1
|
Parisod C. Duplicated gene networks promote 'hopeful' phenotypic variation. Trends Genet 2024; 40:109-111. [PMID: 38272738 DOI: 10.1016/j.tig.2023.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 12/05/2023] [Indexed: 01/27/2024]
Abstract
The consequences of whole-genome duplication (WGD) remain elusive. A new study by Ebadi et al. simulating duplicated gene networks predicts that WGD immediately generates autopolyploids with extreme phenotypes and increases phenotypic variance. Such theoretical work calls for new experimental studies addressing to what extent WGD may be beneficial under environmental changes.
Collapse
Affiliation(s)
- Christian Parisod
- Department of Biology, University of Fribourg, Fribourg, Switzerland.
| |
Collapse
|
2
|
Ebadi M, Bafort Q, Mizrachi E, Audenaert P, Simoens P, Van Montagu M, Bonte D, Van de Peer Y. The duplication of genomes and genetic networks and its potential for evolutionary adaptation and survival during environmental turmoil. Proc Natl Acad Sci U S A 2023; 120:e2307289120. [PMID: 37788315 PMCID: PMC10576144 DOI: 10.1073/pnas.2307289120] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/07/2023] [Indexed: 10/05/2023] Open
Abstract
The importance of whole-genome duplication (WGD) for evolution is controversial. Whereas some view WGD mainly as detrimental and an evolutionary dead end, there is growing evidence that polyploidization can help overcome environmental change, stressful conditions, or periods of extinction. However, despite much research, the mechanistic underpinnings of why and how polyploids might be able to outcompete or outlive nonpolyploids at times of environmental upheaval remain elusive, especially for autopolyploids, in which heterosis effects are limited. On the longer term, WGD might increase both mutational and environmental robustness due to redundancy and increased genetic variation, but on the short-or even immediate-term, selective advantages of WGDs are harder to explain. Here, by duplicating artificially generated Gene Regulatory Networks (GRNs), we show that duplicated GRNs-and thus duplicated genomes-show higher signal output variation than nonduplicated GRNs. This increased variation leads to niche expansion and can provide polyploid populations with substantial advantages to survive environmental turmoil. In contrast, under stable environments, GRNs might be maladaptive to changes, a phenomenon that is exacerbated in duplicated GRNs. We believe that these results provide insights into how genome duplication and (auto)polyploidy might help organisms to adapt quickly to novel conditions and to survive ecological uproar or even cataclysmic events.
Collapse
Affiliation(s)
- Mehrshad Ebadi
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent9052, Belgium
- Center for Plant Systems Biology, VIB, Gent9052, Belgium
| | - Quinten Bafort
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent9052, Belgium
- Center for Plant Systems Biology, VIB, Gent9052, Belgium
| | - Eshchar Mizrachi
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria0028, South Africa
| | - Pieter Audenaert
- Department of Information Technology–IDLab, Ghent University-IMEC, Gent9052, Belgium
| | - Pieter Simoens
- Department of Information Technology–IDLab, Ghent University-IMEC, Gent9052, Belgium
| | - Marc Van Montagu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent9052, Belgium
- Center for Plant Systems Biology, VIB, Gent9052, Belgium
| | - Dries Bonte
- Department of Biology, Terrestrial Ecology Unit, Ghent University, Ghent9000, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent9052, Belgium
- Center for Plant Systems Biology, VIB, Gent9052, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria0028, South Africa
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing210095, China
| |
Collapse
|
3
|
Abstract
Many questions remain about the interplay between adaptive and neutral processes leading to genome expansion and the evolution of cellular complexity. Genome size appears to be tightly linked to the size of the regulatory repertoire of cells (van Nimwegen E. 2003. Scaling laws in the functional content of genomes. Trends Gen. 19(9):479–484). In the context of gene regulation, we here study the interplay between adaptive and nonadaptive forces on genome and regulatory network in a computational model of cell-cycle adaptation to different environments. Starting from the well-known Caulobacter crescentus network, we report on ten replicate in silico evolution experiments where cells evolve cell-cycle control by adapting to increasingly harsh spatial habitats. We find adaptive expansion of the regulatory repertoire of cells. Having a large genome is inherently costly, but also allows for improved cell-cycle behavior. Replicates traverse different evolutionary trajectories leading to distinct eco-evolutionary strategies. In four replicates, cells evolve a generalist strategy to cope with a variety of nutrient levels; in two replicates, different specialist cells evolve for specific nutrient levels; in the remaining four replicates, an intermediate strategy evolves. These diverse evolutionary outcomes reveal the role of contingency in a system under strong selective forces. This study shows that functionality of cells depends on the combination of regulatory network topology and genome organization. For example, the positions of dosage-sensitive genes are exploited to signal to the regulatory network when replication is completed, forming a de novo evolved cell cycle checkpoint. Our results underline the importance of the integration of multiple organizational levels to understand complex gene regulation and the evolution thereof.
Collapse
|
4
|
Sharma G, Barney JN, Westwood JH, Haak DC. Into the weeds: new insights in plant stress. TRENDS IN PLANT SCIENCE 2021; 26:1050-1060. [PMID: 34238685 DOI: 10.1016/j.tplants.2021.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 06/03/2021] [Accepted: 06/10/2021] [Indexed: 06/13/2023]
Abstract
Weeds, plants that thrive in the face of disturbance, have eluded human's attempts at control for >12 000 years, positioning them as a unique group of extreme stress tolerators. The most successful weeds have a suite of traits that enable them to rapidly adapt to environments typified by stress, growing in hostile conditions or subject to massive destruction from agricultural practices. Through their ability to persist and adapt, weeds illuminate principles of evolution and provide insights into weed management and crop improvement. Here we highlight why the time is right to move beyond traditional model systems and leverage weeds to gain a deeper understanding of the mechanisms, adaptations, and genetic and physiological bases for stress tolerance.
Collapse
Affiliation(s)
- Gourav Sharma
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Jacob N Barney
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - James H Westwood
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA.
| | - David C Haak
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA.
| |
Collapse
|
5
|
Manrubia S, Cuesta JA, Aguirre J, Ahnert SE, Altenberg L, Cano AV, Catalán P, Diaz-Uriarte R, Elena SF, García-Martín JA, Hogeweg P, Khatri BS, Krug J, Louis AA, Martin NS, Payne JL, Tarnowski MJ, Weiß M. From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics. Phys Life Rev 2021; 38:55-106. [PMID: 34088608 DOI: 10.1016/j.plrev.2021.03.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/01/2021] [Indexed: 12/21/2022]
Abstract
Understanding how genotypes map onto phenotypes, fitness, and eventually organisms is arguably the next major missing piece in a fully predictive theory of evolution. We refer to this generally as the problem of the genotype-phenotype map. Though we are still far from achieving a complete picture of these relationships, our current understanding of simpler questions, such as the structure induced in the space of genotypes by sequences mapped to molecular structures, has revealed important facts that deeply affect the dynamical description of evolutionary processes. Empirical evidence supporting the fundamental relevance of features such as phenotypic bias is mounting as well, while the synthesis of conceptual and experimental progress leads to questioning current assumptions on the nature of evolutionary dynamics-cancer progression models or synthetic biology approaches being notable examples. This work delves with a critical and constructive attitude into our current knowledge of how genotypes map onto molecular phenotypes and organismal functions, and discusses theoretical and empirical avenues to broaden and improve this comprehension. As a final goal, this community should aim at deriving an updated picture of evolutionary processes soundly relying on the structural properties of genotype spaces, as revealed by modern techniques of molecular and functional analysis.
Collapse
Affiliation(s)
- Susanna Manrubia
- Department of Systems Biology, Centro Nacional de Biotecnología (CSIC), Madrid, Spain; Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain.
| | - José A Cuesta
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain; Departamento de Matemáticas, Universidad Carlos III de Madrid, Leganés, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BiFi), Universidad de Zaragoza, Spain; UC3M-Santander Big Data Institute (IBiDat), Getafe, Madrid, Spain
| | - Jacobo Aguirre
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain; Centro de Astrobiología, CSIC-INTA, ctra. de Ajalvir km 4, 28850 Torrejón de Ardoz, Madrid, Spain
| | - Sebastian E Ahnert
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, UK; The Alan Turing Institute, British Library, 96 Euston Road, London NW1 2DB, UK
| | | | - Alejandro V Cano
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Pablo Catalán
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain; Departamento de Matemáticas, Universidad Carlos III de Madrid, Leganés, Spain
| | - Ramon Diaz-Uriarte
- Department of Biochemistry, Universidad Autónoma de Madrid, Madrid, Spain; Instituto de Investigaciones Biomédicas "Alberto Sols" (UAM-CSIC), Madrid, Spain
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas, I(2)SysBio (CSIC-UV), València, Spain; The Santa Fe Institute, Santa Fe, NM, USA
| | | | - Paulien Hogeweg
- Theoretical Biology and Bioinformatics Group, Utrecht University, the Netherlands
| | - Bhavin S Khatri
- The Francis Crick Institute, London, UK; Department of Life Sciences, Imperial College London, London, UK
| | - Joachim Krug
- Institute for Biological Physics, University of Cologne, Köln, Germany
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford, UK
| | - Nora S Martin
- Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, Cambridge, UK; Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Joshua L Payne
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Marcel Weiß
- Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, Cambridge, UK; Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| |
Collapse
|
6
|
A Review of Unreduced Gametes and Neopolyploids in Alfalfa: How to Fill the Gap between Well-Established Meiotic Mutants and Next-Generation Genomic Resources. PLANTS 2021; 10:plants10050999. [PMID: 34067689 PMCID: PMC8156078 DOI: 10.3390/plants10050999] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/03/2021] [Accepted: 05/12/2021] [Indexed: 01/11/2023]
Abstract
The gene flow mediated by unreduced gametes between diploid and tetraploid plants of the Medicagosativa-coerulea-falcata complex is pivotal for alfalfa breeding. Sexually tetraploidized hybrids could represent the best way to exploit progressive heterosis simultaneously derived from gene diversity, heterozygosity, and polyploidy. Moreover, unreduced gametes combined with parthenogenesis (i.e., apomixis) would enable the cloning of plants through seeds, providing a unique opportunity for the selection of superior genotypes with permanently fixed heterosis. This reproductive strategy has never been detected in the genus Medicago, but features of apomixis, such as restitutional apomeiosis and haploid parthenogenesis, have been reported. By means of an original case study, we demonstrated that sexually tetraploidized plants maintain apomeiosis, but this trait is developmentally independent from parthenogenesis. Alfalfa meiotic mutants producing unreduced egg cells revealed a null or very low capacity for parthenogenesis. The overall achievements reached so far are reviewed and discussed along with the efforts and strategies made for exploiting reproductive mutants that express apomictic elements in alfalfa breeding programs. Although several studies have investigated the cytological mechanisms responsible for 2n gamete formation and the inheritance of this trait, only a very small number of molecular markers and candidate genes putatively linked to unreduced gamete formation have been identified. Furthermore, this scenario has remained almost unchanged over the last two decades. Here, we propose a reverse genetics approach, by exploiting the genomic and transcriptomic resources available in alfalfa. Through a comparison with 9 proteins belonging to Arabidopsis thaliana known for their involvement in 2n gamete production, we identified 47 orthologous genes and evaluated their expression in several tissues, paving the way for novel candidate gene characterization studies. An overall view on strategies suitable to fill the gap between well-established meiotic mutants and next-generation genomic resources is presented and discussed.
Collapse
|
7
|
Van de Peer Y, Ashman TL, Soltis PS, Soltis DE. Polyploidy: an evolutionary and ecological force in stressful times. THE PLANT CELL 2021; 33:11-26. [PMID: 33751096 PMCID: PMC8136868 DOI: 10.1093/plcell/koaa015] [Citation(s) in RCA: 265] [Impact Index Per Article: 88.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/07/2020] [Indexed: 05/10/2023]
Abstract
Polyploidy has been hypothesized to be both an evolutionary dead-end and a source for evolutionary innovation and species diversification. Although polyploid organisms, especially plants, abound, the apparent nonrandom long-term establishment of genome duplications suggests a link with environmental conditions. Whole-genome duplications seem to correlate with periods of extinction or global change, while polyploids often thrive in harsh or disturbed environments. Evidence is also accumulating that biotic interactions, for instance, with pathogens or mutualists, affect polyploids differently than nonpolyploids. Here, we review recent findings and insights on the effect of both abiotic and biotic stress on polyploids versus nonpolyploids and propose that stress response in general is an important and even determining factor in the establishment and success of polyploidy.
Collapse
Affiliation(s)
- Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB - UGent Center for Plant Systems Biology, B-9052 Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611
- Department of Biology, University of Florida, Gainesville, Florida 32611
| |
Collapse
|
8
|
Jandzik D, Stock DW. Differences in developmental potential predict the contrasting patterns of dental diversification in characiform and cypriniform fishes. Proc Biol Sci 2021; 288:20202205. [PMID: 33563123 PMCID: PMC7893225 DOI: 10.1098/rspb.2020.2205] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/12/2021] [Indexed: 11/12/2022] Open
Abstract
Morphological diversification during adaptive radiation may depend on factors external or internal to the lineage. We provide evidence for the latter in characiform fishes (tetras and piranhas), which exhibit extensive dental diversity. Phylogenetic character mapping supported regain of lost teeth as contributing to this diversity. To test for latent potential for dentition that would facilitate its evolutionary expansion, we overexpressed a tooth initiation signal, the tumour necrosis factor pathway ligand ectodysplasin, in a model characiform, the Mexican tetra (Astyanax mexicanus). This manipulation resulted in extensive ectopic dentition, in contrast with its previously reported limited effect in the zebrafish (Danio rerio). Tooth location in the order Cypriniformes, to which the zebrafish belongs, is much more restricted than in characiforms, a pattern that may be explained by differences in the retention of ancestral developmental potential. Our results suggest that differences in evolvability between lineages may lead to contrasting patterns of diversification.
Collapse
Affiliation(s)
- David Jandzik
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
- Department of Zoology, Comenius University in Bratislava, Bratislava 84215, Slovakia
| | - David W. Stock
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
| |
Collapse
|
9
|
Meijer J, van Dijk B, Hogeweg P. Contingent evolution of alternative metabolic network topologies determines whether cross-feeding evolves. Commun Biol 2020; 3:401. [PMID: 32728180 PMCID: PMC7391776 DOI: 10.1038/s42003-020-1107-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 06/19/2020] [Indexed: 12/13/2022] Open
Abstract
Metabolic exchange is widespread in natural microbial communities and an important driver of ecosystem structure and diversity, yet it remains unclear what determines whether microbes evolve division of labor or maintain metabolic autonomy. Here we use a mechanistic model to study how metabolic strategies evolve in a constant, one resource environment, when metabolic networks are allowed to freely evolve. We find that initially identical ancestral communities of digital organisms follow different evolutionary trajectories, as some communities become dominated by a single, autonomous lineage, while others are formed by stably coexisting lineages that cross-feed on essential building blocks. Our results show how without presupposed cellular trade-offs or external drivers such as temporal niches, diverse metabolic strategies spontaneously emerge from the interplay between ecology, spatial structure, and metabolic constraints that arise during the evolution of metabolic networks. Thus, in the long term, whether microbes remain autonomous or evolve metabolic division of labour is an evolutionary contingency.
Collapse
Affiliation(s)
- Jeroen Meijer
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands.
| | - Bram van Dijk
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Paulien Hogeweg
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| |
Collapse
|
10
|
Using digital organisms to study the evolutionary consequences of whole genome duplication and polyploidy. PLoS One 2019; 14:e0220257. [PMID: 31365541 PMCID: PMC6668904 DOI: 10.1371/journal.pone.0220257] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 07/11/2019] [Indexed: 11/21/2022] Open
Abstract
The potential role of whole genome duplication (WGD) in evolution is controversial. Whereas some view WGD mainly as detrimental and an evolutionary ‘dead end’, there is growing evidence that the long-term establishment of polyploidy might be linked to environmental change, stressful conditions, or periods of extinction. However, despite much research, the mechanistic underpinnings of why and how polyploids might be able to outcompete non-polyploids at times of environmental upheaval remain indefinable. Here, we improved our recently developed bio-inspired framework, combining an artificial genome with an agent-based system, to form a population of so-called Digital Organisms (DOs), to examine the impact of WGD on evolution under different environmental scenarios mimicking extinction events of varying strength and frequency. We found that, under stable environments, DOs with non-duplicated genomes formed the majority, if not all, of the population, whereas the numbers of DOs with duplicated genomes increased under dramatically challenging environments. After tracking the evolutionary trajectories of individual genomes in terms of sequence and encoded gene regulatory networks (GRNs), we propose that duplicated GRNs might provide polyploids with better chances to acquire the drastic changes necessary to adapt to challenging conditions, thus endowing DOs with increased adaptive potential under extinction events. In contrast, under stable environments, random mutations might easily render the GRN less well adapted to such environments, a phenomenon that is exacerbated in duplicated, more complex GRNs. We believe that our results provide some additional insights into how genome duplication and polyploidy might help organisms to compete for novel niches and survive ecological turmoil, and confirm the usefulness of our computational simulation in studying the role of WGD in evolution and adaptation, helping to overcome some of the traditional limitations of evolution experiments with model organisms.
Collapse
|
11
|
Carta A, Bedini G, Peruzzi L. Unscrambling phylogenetic effects and ecological determinants of chromosome number in major angiosperm clades. Sci Rep 2018; 8:14258. [PMID: 30250220 PMCID: PMC6155329 DOI: 10.1038/s41598-018-32515-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 09/10/2018] [Indexed: 11/09/2022] Open
Abstract
As variations in the chromosome number are recognized to be of evolutionary interest but are also widely debated in the literature, we aimed to quantitatively test for possible relationships among the chromosome number, plant traits, and environmental factors. In particular, the chromosome number and drivers of its variation were examined in 801 Italian endemic vascular plants, for a total of 1364 accessions. We estimated phylogenetic inertia and adaptation in chromosome number - based on an Ornstein-Uhlenbeck process - and related chromosome numbers with other plant traits and environmental variables. Phylogenetic effects in chromosome number varied among the examined clades but were generally high. Chromosome numbers were poorly related to large scale climatic conditions, while a stronger relationship with categorical variables was found. Specifically, open, disturbed, drought-prone habitats selected for low chromosome numbers, while perennial herbs, living in shaded, stable environments were associated with high chromosome numbers. Altogether, our findings support an evolutionary role of chromosome number variation, and we argue that environmental stability favours higher recombination rates in comparison to unstable environments. In addition, by comparing the results of models testing for the evolvability of 2n and of x, we provide insight into the presumptive ecological significance of polyploidy.
Collapse
Affiliation(s)
- Angelino Carta
- Department of Biology, Unit of Botany, University of Pisa, via Derna 1, 56126, Pisa, Italy.
| | - Gianni Bedini
- Department of Biology, Unit of Botany, University of Pisa, via Derna 1, 56126, Pisa, Italy
| | - Lorenzo Peruzzi
- Department of Biology, Unit of Botany, University of Pisa, via Derna 1, 56126, Pisa, Italy
| |
Collapse
|
12
|
Roux J, Liu J, Robinson-Rechavi M. Selective Constraints on Coding Sequences of Nervous System Genes Are a Major Determinant of Duplicate Gene Retention in Vertebrates. Mol Biol Evol 2018; 34:2773-2791. [PMID: 28981708 PMCID: PMC5850798 DOI: 10.1093/molbev/msx199] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The evolutionary history of vertebrates is marked by three ancient whole-genome duplications: two successive rounds in the ancestor of vertebrates, and a third one specific to teleost fishes. Biased loss of most duplicates enriched the genome for specific genes, such as slow evolving genes, but this selective retention process is not well understood. To understand what drives the long-term preservation of duplicate genes, we characterized duplicated genes in terms of their expression patterns. We used a new method of expression enrichment analysis, TopAnat, applied to in situ hybridization data from thousands of genes from zebrafish and mouse. We showed that the presence of expression in the nervous system is a good predictor of a higher rate of retention of duplicate genes after whole-genome duplication. Further analyses suggest that purifying selection against the toxic effects of misfolded or misinteracting proteins, which is particularly strong in nonrenewing neural tissues, likely constrains the evolution of coding sequences of nervous system genes, leading indirectly to the preservation of duplicate genes after whole-genome duplication. Whole-genome duplications thus greatly contributed to the expansion of the toolkit of genes available for the evolution of profound novelties of the nervous system at the base of the vertebrate radiation.
Collapse
Affiliation(s)
- Julien Roux
- Département d'Ecologie et d'Evolution, Université de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jialin Liu
- Département d'Ecologie et d'Evolution, Université de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Département d'Ecologie et d'Evolution, Université de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| |
Collapse
|
13
|
Abstract
Ploidy is considered a very stable cellular characteristic. Although rare, changes in ploidy play important roles in the acquisition of long-term adaptations. Since these duplications allow the subsequent loss of individual chromosomes and accumulation of mutations, changes in ploidy can also cause genomic instability, and have been found to promote cancer. Despite the importance of the subject, measuring the rate of whole-genome duplications has proven extremely challenging. We have recently measured the rate of diploidization in yeast using long-term, in-lab experiments. We found that spontaneous diploidization occurs frequently, by two different mechanisms: endoreduplication and mating type switching. Despite its common occurrence, spontaneous diploidization is usually selected against, although it can be advantageous under some stressful conditions. Our results have implications for the understanding of evolutionary processes, as well as for the use of yeast cells in biotechnological applications.
Collapse
|
14
|
Spontaneous Changes in Ploidy Are Common in Yeast. Curr Biol 2018; 28:825-835.e4. [PMID: 29502947 DOI: 10.1016/j.cub.2018.01.062] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 12/11/2017] [Accepted: 01/22/2018] [Indexed: 12/19/2022]
Abstract
Changes in ploidy are relatively rare, but play important roles in the development of cancer and the acquisition of long-term adaptations. Genome duplications occur across the tree of life, and can alter the rate of adaptive evolution. Moreover, by allowing the subsequent loss of individual chromosomes and the accumulation of mutations, changes in ploidy can promote genomic instability and/or adaptation. Although many studies have been published in the last years about changes in chromosome number and their evolutionary consequences, tracking and measuring the rate of whole-genome duplications have been extremely challenging. We have systematically studied the appearance of diploid cells among haploid yeast cultures evolving for over 100 generations in different media. We find that spontaneous diploidization is a relatively common event, which is usually selected against, but under certain stressful conditions may become advantageous. Furthermore, we were able to detect and distinguish between two different mechanisms of diploidization, one that requires whole-genome duplication (endoreduplication) and a second that involves mating-type switching despite the use of heterothallic strains. Our results have important implications for our understanding of evolution and adaptation in fungal pathogens and the development of cancer, and for the use of yeast cells in biotechnological applications.
Collapse
|
15
|
Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes. PLoS Genet 2017; 13:e1006777. [PMID: 28594822 PMCID: PMC5465968 DOI: 10.1371/journal.pgen.1006777] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 04/24/2017] [Indexed: 11/19/2022] Open
Abstract
Root-knot nematodes (genus Meloidogyne) exhibit a diversity of reproductive modes ranging from obligatory sexual to fully asexual reproduction. Intriguingly, the most widespread and devastating species to global agriculture are those that reproduce asexually, without meiosis. To disentangle this surprising parasitic success despite the absence of sex and genetic exchanges, we have sequenced and assembled the genomes of three obligatory ameiotic and asexual Meloidogyne. We have compared them to those of relatives able to perform meiosis and sexual reproduction. We show that the genomes of ameiotic asexual Meloidogyne are large, polyploid and made of duplicated regions with a high within-species average nucleotide divergence of ~8%. Phylogenomic analysis of the genes present in these duplicated regions suggests that they originated from multiple hybridization events and are thus homoeologs. We found that up to 22% of homoeologous gene pairs were under positive selection and these genes covered a wide spectrum of predicted functional categories. To biologically assess functional divergence, we compared expression patterns of homoeologous gene pairs across developmental life stages using an RNAseq approach in the most economically important asexually-reproducing nematode. We showed that >60% of homoeologous gene pairs display diverged expression patterns. These results suggest a substantial functional impact of the genome structure. Contrasting with high within-species nuclear genome divergence, mitochondrial genome divergence between the three ameiotic asexuals was very low, signifying that these putative hybrids share a recent common maternal ancestor. Transposable elements (TE) cover a ~1.7 times higher proportion of the genomes of the ameiotic asexual Meloidogyne compared to the sexual relative and might also participate in their plasticity. The intriguing parasitic success of asexually-reproducing Meloidogyne species could be partly explained by their TE-rich composite genomes, resulting from allopolyploidization events, and promoting plasticity and functional divergence between gene copies in the absence of sex and meiosis.
Collapse
|
16
|
Cuypers TD, Rutten JP, Hogeweg P. Evolution of evolvability and phenotypic plasticity in virtual cells. BMC Evol Biol 2017; 17:60. [PMID: 28241744 PMCID: PMC5329926 DOI: 10.1186/s12862-017-0918-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 02/18/2017] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Changing environmental conditions pose a challenge for the survival of species. To meet this challenge organisms adapt their phenotype by physiological regulation (phenotypic plasticity) or by evolving. Regulatory mechanisms that ensure a constant internal environment in the face of continuous external fluctuations (homeostasis) are ubiquitous and essential for survival. However, more drastic and enduring environmental change, often requires lineages to adapt by mutating. In vitro evolutionary experiments with microbes show that adaptive, large phenotypic changes occur remarkably quickly, requiring only a few mutations. It has been proposed that the high evolvability demonstrated by these microbes, is an evolved property. If both regulation (phenotypic plasticity) and evolvability can evolve as strategies to adapt to change, what are the conditions that favour the emergence of either of these strategy? Does evolution of one strategy hinder or facilitate evolution of the other strategy? RESULTS Here we investigate this with computational evolutionary modelling in populations of Virtual Cells. During a preparatory evolutionary phase, Virtual Cells evolved homeostasis regulation for internal metabolite concentrations in a fluctuating environment. The resulting wild-type Virtual Cell strains (WT-VCS) were then exposed to periodic, drastic environmental changes, while maintaining selection on homeostasis regulation. In different sets of simulations the nature and frequencies of environmental change were varied. Pre-evolved WT-VCS were highly evolvable, showing rapid evolutionary adaptation after novel environmental change. Moreover, continued low frequency changes resulted in evolutionary restructuring of the genome that enables even faster adaptation with very few mutations. In contrast, when change frequency is high, lineages evolve phenotypic plasticity that allows them to be fit in different environments without mutations. Yet, evolving phenotypic plasticity is a comparatively slow process. Under intermediate change frequencies, both strategies occur. CONCLUSIONS We conclude that evolving a homeostasis mechanisms predisposes lineage to be evolvable to novel environmental conditions. Moreover, after continued evolution, evolvability can be a viable alternative with comparable fitness to regulated phenotypic plasticity in all but the most rapidly changing environments.
Collapse
Affiliation(s)
- Thomas D Cuypers
- Theoretical Biology Group, Utrecht University, Padualaan 8, Utrecht, 3584, CH, The Netherlands.
| | - Jacob P Rutten
- Theoretical Biology Group, Utrecht University, Padualaan 8, Utrecht, 3584, CH, The Netherlands
| | - Paulien Hogeweg
- Theoretical Biology Group, Utrecht University, Padualaan 8, Utrecht, 3584, CH, The Netherlands
| |
Collapse
|
17
|
Liu S, Luo J, Chai J, Ren L, Zhou Y, Huang F, Liu X, Chen Y, Zhang C, Tao M, Lu B, Zhou W, Lin G, Mai C, Yuan S, Wang J, Li T, Qin Q, Feng H, Luo K, Xiao J, Zhong H, Zhao R, Duan W, Song Z, Wang Y, Wang J, Zhong L, Wang L, Ding Z, Du Z, Lu X, Gao Y, Murphy RW, Liu Y, Meyer A, Zhang YP. Genomic incompatibilities in the diploid and tetraploid offspring of the goldfish × common carp cross. Proc Natl Acad Sci U S A 2016; 113:1327-32. [PMID: 26768847 PMCID: PMC4747765 DOI: 10.1073/pnas.1512955113] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Polyploidy is much rarer in animals than in plants but it is not known why. The outcome of combining two genomes in vertebrates remains unpredictable, especially because polyploidization seldom shows positive effects and more often results in lethal consequences because viable gametes fail to form during meiosis. Fortunately, the goldfish (maternal) × common carp (paternal) hybrids have reproduced successfully up to generation 22, and this hybrid lineage permits an investigation into the genomics of hybridization and tetraploidization. The first two generations of these hybrids are diploids, and subsequent generations are tetraploids. Liver transcriptomes from four generations and their progenitors reveal chimeric genes (>9%) and mutations of orthologous genes. Characterizations of 18 randomly chosen genes from genomic DNA and cDNA confirm the chimera. Some of the chimeric and differentially expressed genes relate to mutagenesis, repair, and cancer-related pathways in 2nF1. Erroneous DNA excision between homologous parental genes may drive the high percentage of chimeric genes, or even more potential mechanisms may result in this phenomenon. Meanwhile, diploid offspring show paternal-biased expression, yet tetraploids show maternal-biased expression. These discoveries reveal that fast and unstable changes are mainly deleterious at the level of transcriptomes although some offspring still survive their genomic abnormalities. In addition, the synthetic effect of genome shock might have resulted in greatly reduced viability of 2nF2 hybrid offspring. The goldfish × common carp hybrids constitute an ideal system for unveiling the consequences of intergenomic interactions in hybrid vertebrate genomes and their fertility.
Collapse
Affiliation(s)
- Shaojun Liu
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China;
| | - Jing Luo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China
| | - Jing Chai
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Li Ren
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Yi Zhou
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Feng Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China
| | - Xiaochuan Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China
| | - Yubao Chen
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Chun Zhang
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Min Tao
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Bin Lu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China
| | - Wei Zhou
- School of Software, Yunnan University, Kunming, 650091, Yunnan, China
| | - Guoliang Lin
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China
| | - Chao Mai
- School of Software, Yunnan University, Kunming, 650091, Yunnan, China
| | - Shuo Yuan
- School of Software, Yunnan University, Kunming, 650091, Yunnan, China
| | - Jun Wang
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Tao Li
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Qinbo Qin
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Hao Feng
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Kaikun Luo
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Jun Xiao
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Huan Zhong
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Rurong Zhao
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Wei Duan
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Zhenyan Song
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Yanqin Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China
| | - Jing Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China
| | - Li Zhong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China
| | - Lu Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China
| | - Zhaoli Ding
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Zhenglin Du
- Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, China
| | - Xuemei Lu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yun Gao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China; Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON, Canada M5S 2C6
| | - Yun Liu
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Axel Meyer
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Ya-Ping Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China;
| |
Collapse
|
18
|
Marques CL, Fernández I, Viegas MN, Cox CJ, Martel P, Rosa J, Cancela ML, Laizé V. Comparative analysis of zebrafish bone morphogenetic proteins 2, 4 and 16: molecular and evolutionary perspectives. Cell Mol Life Sci 2016; 73:841-57. [PMID: 26341094 PMCID: PMC11108344 DOI: 10.1007/s00018-015-2024-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 07/27/2015] [Accepted: 08/14/2015] [Indexed: 11/24/2022]
Abstract
BMP2, BMP4 and BMP16 form a subfamily of bone morphogenetic proteins acting as pleiotropic growth factors during development and as bone inducers during osteogenesis. BMP16 is the most recent member of this subfamily and basic data regarding protein structure and function, and spatio-temporal gene expression is still scarce. In this work, insights on BMP16 were provided through the comparative analysis of structural and functional data for zebrafish BMP2a, BMP2b, BMP4 and BMP16 genes and proteins, determined from three-dimensional models, patterns of gene expression during development and in adult tissues, regulation by retinoic acid and capacity to activate BMP-signaling pathway. Structures of Bmp2a, Bmp2b, Bmp4 and Bmp16 were found to be remarkably similar; with residues involved in receptor binding being highly conserved. All proteins could activate the BMP-signaling pathway, suggesting that they share a common function. On the contrary, stage- and tissue-specific expression of bmp2, bmp4 and bmp16 suggested the genes might be differentially regulated (e.g. different transcription factors, enhancers and/or regulatory modules) but also that they are involved in distinct physiological processes, although with the same function. Retinoic acid, a morphogen known to interact with BMP-signaling during bone formation, was shown to down-regulate the expression of bmp2, bmp4 and bmp16, although to different extents. Taxonomic and phylogenetic analyses indicated that bmp16 diverged before bmp2 and bmp4, is not restricted to teleost fish lineage as previously reported, and that it probably arose from a whole genomic duplication event that occurred early in vertebrate evolution and disappeared in various tetrapod lineages through independent events.
Collapse
Affiliation(s)
- Cátia L Marques
- Centre of Marine Sciences (CCMAR), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
- PhD Program in Biomedical Sciences, University of Algarve, Faro, Portugal
- Department of Biomedical Sciences and Medicine (DCBM), University of Algarve, Faro, Portugal
| | - Ignacio Fernández
- Centre of Marine Sciences (CCMAR), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Michael N Viegas
- Centre of Marine Sciences (CCMAR), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Cymon J Cox
- Centre of Marine Sciences (CCMAR), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Paulo Martel
- Centre for Molecular and Structural Biomedicine (CBME/IBB-LA), University of Algarve, Faro, Portugal
| | - Joana Rosa
- Centre of Marine Sciences (CCMAR), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
- PhD Program in Biomedical Sciences, University of Algarve, Faro, Portugal
- Department of Biomedical Sciences and Medicine (DCBM), University of Algarve, Faro, Portugal
| | - M Leonor Cancela
- Centre of Marine Sciences (CCMAR), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
- Department of Biomedical Sciences and Medicine (DCBM), University of Algarve, Faro, Portugal
| | - Vincent Laizé
- Centre of Marine Sciences (CCMAR), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.
- Department of Biomedical Sciences and Medicine (DCBM), University of Algarve, Faro, Portugal.
| |
Collapse
|
19
|
Mason AS, Pires JC. Unreduced gametes: meiotic mishap or evolutionary mechanism? Trends Genet 2015; 31:5-10. [DOI: 10.1016/j.tig.2014.09.011] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 09/22/2014] [Accepted: 09/24/2014] [Indexed: 10/24/2022]
|
20
|
Conant GC, Birchler JA, Pires JC. Dosage, duplication, and diploidization: clarifying the interplay of multiple models for duplicate gene evolution over time. CURRENT OPINION IN PLANT BIOLOGY 2014; 19:91-8. [PMID: 24907529 DOI: 10.1016/j.pbi.2014.05.008] [Citation(s) in RCA: 172] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 05/06/2014] [Accepted: 05/08/2014] [Indexed: 05/04/2023]
Abstract
Requirements to maintain dosage balance shape many genome-scale patterns in organisms, including the resolution of whole genome duplications (WGD), as well as the varied effects of aneuploidy, segmental duplications, tandem duplications, gene copy number variations (CNV), and epigenetic marks. Like neofunctionalization and subfunctionalization, the impact of absolute and relative dosage varies over time. These variations are of particular importance in understanding the role of dosage in the evolution of polyploid organisms. Numerous investigations have found the consequences of polyploidy remain distinct from small-scale duplications (SSD). This observation is significant as all flowering plants have experienced at least two ancient polyploid events, and many angiosperm lineages have undergone additional rounds of polyploidy. Intriguingly, recent studies indicate a link between how epigenetic marks in recent allopolyploids may induce immediate changes in gene expression and the longer-term patterns of biased fractionation and chromosomal evolution. We argue that dosage effects represent one aspect of an emerging pluralistic framework, a framework that will use biophysics, genomic technologies, and systems-level models of cells to broaden our view of how genomes evolve.
Collapse
Affiliation(s)
- Gavin C Conant
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, United States; Informatics Institute, University of Missouri, Columbia, MO 65211, United States.
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, United States.
| | - J Chris Pires
- Informatics Institute, University of Missouri, Columbia, MO 65211, United States; Division of Biological Sciences, University of Missouri, Columbia, MO 65211, United States.
| |
Collapse
|