bread that gave rise to modern commercial baking yeast, and the genetic and genomic changes that accompanied this. We illustrate the genetic and phenotypic variation that has been documented in baking strains and wild strains, and how this variation might be used for baking strain improvement. While we continue to improve our understanding of how baking strains have adapted to bread dough, we conclude by highlighting some of the remaining open questions in the field.
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Affiliation(s)
- Caitlin Lahue
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States
| | - Anne A. Madden
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States
| | - Robert R. Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Caiti Smukowski Heil
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
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Sui Y, Qi L, Wu JK, Wen XP, Tang XX, Ma ZJ, Wu XC, Zhang K, Kokoska RJ, Zheng DQ, Petes TD. Genome-wide mapping of spontaneous genetic alterations in diploid yeast cells. Proc Natl Acad Sci U S A 2020; 117:28191-28200. [PMID: 33106417 PMCID: PMC7668089 DOI: 10.1073/pnas.2018633117] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Genomic alterations including single-base mutations, deletions and duplications, translocations, mitotic recombination events, and chromosome aneuploidy generate genetic diversity. We examined the rates of all of these genetic changes in a diploid strain of Saccharomyces cerevisiae by whole-genome sequencing of many independent isolates (n = 93) subcloned about 100 times in unstressed growth conditions. The most common alterations were point mutations and small (<100 bp) insertion/deletions (n = 1,337) and mitotic recombination events (n = 1,215). The diploid cells of most eukaryotes are heterozygous for many single-nucleotide polymorphisms (SNPs). During mitotic cell divisions, recombination can produce derivatives of these cells that have become homozygous for the polymorphisms, termed loss-of-heterozygosity (LOH) events. LOH events can change the phenotype of the cells and contribute to tumor formation in humans. We observed two types of LOH events: interstitial events (conversions) resulting in a short LOH tract (usually less than 15 kb) and terminal events (mostly cross-overs) in which the LOH tract extends to the end of the chromosome. These two types of LOH events had different distributions, suggesting that they may have initiated by different mechanisms. Based on our results, we present a method of calculating the probability of an LOH event for individual SNPs located throughout the genome. We also identified several hotspots for chromosomal rearrangements (large deletions and duplications). Our results provide insights into the relative importance of different types of genetic alterations produced during vegetative growth.
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Affiliation(s)
- Yang Sui
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, 316021 Zhoushan, China
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27705
| | - Lei Qi
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, 316021 Zhoushan, China
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27705
| | - Jian-Kun Wu
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, 316021 Zhoushan, China
| | - Xue-Ping Wen
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, 316021 Zhoushan, China
| | - Xing-Xing Tang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, 316021 Zhoushan, China
| | - Zhong-Jun Ma
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, 316021 Zhoushan, China
| | - Xue-Chang Wu
- Institute of Microbiology, College of Life Science, Zhejiang University, 310058 Hangzhou, China
| | - Ke Zhang
- Institute of Microbiology, College of Life Science, Zhejiang University, 310058 Hangzhou, China;
| | - Robert J Kokoska
- Physical Sciences Directorate, United States Army Research Office, Research Triangle Park, NC 27709
| | - Dao-Qiong Zheng
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, 316021 Zhoushan, China;
| | - Thomas D Petes
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27705;
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Molinet J, Cubillos FA. Wild Yeast for the Future: Exploring the Use of Wild Strains for Wine and Beer Fermentation. Front Genet 2020; 11:589350. [PMID: 33240332 PMCID: PMC7667258 DOI: 10.3389/fgene.2020.589350] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/28/2020] [Indexed: 01/05/2023] Open
Abstract
The continuous usage of single Saccharomyces cerevisiae strains as starter cultures in fermentation led to the domestication and propagation of highly specialized strains in fermentation, resulting in the standardization of wines and beers. In this way, hundreds of commercial strains have been developed to satisfy producers’ and consumers’ demands, including beverages with high/low ethanol content, nutrient deprivation tolerance, diverse aromatic profiles, and fast fermentations. However, studies in the last 20 years have demonstrated that the genetic and phenotypic diversity in commercial S. cerevisiae strains is low. This lack of diversity limits alternative wines and beers, stressing the need to explore new genetic resources to differentiate each fermentation product. In this sense, wild strains harbor a higher than thought genetic and phenotypic diversity, representing a feasible option to generate new fermentative beverages. Numerous recent studies have identified alleles in wild strains that could favor phenotypes of interest, such as nitrogen consumption, tolerance to cold or high temperatures, and the production of metabolites, such as glycerol and aroma compounds. Here, we review the recent literature on the use of commercial and wild S. cerevisiae strains in wine and beer fermentation, providing molecular evidence of the advantages of using wild strains for the generation of improved genetic stocks for the industry according to the product style.
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Affiliation(s)
- Jennifer Molinet
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile.,ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBIO), Santiago, Chile
| | - Francisco A Cubillos
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile.,ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBIO), Santiago, Chile
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Loss of Heterozygosity and Base Mutation Rates Vary Among Saccharomyces cerevisiae Hybrid Strains. G3-GENES GENOMES GENETICS 2020; 10:3309-3319. [PMID: 32727920 PMCID: PMC7466981 DOI: 10.1534/g3.120.401551] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A growing body of evidence suggests that mutation rates exhibit intra-species specific variation. We estimated genome-wide loss of heterozygosity (LOH), gross chromosomal changes, and single nucleotide mutation rates to determine intra-species specific differences in hybrid and homozygous strains of Saccharomyces cerevisiae. The mutation accumulation lines of the S. cerevisiae hybrid backgrounds - S288c/YJM789 (S/Y) and S288c/RM11-1a (S/R) were analyzed along with the homozygous diploids RM11, S288c, and YJM145. LOH was extensive in both S/Y and S/R hybrid backgrounds. The S/Y background also showed longer LOH tracts, gross chromosomal changes, and aneuploidy. Short copy number aberrations were observed in the S/R background. LOH data from the S/Y and S/R hybrids were used to construct a LOH map for S288c to identify hotspots. Further, we observe up to a sixfold difference in single nucleotide mutation rates among the S. cerevisiae S/Y and S/R genetic backgrounds. Our results demonstrate LOH is common during mitotic divisions in S. cerevisiae hybrids and also highlight genome-wide differences in LOH patterns and rates of single nucleotide mutations between commonly used S. cerevisiae hybrid genetic backgrounds.
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44
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Heat shock drives genomic instability and phenotypic variations in yeast. AMB Express 2020; 10:146. [PMID: 32804300 PMCID: PMC7431486 DOI: 10.1186/s13568-020-01091-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 08/11/2020] [Indexed: 12/28/2022] Open
Abstract
High temperature causes ubiquitous environmental stress to microorganisms, but studies have not fully explained whether and to what extent heat shock would affect genome stability. Hence, this study explored heat-shock-induced genomic alterations in the yeast Saccharomyces cerevisiae. Using genetic screening systems and customized single nucleotide polymorphism (SNP) microarrays, we found that heat shock (52 °C) for several minutes could heighten mitotic recombination by at least one order of magnitude. More than half of heat-shock-induced mitotic recombinations were likely to be initiated by DNA breaks in the S/G2 phase of the cell cycle. Chromosomal aberration, mainly trisomy, was elevated hundreds of times in heat-shock-treated cells than in untreated cells. Distinct chromosomal instability patterns were also observed between heat-treated and carbendazim-treated yeast cells. Finally, we demonstrated that heat shock stimulates fast phenotypic evolutions (such as tolerance to ethanol, vanillin, fluconazole, and tunicamycin) in the yeast population. This study not only provided novel insights into the effect of temperature fluctuations on genomic integrity but also developed a simple protocol to generate an aneuploidy mutant of yeast.
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Koonthongkaew J, Toyokawa Y, Ohashi M, Large CRL, Dunham MJ, Takagi H. Effect of the Ala234Asp replacement in mitochondrial branched-chain amino acid aminotransferase on the production of BCAAs and fusel alcohols in yeast. Appl Microbiol Biotechnol 2020. [PMID: 32776205 DOI: 10.1101/2020.06.26.166157] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In the yeast Saccharomyces cerevisiae, the mitochondrial branched-chain amino acid (BCAA) aminotransferase Bat1 plays an important role in the synthesis of BCAAs (valine, leucine, and isoleucine). Our upcoming study (Large et al. bioRχiv. 10.1101/2020.06.26.166157, Large et al. 2020) will show that the heterozygous tetraploid beer yeast strain, Wyeast 1056, which natively has a variant causing one amino acid substitution of Ala234Asp in Bat1 on one of the four chromosomes, produced higher levels of BCAA-derived fusel alcohols in the brewer's wort medium than a derived strain lacking this mutation. Here, we investigated the physiological role of the A234D variant Bat1 in S. cerevisiae. Both bat1∆ and bat1A234D cells exhibited the same phenotypes relative to the wild-type Bat1 strain-namely, a repressive growth rate in the logarithmic phase; decreases in intracellular valine and leucine content in the logarithmic and stationary growth phases, respectively; an increase in fusel alcohol content in culture medium; and a decrease in the carbon dioxide productivity. These results indicate that amino acid change from Ala to Asp at position 234 led to a functional impairment of Bat1, although homology modeling suggests that Asp234 in the variant Bat1 did not inhibit enzymatic activity directly. KEY POINTS: • Yeast cells expressing Bat1A234D exhibited a slower growth phenotype. • The Val and Leu levels were decreased in yeast cells expressing Bat1A234D. • The A234D substitution causes a loss-of-function in Bat1. • The A234D substitution in Bat1 increased fusel alcohol production in yeast cells.
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Affiliation(s)
- Jirasin Koonthongkaew
- Division of Biological Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara, 630-0192, Japan
| | - Yoichi Toyokawa
- Division of Biological Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara, 630-0192, Japan
| | - Masataka Ohashi
- Nara Prefecture Institute of Industrial Development, 129-1 Kashiwagi-cho, Nara, Nara, 630-8031, Japan
| | - Christopher R L Large
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA, 98195, USA
| | - Maitreya J Dunham
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA, 98195, USA
| | - Hiroshi Takagi
- Division of Biological Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara, 630-0192, Japan.
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Gabaldón T. Hybridization and the origin of new yeast lineages. FEMS Yeast Res 2020; 20:5870662. [PMID: 32658267 PMCID: PMC7394516 DOI: 10.1093/femsyr/foaa040] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 07/10/2020] [Indexed: 12/16/2022] Open
Abstract
Hybrids originate from the mating of two diverged organisms, resulting in novel lineages that have chimeric genomes. Hybrids may exhibit unique phenotypic traits that are not necessarily intermediate between those present in the progenitors. These unique traits may enable them to thrive in new environments. Many hybrid lineages have been discovered among yeasts in the Saccharomycotina, of which many have industrial or clinical relevance, but this might reflect a bias toward investigating species with relevance to humans. Hybridization has also been proposed to be at the root of the whole-genome duplication in the lineage leading to Saccharomyces cerevisiae. Thus, hybridization seems to have played a prominent role in the evolution of Saccharomycotina yeasts, although it is still unclear how common this evolutionary process has been during the evolution of this and other fungal clades. Similarly, the evolutionary aftermath of hybridization, including implications at the genomic, transcriptional, physiological or ecological levels, remains poorly understood. In this review, I survey recent findings from genomic analysis of yeast hybrids of industrial or clinical relevance, and discuss the evolutionary implications of genomic hybridization for the origin of new lineages, including when such hybridization results in a whole-genome duplication.
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Affiliation(s)
- Toni Gabaldón
- Barcelona Supercomputing Centre (BSC-CNS), Jordi Girona 29, 08034 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
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de Witt RN, Kroukamp H, Van Zyl WH, Paulsen IT, Volschenk H. QTL analysis of natural Saccharomyces cerevisiae isolates reveals unique alleles involved in lignocellulosic inhibitor tolerance. FEMS Yeast Res 2020; 19:5528620. [PMID: 31276593 DOI: 10.1093/femsyr/foz047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 07/03/2019] [Indexed: 12/13/2022] Open
Abstract
Decoding the genetic basis of lignocellulosic inhibitor tolerance in Saccharomyces cerevisiae is crucial for rational engineering of bioethanol strains with enhanced robustness. The genetic diversity of natural strains present an invaluable resource for the exploration of complex traits of industrial importance from a pan-genomic perspective to complement the limited range of specialised, tolerant industrial strains. Natural S. cerevisiae isolates have lately garnered interest as a promising toolbox for engineering novel, genetically encoded tolerance phenotypes into commercial strains. To this end, we investigated the genetic basis for lignocellulosic inhibitor tolerance of natural S. cerevisiae isolates. A total of 12 quantitative trait loci underpinning tolerance were identified by next-generation sequencing linked bulk-segregant analysis of superior interbred pools. Our findings corroborate the current perspective of lignocellulosic inhibitor tolerance as a multigenic, complex trait. Apart from a core set of genetic variants required for inhibitor tolerance, an additional genetic background-specific response was observed. Functional analyses of the identified genetic loci revealed the uncharacterised ORF, YGL176C and the bud-site selection XRN1/BUD13 as potentially beneficial alleles contributing to tolerance to a complex lignocellulosic inhibitor mixture. We present evidence for the consideration of both regulatory and coding sequence variants for strain improvement.
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Affiliation(s)
- R N de Witt
- Department of Microbiology, Stellenbosch University, De Beer Street, Stellenbosch 7600, Western Cape, South Africa
| | - H Kroukamp
- Department of Molecular Sciences, Macquarie University, Balaclava Rd, North Ryde, NSW 2109, Australia
| | - W H Van Zyl
- Department of Microbiology, Stellenbosch University, De Beer Street, Stellenbosch 7600, Western Cape, South Africa
| | - I T Paulsen
- Department of Molecular Sciences, Macquarie University, Balaclava Rd, North Ryde, NSW 2109, Australia
| | - H Volschenk
- Department of Microbiology, Stellenbosch University, De Beer Street, Stellenbosch 7600, Western Cape, South Africa
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Gorter de Vries AR, Pronk JT, Daran JMG. Lager-brewing yeasts in the era of modern genetics. FEMS Yeast Res 2020; 19:5573808. [PMID: 31553794 PMCID: PMC6790113 DOI: 10.1093/femsyr/foz063] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 09/23/2019] [Indexed: 12/11/2022] Open
Abstract
The yeast Saccharomyces pastorianus is responsible for the annual worldwide production of almost 200 billion liters of lager-type beer. S. pastorianus is a hybrid of Saccharomyces cerevisiae and Saccharomyces eubayanus that has been studied for well over a century. Scientific interest in S. pastorianus intensified upon the discovery, in 2011, of its S. eubayanus ancestor. Moreover, advances in whole-genome sequencing and genome editing now enable deeper exploration of the complex hybrid and aneuploid genome architectures of S. pastorianus strains. These developments not only provide novel insights into the emergence and domestication of S. pastorianus but also generate new opportunities for its industrial application. This review paper combines historical, technical and socioeconomic perspectives to analyze the evolutionary origin and genetics of S. pastorianus. In addition, it provides an overview of available methods for industrial strain improvement and an outlook on future industrial application of lager-brewing yeasts. Particular attention is given to the ongoing debate on whether current S. pastorianus originates from a single or multiple hybridization events and to the potential role of genome editing in developing industrial brewing yeast strains.
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Affiliation(s)
- Arthur R Gorter de Vries
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Jean-Marc G Daran
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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Hovhannisyan H, Saus E, Ksiezopolska E, Hinks Roberts AJ, Louis EJ, Gabaldón T. Integrative Omics Analysis Reveals a Limited Transcriptional Shock After Yeast Interspecies Hybridization. Front Genet 2020; 11:404. [PMID: 32457798 PMCID: PMC7221068 DOI: 10.3389/fgene.2020.00404] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 03/30/2020] [Indexed: 12/30/2022] Open
Abstract
The formation of interspecific hybrids results in the coexistence of two diverged genomes within the same nucleus. It has been hypothesized that negative epistatic interactions and regulatory interferences between the two sub-genomes may elicit a so-called genomic shock involving, among other alterations, broad transcriptional changes. To assess the magnitude of this shock in hybrid yeasts, we investigated the transcriptomic differences between a newly formed Saccharomyces cerevisiae × Saccharomyces uvarum diploid hybrid and its diploid parentals, which diverged ∼20 mya. RNA sequencing (RNA-Seq) based allele-specific expression (ASE) analysis indicated that gene expression changes in the hybrid genome are limited, with only ∼1-2% of genes significantly altering their expression with respect to a non-hybrid context. In comparison, a thermal shock altered six times more genes. Furthermore, differences in the expression between orthologous genes in the two parental species tended to be diminished for the corresponding homeologous genes in the hybrid. Finally, and consistent with the RNA-Seq results, we show a limited impact of hybridization on chromatin accessibility patterns, as assessed with assay for transposase-accessible chromatin using sequencing (ATAC-Seq). Overall, our results suggest a limited genomic shock in a newly formed yeast hybrid, which may explain the high frequency of successful hybridization in these organisms.
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Affiliation(s)
- Hrant Hovhannisyan
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Health and Life Sciences. Universitat Pompeu Fabra, Barcelona, Spain
| | - Ester Saus
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Health and Life Sciences. Universitat Pompeu Fabra, Barcelona, Spain
| | - Ewa Ksiezopolska
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Health and Life Sciences. Universitat Pompeu Fabra, Barcelona, Spain
| | - Alex J. Hinks Roberts
- Centre for Genetic Architecture of Complex Traits, University of Leicester, Leicester, United Kingdom
| | - Edward J. Louis
- Centre for Genetic Architecture of Complex Traits, University of Leicester, Leicester, United Kingdom
| | - Toni Gabaldón
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Health and Life Sciences. Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
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The Transcriptional Aftermath in Two Independently Formed Hybrids of the Opportunistic Pathogen Candida orthopsilosis. mSphere 2020; 5:5/3/e00282-20. [PMID: 32376704 PMCID: PMC7203458 DOI: 10.1128/msphere.00282-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
How new pathogens emerge is an important question that remains largely unanswered. Some emerging yeast pathogens are hybrids originated through the crossing of two different species, but how hybridization contributes to higher virulence is unclear. Here, we show that hybrids selectively retain gene regulation plasticity inherited from the two parents and that this plasticity affects genes involved in virulence. Interspecific hybridization can drive evolutionary adaptation to novel environments. The Saccharomycotina clade of budding yeasts includes many hybrid lineages, and hybridization has been proposed as a source for new pathogenic species. Candida orthopsilosis is an emerging opportunistic pathogen for which most clinical isolates are hybrids, each derived from one of at least four independent crosses between the same two parental lineages. To gain insight into the transcriptomic aftermath of hybridization in these pathogens, we analyzed allele-specific gene expression in two independently formed hybrid strains and in a homozygous strain representative of one parental lineage. Our results show that the effect of hybridization on overall gene expression is rather limited, affecting ∼4% of the genes studied. However, we identified a larger effect in terms of imbalanced allelic expression, affecting ∼9.5% of the heterozygous genes in the hybrids. This effect was larger in the hybrid with more extensive loss of heterozygosity, which may indicate a tendency to avoid loss of heterozygosity in these genes. Consistently, the number of shared genes with allele-specific expression in the two independently formed hybrids was higher than random expectation, suggesting selective retention. Some of the imbalanced genes have functions related to pathogenicity, including zinc transport and superoxide dismutase activities. While it remains unclear whether the observed imbalanced genes play a role in virulence, our results suggest that differences in allele-specific expression may add an additional layer of phenotypic plasticity to traits related to virulence in C. orthopsilosis hybrids. IMPORTANCE How new pathogens emerge is an important question that remains largely unanswered. Some emerging yeast pathogens are hybrids originated through the crossing of two different species, but how hybridization contributes to higher virulence is unclear. Here, we show that hybrids selectively retain gene regulation plasticity inherited from the two parents and that this plasticity affects genes involved in virulence.
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