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Horvath R, Minadakis N, Bourgeois Y, Roulin AC. The evolution of transposable elements in Brachypodium distachyon is governed by purifying selection, while neutral and adaptive processes play a minor role. eLife 2024; 12:RP93284. [PMID: 38606833 PMCID: PMC11014726 DOI: 10.7554/elife.93284] [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: 04/13/2024] Open
Abstract
Understanding how plants adapt to changing environments and the potential contribution of transposable elements (TEs) to this process is a key question in evolutionary genomics. While TEs have recently been put forward as active players in the context of adaptation, few studies have thoroughly investigated their precise role in plant evolution. Here, we used the wild Mediterranean grass Brachypodium distachyon as a model species to identify and quantify the forces acting on TEs during the adaptation of this species to various conditions, across its entire geographic range. Using sequencing data from more than 320 natural B. distachyon accessions and a suite of population genomics approaches, we reveal that putatively adaptive TE polymorphisms are rare in wild B. distachyon populations. After accounting for changes in past TE activity, we show that only a small proportion of TE polymorphisms evolved neutrally (<10%), while the vast majority of them are under moderate purifying selection regardless of their distance to genes. TE polymorphisms should not be ignored when conducting evolutionary studies, as they can be linked to adaptation. However, our study clearly shows that while they have a large potential to cause phenotypic variation in B. distachyon, they are not favored during evolution and adaptation over other types of mutations (such as point mutations) in this species.
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Affiliation(s)
- Robert Horvath
- Department of Plant and Microbial Biology, University of ZurichZurichSwitzerland
| | - Nikolaos Minadakis
- Department of Plant and Microbial Biology, University of ZurichZurichSwitzerland
| | - Yann Bourgeois
- DIADE, University of Montpellier, CIRAD, IRDMontpellierFrance
- University of PortsmouthPortsmouthUnited Kingdom
| | - Anne C Roulin
- Department of Plant and Microbial Biology, University of ZurichZurichSwitzerland
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2
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De Kort H, Legrand S, Honnay O, Buckley J. Transposable elements maintain genome-wide heterozygosity in inbred populations. Nat Commun 2022; 13:7022. [PMID: 36396660 PMCID: PMC9672359 DOI: 10.1038/s41467-022-34795-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 11/08/2022] [Indexed: 11/18/2022] Open
Abstract
Elevated levels of inbreeding increase the risk of inbreeding depression and extinction, yet many inbred species are widespread, suggesting that inbreeding has little impact on evolutionary potential. Here, we explore the potential for transposable elements (TEs) to maintain genetic variation in functional genomic regions under extreme inbreeding. Capitalizing on the mixed mating system of Arabidopsis lyrata, we assess genome-wide heterozygosity and signatures of selection at single nucleotide polymorphisms near transposable elements across an inbreeding gradient. Under intense inbreeding, we find systematically elevated heterozygosity downstream of several TE superfamilies, associated with signatures of balancing selection. In addition, we demonstrate increased heterozygosity in stress-responsive genes that consistently occur downstream of TEs. We finally reveal that TE superfamilies are associated with specific signatures of selection that are reproducible across independent evolutionary lineages of A. lyrata. Together, our study provides an important hypothesis for the success of self-fertilizing species.
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Affiliation(s)
- Hanne De Kort
- grid.5596.f0000 0001 0668 7884Plant Conservation and Population Biology, University of Leuven, Kasteelpark Arenberg 31-2435, BE-3001 Leuven, Belgium
| | - Sylvain Legrand
- grid.503422.20000 0001 2242 6780Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | - Olivier Honnay
- grid.5596.f0000 0001 0668 7884Plant Conservation and Population Biology, University of Leuven, Kasteelpark Arenberg 31-2435, BE-3001 Leuven, Belgium
| | - James Buckley
- grid.11201.330000 0001 2219 0747School of Biological and Marine Sciences, University of Plymouth, Plymouth, PL1 2BT UK
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3
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Huang Y, Shukla H, Lee YCG. Species-specific chromatin landscape determines how transposable elements shape genome evolution. eLife 2022; 11:81567. [PMID: 35997258 PMCID: PMC9398452 DOI: 10.7554/elife.81567] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 07/15/2022] [Indexed: 11/30/2022] Open
Abstract
Transposable elements (TEs) are selfish genetic parasites that increase their copy number at the expense of host fitness. The ‘success’, or genome-wide abundance, of TEs differs widely between species. Deciphering the causes for this large variety in TE abundance has remained a central question in evolutionary genomics. We previously proposed that species-specific TE abundance could be driven by the inadvertent consequences of host-direct epigenetic silencing of TEs—the spreading of repressive epigenetic marks from silenced TEs into adjacent sequences. Here, we compared this TE-mediated local enrichment of repressive marks, or ‘the epigenetic effect of TEs’, in six species in the Drosophila melanogaster subgroup to dissect step-by-step the role of such effect in determining genomic TE abundance. We found that TE-mediated local enrichment of repressive marks is prevalent and substantially varies across and even within species. While this TE-mediated effect alters the epigenetic states of adjacent genes, we surprisingly discovered that the transcription of neighboring genes could reciprocally impact this spreading. Importantly, our multi-species analysis provides the power and appropriate phylogenetic resolution to connect species-specific host chromatin regulation, TE-mediated epigenetic effects, the strength of natural selection against TEs, and genomic TE abundance unique to individual species. Our findings point toward the importance of host chromatin landscapes in shaping genome evolution through the epigenetic effects of a selfish genetic parasite. All the instructions required for life are encoded in the set of DNA present in a cell. It therefore seems natural to think that every bit of this genetic information should serve the organism. And yet most species carry parasitic ‘transposable’ sequences, or transposons, whose only purpose is to multiply and insert themselves at other positions in the genome. It is possible for cells to suppress these selfish elements. Chemical marks can be deposited onto the DNA to temporarily ‘silence’ transposons and prevent them from being able to move and replicate. However, this sometimes comes at a cost: the repressive chemical modifications can spread to nearby genes that are essential for the organism and perturb their function. Strangely, the prevalence of transposons varies widely across the tree of life. These sequences form the majority of the genome of certain species – in fact, they represent about half of the human genetic information. But their abundance is much lower in other organisms, forming a measly 6% of the genome of puffer fish for instance. Even amongst fruit fly species, the prevalence of transposable elements can range between 2% and 25%. What explains such differences? Huang et al. set out to examine this question through the lens of transposon silencing, systematically comparing how this process impacts nearby regions in six species of fruit flies. This revealed variations in the strength of the side effects associated with transposon silencing, resulting in different levels of perturbation on neighbouring genes. A stronger impact was associated with the species having fewer transposons in its genome, suggesting that an evolutionary pressure is at work to keep the abundance of transposons at a low level in these species. Further analyses showed that the genes which determine how silencing marks are distributed may also be responsible for the variations in the impact of transposon silencing. They could therefore be the ones driving differences in the abundance of transposons between species. Overall, this work sheds light on the complex mechanisms shaping the evolution of genomes, and it may help to better understand how transposons are linked to processes such as aging and cancer.
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Affiliation(s)
- Yuheng Huang
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, United States
| | - Harsh Shukla
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, United States
| | - Yuh Chwen G Lee
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, United States
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4
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The challenges of predicting transposable element activity in hybrids. Curr Genet 2021; 67:567-572. [PMID: 33738571 DOI: 10.1007/s00294-021-01169-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 02/07/2023]
Abstract
Transposable elements (TEs) are ubiquitous mobile genetic elements that hold both disruptive and adaptive potential for species. It has long been postulated that their activity may be triggered by hybridization, a hypothesis that received mixed support from studies in various species. While host defense mechanisms against TEs are being elucidated, the increasing volume of genomic data and bioinformatic tools specialized in TE detection enable in-depth characterization of TEs at the levels of species and populations. Here, I borrow elements from the genome ecology theory to illustrate how knowledge of the diversity of TEs and host defense mechanisms may help predict the activity of TEs in the face of hybridization, and how current limitations make this task especially challenging.
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5
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Burns R, Mandáková T, Gunis J, Soto-Jiménez LM, Liu C, Lysak MA, Novikova PY, Nordborg M. Gradual evolution of allopolyploidy in Arabidopsis suecica. Nat Ecol Evol 2021; 5:1367-1381. [PMID: 34413506 PMCID: PMC8484011 DOI: 10.1038/s41559-021-01525-w] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 07/01/2021] [Indexed: 02/06/2023]
Abstract
Most diploid organisms have polyploid ancestors. The evolutionary process of polyploidization is poorly understood but has frequently been conjectured to involve some form of 'genome shock', such as genome reorganization and subgenome expression dominance. Here we study polyploidization in Arabidopsis suecica, a post-glacial allopolyploid species formed via hybridization of Arabidopsis thaliana and Arabidopsis arenosa. We generated a chromosome-level genome assembly of A. suecica and complemented it with polymorphism and transcriptome data from all species. Despite a divergence around 6 million years ago (Ma) between the ancestral species and differences in their genome composition, we see no evidence of a genome shock: the A. suecica genome is colinear with the ancestral genomes; there is no subgenome dominance in expression; and transposon dynamics appear stable. However, we find changes suggesting gradual adaptation to polyploidy. In particular, the A. thaliana subgenome shows upregulation of meiosis-related genes, possibly to prevent aneuploidy and undesirable homeologous exchanges that are observed in synthetic A. suecica, and the A. arenosa subgenome shows upregulation of cyto-nuclear processes, possibly in response to the new cytoplasmic environment of A. suecica, with plastids maternally inherited from A. thaliana. These changes are not seen in synthetic hybrids, and thus are likely to represent subsequent evolution.
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Affiliation(s)
- Robin Burns
- grid.24194.3a0000 0000 9669 8503Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Terezie Mandáková
- grid.10267.320000 0001 2194 0956CEITEC - Central European Institute of Technology, and Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Joanna Gunis
- grid.24194.3a0000 0000 9669 8503Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Luz Mayela Soto-Jiménez
- grid.24194.3a0000 0000 9669 8503Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Chang Liu
- grid.9464.f0000 0001 2290 1502Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Martin A. Lysak
- grid.10267.320000 0001 2194 0956CEITEC - Central European Institute of Technology, and Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Polina Yu. Novikova
- grid.511033.5VIB-UGent Center for Plant Systems Biology, Ghent, Belgium ,grid.419498.90000 0001 0660 6765Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Magnus Nordborg
- grid.24194.3a0000 0000 9669 8503Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
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6
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Hénault M, Marsit S, Charron G, Landry CR. The effect of hybridization on transposable element accumulation in an undomesticated fungal species. eLife 2020; 9:e60474. [PMID: 32955438 PMCID: PMC7584455 DOI: 10.7554/elife.60474] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 09/21/2020] [Indexed: 12/24/2022] Open
Abstract
Transposable elements (TEs) are mobile genetic elements that can profoundly impact the evolution of genomes and species. A long-standing hypothesis suggests that hybridization could deregulate TEs and trigger their accumulation, although it received mixed support from studies mostly in plants and animals. Here, we tested this hypothesis in fungi using incipient species of the undomesticated yeast Saccharomyces paradoxus. Population genomic data revealed no signature of higher transposition in natural hybrids. As we could not rule out the elimination of past transposition increase signatures by natural selection, we performed a laboratory evolution experiment on a panel of artificial hybrids to measure TE accumulation in the near absence of selection. Changes in TE copy numbers were not predicted by the level of evolutionary divergence between the parents of a hybrid genotype. Rather, they were highly dependent on the individual hybrid genotypes, showing that strong genotype-specific deterministic factors govern TE accumulation in yeast hybrids.
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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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7
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Woodruff GC, Teterina AA. Degradation of the Repetitive Genomic Landscape in a Close Relative of Caenorhabditis elegans. Mol Biol Evol 2020; 37:2549-2567. [PMID: 32359146 PMCID: PMC7475029 DOI: 10.1093/molbev/msaa107] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The abundance, diversity, and genomic distribution of repetitive elements is highly variable among species. These patterns are thought to be driven in part by reproductive mode and the interaction of selection and recombination, and recombination rates typically vary by chromosomal position. In the nematode Caenorhabditis elegans, repetitive elements are enriched at chromosome arms and depleted on centers, and this mirrors the chromosomal distributions of other genomic features such as recombination rate. How conserved is this genomic landscape of repeats, and what evolutionary forces maintain it? To address this, we compared the genomic organization of repetitive elements across five Caenorhabditis species with chromosome-level assemblies. As previously reported, repeat content is enriched on chromosome arms in most Caenorhabditis species, and no obvious patterns of repeat content associated with reproductive mode were observed. However, the fig-associated C. inopinata has experienced repetitive element expansion and reveals no association of global repeat density with chromosome position. Patterns of repeat superfamily specific distributions reveal this global pattern is driven largely by a few repeat superfamilies that in C. inopinata have expanded in number and have weak associations with chromosome position. Additionally, 15% of predicted protein-coding genes in C. inopinata align to transposon-related proteins. When these are excluded, C. inopinata has no enrichment of genes in chromosome centers, in contrast to its close relatives who all have such clusters. Forward evolutionary simulations reveal that chromosomal heterogeneity in recombination rate alone can generate structured repetitive genomic landscapes when insertions are weakly deleterious, whereas chromosomal heterogeneity in the fitness effects of transposon insertion can promote such landscapes across a variety of evolutionary scenarios. Thus, patterns of gene density along chromosomes likely contribute to global repetitive landscapes in this group, although other historical or genomic factors are needed to explain the idiosyncrasy of genomic organization of various transposable element taxa within C. inopinata. Taken together, these results highlight the power of comparative genomics and evolutionary simulations in testing hypotheses regarding the causes of genome organization.
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Affiliation(s)
- Gavin C Woodruff
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR
| | - Anastasia A Teterina
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR
- Center of Parasitology, Severtsov Institute of Ecology and Evolution RAS, Moscow, Russia
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8
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A Tale of Two Families: Whole Genome and Segmental Duplications Underlie Glutamine Synthetase and Phosphoenolpyruvate Carboxylase Diversity in Narrow-Leafed Lupin ( Lupinus angustifolius L.). Int J Mol Sci 2020; 21:ijms21072580. [PMID: 32276381 PMCID: PMC7177731 DOI: 10.3390/ijms21072580] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/04/2020] [Accepted: 04/06/2020] [Indexed: 01/04/2023] Open
Abstract
Narrow-leafed lupin (Lupinus angustifolius L.) has recently been supplied with advanced genomic resources and, as such, has become a well-known model for molecular evolutionary studies within the legume family—a group of plants able to fix nitrogen from the atmosphere. The phylogenetic position of lupins in Papilionoideae and their evolutionary distance to other higher plants facilitates the use of this model species to improve our knowledge on genes involved in nitrogen assimilation and primary metabolism, providing novel contributions to our understanding of the evolutionary history of legumes. In this study, we present a complex characterization of two narrow-leafed lupin gene families—glutamine synthetase (GS) and phosphoenolpyruvate carboxylase (PEPC). We combine a comparative analysis of gene structures and a synteny-based approach with phylogenetic reconstruction and reconciliation of the gene family and species history in order to examine events underlying the extant diversity of both families. Employing the available evidence, we show the impact of duplications on the initial complement of the analyzed gene families within the genistoid clade and posit that the function of duplicates has been largely retained. In terms of a broader perspective, our results concerning GS and PEPC gene families corroborate earlier findings pointing to key whole genome duplication/triplication event(s) affecting the genistoid lineage.
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9
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Mattila TM, Laenen B, Slotte T. Population Genomics of Transitions to Selfing in Brassicaceae Model Systems. Methods Mol Biol 2020; 2090:269-287. [PMID: 31975171 DOI: 10.1007/978-1-0716-0199-0_11] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Many plants harbor complex mechanisms that promote outcrossing and efficient pollen transfer. These include floral adaptations as well as genetic mechanisms, such as molecular self-incompatibility (SI) systems. The maintenance of such systems over long evolutionary timescales suggests that outcrossing is favorable over a broad range of conditions. Conversely, SI has repeatedly been lost, often in association with transitions to self-fertilization (selfing). This transition is favored when the short-term advantages of selfing outweigh the costs, primarily inbreeding depression. The transition to selfing is expected to have major effects on population genetic variation and adaptive potential, as well as on genome evolution. In the Brassicaceae, many studies on the population genetic, gene regulatory, and genomic effects of selfing have centered on the model plant Arabidopsis thaliana and the crucifer genus Capsella. The accumulation of population genomics datasets have allowed detailed investigation of where, when and how the transition to selfing occurred. Future studies will take advantage of the development of population genetics theory on the impact of selfing, especially regarding positive selection. Furthermore, investigation of systems including recent transitions to selfing, mixed mating populations and/or multiple independent replicates of the same transition will facilitate dissecting the effects of mating system variation from processes driven by demography.
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Affiliation(s)
- Tiina M Mattila
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Benjamin Laenen
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Tanja Slotte
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.
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10
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Abstract
A major current molecular evolution challenge is to link comparative genomic patterns to species' biology and ecology. Breeding systems are pivotal because they affect many population genetic processes and thus genome evolution. We review theoretical predictions and empirical evidence about molecular evolutionary processes under three distinct breeding systems-outcrossing, selfing, and asexuality. Breeding systems may have a profound impact on genome evolution, including molecular evolutionary rates, base composition, genomic conflict, and possibly genome size. We present and discuss the similarities and differences between the effects of selfing and clonality. In reverse, comparative and population genomic data and approaches help revisiting old questions on the long-term evolution of breeding systems.
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Affiliation(s)
- Sylvain Glémin
- Institut des Sciences de l'Evolution, UMR5554, Université Montpellier II, Montpellier, France
| | - Clémentine M François
- Institut des Sciences de l'Evolution, UMR5554, Université Montpellier II, Montpellier, France
| | - Nicolas Galtier
- Institut des Sciences de l'Evolution, UMR5554, Université Montpellier II, Montpellier, France.
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11
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Fine-Grained Analysis of Spontaneous Mutation Spectrum and Frequency in Arabidopsis thaliana. Genetics 2018; 211:703-714. [PMID: 30514707 PMCID: PMC6366913 DOI: 10.1534/genetics.118.301721] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 11/29/2018] [Indexed: 01/17/2023] Open
Abstract
Mutations are the ultimate source of all genetic variation. However, few direct estimates of the contribution of mutation to molecular genetic variation are available. To address this issue, we first analyzed the rate and spectrum of mutations in the Arabidopsis thaliana reference accession after 25 generations of single-seed descent. We then compared the mutation profile in these mutation accumulation (MA) lines against genetic variation observed in the 1001 Genomes Project. The estimated haploid single nucleotide mutation (SNM) rate for A. thaliana is 6.95 × 10−9 (SE ± 2.68 × 10−10) per site per generation, with SNMs having higher frequency in transposable elements (TEs) and centromeric regions. The estimated indel mutation rate is 1.30 × 10−9 (±1.07 × 10−10) per site per generation, with deletions being more frequent and larger than insertions. Among the 1694 unique SNMs identified in the MA lines, the positions of 389 SNMs (23%) coincide with biallelic SNPs from the 1001 Genomes population, and in 289 (17%) cases the changes are identical. Of the 329 unique indels identified in the MA lines, 96 (29%) overlap with indels from the 1001 Genomes dataset, and 16 indels (5% of the total) are identical. These overlap frequencies are significantly higher than expected, suggesting that de novo mutations are not uniformly distributed and arise at polymorphic sites more frequently than assumed. These results suggest that high mutation rate potentially contributes to high polymorphism and low mutation rate to reduced polymorphism in natural populations providing insights of mutational inputs in generating natural genetic diversity.
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12
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Göbel U, Arce AL, He F, Rico A, Schmitz G, de Meaux J. Robustness of Transposable Element Regulation but No Genomic Shock Observed in Interspecific Arabidopsis Hybrids. Genome Biol Evol 2018; 10:1403-1415. [PMID: 29788048 PMCID: PMC6007786 DOI: 10.1093/gbe/evy095] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2018] [Indexed: 12/23/2022] Open
Abstract
The merging of two divergent genomes in a hybrid is believed to trigger a “genomic shock”, disrupting gene regulation and transposable element (TE) silencing. Here, we tested this expectation by comparing the pattern of expression of transposable elements in their native and hybrid genomic context. For this, we sequenced the transcriptome of the Arabidopsis thaliana genotype Col-0, the A. lyrata genotype MN47 and their F1 hybrid. Contrary to expectations, we observe that the level of TE expression in the hybrid is strongly correlated to levels in the parental species. We detect that at most 1.1% of expressed transposable elements belonging to two specific subfamilies change their expression level upon hybridization. Most of these changes, however, are of small magnitude. We observe that the few hybrid-specific modifications in TE expression are more likely to occur when TE insertions are close to genes. In addition, changes in epigenetic histone marks H3K9me2 and H3K27me3 following hybridization do not coincide with TEs with changed expression. Finally, we further examined TE expression in parents and hybrids exposed to severe dehydration stress. Despite the major reorganization of gene and TE expression by stress, we observe that hybridization does not lead to increased disorganization of TE expression in the hybrid. Although our study did not examine TE transposition activity in hybrids, the examination of the transcriptome shows that TE expression is globally robust to hybridization. The term “genomic shock” is perhaps not appropriate to describe transcriptional modification in a viable hybrid merging divergent genomes.
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Affiliation(s)
- Ulrike Göbel
- Botanical Institute, University of Cologne, Germany
| | - Agustin L Arce
- Laboratorio de Biología del ARN, Instituto de Agrobiotecnología del Litoral (CONICET-UNL), 3000 Santa Fe, Argentina
| | - Fei He
- Botanical Institute, University of Cologne, Germany
| | - Alain Rico
- Thermo Fisher Scientific, Villebon-sur-Yvette, France
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13
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Horvath R, Slotte T. The Role of Small RNA-Based Epigenetic Silencing for Purifying Selection on Transposable Elements in Capsella grandiflora. Genome Biol Evol 2018; 9:2911-2920. [PMID: 29036316 PMCID: PMC5737465 DOI: 10.1093/gbe/evx206] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2017] [Indexed: 12/13/2022] Open
Abstract
To avoid negative effects of transposable element (TE) proliferation, plants epigenetically silence TEs using a number of mechanisms, including RNA-directed DNA methylation. These epigenetic modifications can extend outside the boundaries of TE insertions and lead to silencing of nearby genes, resulting in a trade-off between TE silencing and interference with nearby gene regulation. Therefore, purifying selection is expected to remove silenced TE insertions near genes more efficiently and prevent their accumulation within a population. To explore how effects of TE silencing on gene regulation shapes purifying selection on TEs, we analyzed whole genome sequencing data from 166 individuals of a large population of the outcrossing species Capsella grandiflora. We found that most TEs are rare, and in chromosome arms, silenced TEs are exposed to stronger purifying selection than those that are not silenced by 24-nucleotide small RNAs, especially with increasing proximity to genes. An age-of-allele test of neutrality on a subset of TEs supports our inference of purifying selection on silenced TEs, suggesting that our results are robust to varying transposition rates. Our results provide new insights into the processes affecting the accumulation of TEs in an outcrossing species and support the view that epigenetic silencing of TEs results in a trade-off between preventing TE proliferation and interference with nearby gene regulation. We also suggest that in the centromeric and pericentromeric regions, the negative aspects of epigenetic TE silencing are missing.
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Affiliation(s)
- Robert Horvath
- Science for Life Laboratory, Department of Ecology, Environment and Plant Sciences, Stockholm University, Sweden
| | - Tanja Slotte
- Science for Life Laboratory, Department of Ecology, Environment and Plant Sciences, Stockholm University, Sweden
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14
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Bonchev G, Willi Y. Accumulation of transposable elements in selfing populations of Arabidopsis lyrata supports the ectopic recombination model of transposon evolution. THE NEW PHYTOLOGIST 2018; 219:767-778. [PMID: 29757461 DOI: 10.1111/nph.15201] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 04/01/2018] [Indexed: 06/08/2023]
Abstract
Transposable elements (TE) can constitute a large fraction of plant genomes, yet our understanding of their evolution and fitness effect is still limited. Here we tested several models of evolution that make specific predictions about differences in TE abundance between selfing and outcrossing taxa, and between small and large populations. We estimated TE abundance in multiple populations of North American Arabidopsis lyrata differing in mating system and long-term size, using transposon insertion display on several TE families. Selfing populations had higher TE copy numbers per individual and higher TE allele frequencies, supporting models which assume that selection against TEs acts predominantly against heterozygotes via the process of ectopic recombination. In outcrossing populations differing in long-term size, the data supported neither a model of density-regulated transposition nor a model of direct deleterious effect. Instead, the population structure of TEs revealed that outcrossing populations tended to split into western and eastern groups - as previously detected using microsatellite markers - whereas selfing populations from west and east were less differentiated. This, too, agrees with the model of ectopic recombination. Overall, our results suggest that TE elements are nearly neutral except for their deleterious potential to disturb meiosis in the heterozygous state.
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Affiliation(s)
- Georgi Bonchev
- Institute of Biology, Evolutionary Botany, University of Neuchâtel, Neuchâtel, 2000, Switzerland
- Institute of Plant Physiology and Genetics, Laboratory of Genome Dynamics and Stability, Bulgarian Academy of Sciences, Sofia, 1113, Bulgaria
| | - Yvonne Willi
- Institute of Biology, Evolutionary Botany, University of Neuchâtel, Neuchâtel, 2000, Switzerland
- Department of Environmental Sciences, University of Basel, Basel, 4056, Switzerland
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15
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Han MJ, Xu HE, Xiong XM, Zhang HH. Evolutionary dynamics of transposable elements during silkworm domestication. Genes Genomics 2018; 40:1041-1051. [DOI: 10.1007/s13258-018-0713-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 05/31/2018] [Indexed: 11/24/2022]
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16
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Serrato-Capuchina A, Matute DR. The Role of Transposable Elements in Speciation. Genes (Basel) 2018; 9:E254. [PMID: 29762547 PMCID: PMC5977194 DOI: 10.3390/genes9050254] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/26/2018] [Accepted: 04/26/2018] [Indexed: 01/20/2023] Open
Abstract
Understanding the phenotypic and molecular mechanisms that contribute to genetic diversity between and within species is fundamental in studying the evolution of species. In particular, identifying the interspecific differences that lead to the reduction or even cessation of gene flow between nascent species is one of the main goals of speciation genetic research. Transposable elements (TEs) are DNA sequences with the ability to move within genomes. TEs are ubiquitous throughout eukaryotic genomes and have been shown to alter regulatory networks, gene expression, and to rearrange genomes as a result of their transposition. However, no systematic effort has evaluated the role of TEs in speciation. We compiled the evidence for TEs as potential causes of reproductive isolation across a diversity of taxa. We find that TEs are often associated with hybrid defects that might preclude the fusion between species, but that the involvement of TEs in other barriers to gene flow different from postzygotic isolation is still relatively unknown. Finally, we list a series of guides and research avenues to disentangle the effects of TEs on the origin of new species.
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Affiliation(s)
- Antonio Serrato-Capuchina
- Biology Department, Genome Sciences Building, University of North Carolina, Chapel Hill, NC 27514, USA.
| | - Daniel R Matute
- Biology Department, Genome Sciences Building, University of North Carolina, Chapel Hill, NC 27514, USA.
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17
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Dubin MJ, Mittelsten Scheid O, Becker C. Transposons: a blessing curse. CURRENT OPINION IN PLANT BIOLOGY 2018; 42:23-29. [PMID: 29453028 DOI: 10.1016/j.pbi.2018.01.003] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/11/2018] [Accepted: 01/16/2018] [Indexed: 05/18/2023]
Abstract
The genomes of most plant species are dominated by transposable elements (TEs). Once considered as 'junk DNA', TEs are now known to have a major role in driving genome evolution. Over the last decade, it has become apparent that some stress conditions and other environmental stimuli can drive bursts of activity of certain TE families and consequently new TE insertions. These can give rise to altered gene expression patterns and phenotypes, with new TE insertions sometimes causing flanking genes to become transcriptionally responsive to the same stress conditions that activated the TE in the first place. Such connections between TE-mediated increases in diversity and an accelerated rate of genome evolution provide powerful mechanisms for plants to adapt more rapidly to new environmental conditions. This review will focus on environmentally induced transposition, the mechanisms by which it alters gene expression, and the consequences for plant genome evolution and breeding.
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Affiliation(s)
- Manu J Dubin
- Université de Lille CNRS, UMR 8198-Evo-Eco-Paleo, Lille, France.
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Claude Becker
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria.
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18
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Lee YCG, Karpen GH. Pervasive epigenetic effects of Drosophila euchromatic transposable elements impact their evolution. eLife 2017; 6. [PMID: 28695823 PMCID: PMC5505702 DOI: 10.7554/elife.25762] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 06/09/2017] [Indexed: 12/21/2022] Open
Abstract
Transposable elements (TEs) are widespread genomic parasites, and their evolution has remained a critical question in evolutionary genomics. Here, we study the relatively unexplored epigenetic impacts of TEs and provide the first genome-wide quantification of such effects in D. melanogaster and D. simulans. Surprisingly, the spread of repressive epigenetic marks (histone H3K9me2) to nearby DNA occurs at >50% of euchromatic TEs, and can extend up to 20 kb. This results in differential epigenetic states of genic alleles and, in turn, selection against TEs. Interestingly, the lower TE content in D. simulans compared to D. melanogaster correlates with stronger epigenetic effects of TEs and higher levels of host genetic factors known to promote epigenetic silencing. Our study demonstrates that the epigenetic effects of euchromatic TEs, and host genetic factors modulating such effects, play a critical role in the evolution of TEs both within and between species. DOI:http://dx.doi.org/10.7554/eLife.25762.001 The DNA inside an organism encodes all the instructions needed for the organism to develop and work properly. Organisms carefully organize and maintain their DNA (collectively known as the genome) so that the genetic information remains intact and the cell can understand the instructions. However, there are some pieces of DNA that are capable of moving around the genome. For example, pieces known as transposable elements can make new copies of themselves and jump into new locations in the genome. Most transposons do not appear to have any important roles, and in fact they are usually harmful to organisms. Despite this, transposons are present in the genomes of almost all species. The number of transposons in a genome varies greatly between individuals and species, but it is not clear why this is the case. Organisms have evolved ways to limit the damage caused by transposons. For example, many cells package regions of DNA containing transposons into a tightly packed structure known as heterochromatin. However, this type of DNA packaging sometimes spreads to neighboring sections of DNA. This is a problem because cells are not usually able to read the information contained within heterochromatin. This means that transposons can prevent some instructions from being produced when they should be. Lee and Karpen used fruit flies to investigate to what extent transposons harm organisms by changing the way DNA is packaged, and whether this influences how transposons evolve. The experiments show that that more than half of the transposons in fruit flies cause neighboring sections of DNA to be packaged into heterochromatin. This can negatively impact up to 20% of genes in the genome. As a result, transposons that have harmful effects on DNA packaging are more likely to be lost from the fly population during evolution than transposons that do not have harmful effects. Fruit fly species containing transposons that tend to package more neighboring sections of DNA into heterochromatin generally have fewer transposons than genomes containing less harmful transposons. The findings of Lee and Karpen provide new insight as to why the numbers of transposons vary among organisms. The next challenge is to find out whether transposons that alter how DNA is packaged are also common in primates and other animals. DOI:http://dx.doi.org/10.7554/eLife.25762.002
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Affiliation(s)
- Yuh Chwen G Lee
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States.,Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, United States
| | - Gary H Karpen
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States.,Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, United States
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19
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Abstract
Comparing genomes of closely related genotypes from populations with distinct demographic histories can help reveal the impact of effective population size on genome evolution. For this purpose, we present a high quality genome assembly of Daphnia pulex (PA42), and compare this with the first sequenced genome of this species (TCO), which was derived from an isolate from a population with >90% reduction in nucleotide diversity. PA42 has numerous similarities to TCO at the gene level, with an average amino acid sequence identity of 98.8 and >60% of orthologous proteins identical. Nonetheless, there is a highly elevated number of genes in the TCO genome annotation, with ∼7000 excess genes appearing to be false positives. This view is supported by the high GC content, lack of introns, and short length of these suspicious gene annotations. Consistent with the view that reduced effective population size can facilitate the accumulation of slightly deleterious genomic features, we observe more proliferation of transposable elements (TEs) and a higher frequency of gained introns in the TCO genome.
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20
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Suryawanshi V, Talke IN, Weber M, Eils R, Brors B, Clemens S, Krämer U. Between-species differences in gene copy number are enriched among functions critical for adaptive evolution in Arabidopsis halleri. BMC Genomics 2016; 17:1034. [PMID: 28155655 PMCID: PMC5259951 DOI: 10.1186/s12864-016-3319-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background Gene copy number divergence between species is a form of genetic polymorphism that contributes significantly to both genome size and phenotypic variation. In plants, copy number expansions of single genes were implicated in cultivar- or species-specific tolerance of high levels of soil boron, aluminium or calamine-type heavy metals, respectively. Arabidopsis halleri is a zinc- and cadmium-hyperaccumulating extremophile species capable of growing on heavy-metal contaminated, toxic soils. In contrast, its non-accumulating sister species A. lyrata and the closely related reference model species A. thaliana exhibit merely basal metal tolerance. Results For a genome-wide assessment of the role of copy number divergence (CND) in lineage-specific environmental adaptation, we conducted cross-species array comparative genome hybridizations of three plant species and developed a global signal scaling procedure to adjust for sequence divergence. In A. halleri, transition metal homeostasis functions are enriched twofold among the genes detected as copy number expanded. Moreover, biotic stress functions including mostly disease Resistance (R) gene-related genes are enriched twofold among genes detected as copy number reduced, when compared to the abundance of these functions among all genes. Conclusions Our results provide genome-wide support for a link between evolutionary adaptation and CND in A. halleri as shown previously for Heavy metal ATPase4. Moreover our results support the hypothesis that elemental defences, which result from the hyperaccumulation of toxic metals, allow the reduction of classical defences against biotic stress as a trade-off. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3319-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vasantika Suryawanshi
- Department of Plant Physiology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, 44801, Germany.,BioQuant, University of Heidelberg, Im Neuenheimer Feld 267, Heidelberg, 69120, Germany
| | - Ina N Talke
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam, 14476, Germany
| | - Michael Weber
- Department of Plant Physiology, University of Bayreuth, Universitätsstrasse 30, Bayreuth, 95447, Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics, DKFZ, Im Neuenheimer Feld 280, Heidelberg, 69121, Germany.,BioQuant, University of Heidelberg, Im Neuenheimer Feld 267, Heidelberg, 69120, Germany.,Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 364, Heidelberg, 69120, Germany
| | - Benedikt Brors
- Division of Theoretical Bioinformatics, DKFZ, Im Neuenheimer Feld 280, Heidelberg, 69121, Germany
| | - Stephan Clemens
- Department of Plant Physiology, University of Bayreuth, Universitätsstrasse 30, Bayreuth, 95447, Germany
| | - Ute Krämer
- Department of Plant Physiology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, 44801, Germany. .,BioQuant, University of Heidelberg, Im Neuenheimer Feld 267, Heidelberg, 69120, Germany.
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21
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Ferreira de Carvalho J, de Jager V, van Gurp TP, Wagemaker NCAM, Verhoeven KJF. Recent and dynamic transposable elements contribute to genomic divergence under asexuality. BMC Genomics 2016; 17:884. [PMID: 27821059 PMCID: PMC5100183 DOI: 10.1186/s12864-016-3234-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 11/01/2016] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Transposable elements (TEs) are mobile pieces of genetic information with high mutagenic potential for the host genome. Transposition is often neutral or deleterious but may also generate potentially adaptive genetic variation. This additional source of variation could be especially relevant in non-recombining species reproducing asexually. However, evidence is lacking to determine the relevance of TEs in plant asexual genome evolution and their associated effects. Here, we characterize the repetitive fraction of the genome of the common dandelion, Taraxacum officinale and compare it between five accessions from the same apomictic lineage. The main objective of this study is to evaluate the extent of within-lineage divergence attributed to TE content and activity. We examined the repetitive genomic contribution, diversity, transcription and methylation changes to characterize accession-specific TEs. RESULTS Using low-coverage genomic sequencing, we report a highly heterogeneous TE compartment in the triploid apomict T. officinale representing up to 38.6 % of the homoploid genome. The repetitive compartment is dominated by LTR retrotransposon families accompanied by few non-LTR retrotransposons and DNA transposons. Up to half of the repeat clusters are biased towards very high read identity, indicating recent and potentially ongoing activity of these TE families. Interestingly, the five accessions are divided into two main clades based on their TE composition. Clade 2 is more dynamic than clade 1 with higher abundance of Gypsy Chromovirus sequences and transposons. Furthermore, a few low-abundant genomic TE clusters exhibit high level of transcription in two of the accessions analysed. Using reduced representation bisulfite sequencing, we detected 18.9 % of loci differentially methylated, of which 25.4 and 40.7 % are annotated as TEs or functional genes, respectively. Additionally, we show clear evidence for accession-specific TE families that are differentially transcribed and differentially methylated within the apomictic lineage, including one Copia Ale II LTR element and a PIF-Harbinger DNA transposon. CONCLUSION We report here a very young and dynamic repetitive compartment that enhances divergence within one asexual lineage of T. officinale. We speculate that accession-specific TE families that are both transcriptionally and epigenetically variable are more prone to trigger changes in expression on nearby coding sequences. These findings emphasize the potential of TE-induced mutations on functional genes during asexual genome evolution.
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Affiliation(s)
- Julie Ferreira de Carvalho
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Victor de Jager
- Bioinformatic Support Group, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Thomas P. van Gurp
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Niels C. A. M. Wagemaker
- Experimental Plant Ecology, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Koen J. F. Verhoeven
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
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22
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Methods for accurate quantification of LTR-retrotransposon copy number using short-read sequence data: a case study in Sorghum. Mol Genet Genomics 2016; 291:1871-83. [PMID: 27295958 DOI: 10.1007/s00438-016-1225-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 05/31/2016] [Indexed: 10/21/2022]
Abstract
Transposable elements (TEs) are ubiquitous in eukaryotic genomes and their mobility impacts genome structure and function in myriad ways. Because of their abundance, activity, and repetitive nature, the characterization and analysis of TEs remain challenging, particularly from short-read sequencing projects. To overcome this difficulty, we have developed a method that estimates TE copy number from short-read sequences. To test the accuracy of our method, we first performed an in silico analysis of the reference Sorghum bicolor genome, using both reference-based and de novo approaches. The resulting TE copy number estimates were strikingly similar to the annotated numbers. We then tested our method on real short-read data by estimating TE copy numbers in several accessions of S. bicolor and its close relative S. propinquum. Both methods effectively identify and rank similar TE families from highest to lowest abundance. We found that de novo characterization was effective at capturing qualitative variation, but underestimated the abundance of some TE families, specifically families of more ancient origin. Also, interspecific reference-based mapping of S. propinquum reads to the S. bicolor database failed to fully describe TE content in S. propinquum, indicative of recent TE activity leading to changes in the respective repetitive landscapes over very short evolutionary timescales. We conclude that reference-based analyses are best suited for within-species comparisons, while de novo approaches are more reliable for evolutionarily distant comparisons.
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23
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Quadrana L, Bortolini Silveira A, Mayhew GF, LeBlanc C, Martienssen RA, Jeddeloh JA, Colot V. The Arabidopsis thaliana mobilome and its impact at the species level. eLife 2016; 5. [PMID: 27258693 PMCID: PMC4917339 DOI: 10.7554/elife.15716] [Citation(s) in RCA: 197] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 06/01/2016] [Indexed: 01/07/2023] Open
Abstract
Transposable elements (TEs) are powerful motors of genome evolution yet a comprehensive assessment of recent transposition activity at the species level is lacking for most organisms. Here, using genome sequencing data for 211 Arabidopsis thaliana accessions taken from across the globe, we identify thousands of recent transposition events involving half of the 326 TE families annotated in this plant species. We further show that the composition and activity of the 'mobilome' vary extensively between accessions in relation to climate and genetic factors. Moreover, TEs insert equally throughout the genome and are rapidly purged by natural selection from gene-rich regions because they frequently affect genes, in multiple ways. Remarkably, loci controlling adaptive responses to the environment are the most frequent transposition targets observed. These findings demonstrate the pervasive, species-wide impact that a rich mobilome can have and the importance of transposition as a recurrent generator of large-effect alleles.
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Affiliation(s)
- Leandro Quadrana
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Ecole Normale Supérieure, Paris, France
| | - Amanda Bortolini Silveira
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Ecole Normale Supérieure, Paris, France
| | | | - Chantal LeBlanc
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
| | - Robert A Martienssen
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Gordon and Betty Moore Foundation, Palo Alto, United States.,Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | | | - Vincent Colot
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Ecole Normale Supérieure, Paris, France
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Macas J, Novák P, Pellicer J, Čížková J, Koblížková A, Neumann P, Fuková I, Doležel J, Kelly LJ, Leitch IJ. In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae. PLoS One 2015; 10:e0143424. [PMID: 26606051 PMCID: PMC4659654 DOI: 10.1371/journal.pone.0143424] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 11/04/2015] [Indexed: 01/30/2023] Open
Abstract
The differential accumulation and elimination of repetitive DNA are key drivers of genome size variation in flowering plants, yet there have been few studies which have analysed how different types of repeats in related species contribute to genome size evolution within a phylogenetic context. This question is addressed here by conducting large-scale comparative analysis of repeats in 23 species from four genera of the monophyletic legume tribe Fabeae, representing a 7.6-fold variation in genome size. Phylogenetic analysis and genome size reconstruction revealed that this diversity arose from genome size expansions and contractions in different lineages during the evolution of Fabeae. Employing a combination of low-pass genome sequencing with novel bioinformatic approaches resulted in identification and quantification of repeats making up 55–83% of the investigated genomes. In turn, this enabled an analysis of how each major repeat type contributed to the genome size variation encountered. Differential accumulation of repetitive DNA was found to account for 85% of the genome size differences between the species, and most (57%) of this variation was found to be driven by a single lineage of Ty3/gypsy LTR-retrotransposons, the Ogre elements. Although the amounts of several other lineages of LTR-retrotransposons and the total amount of satellite DNA were also positively correlated with genome size, their contributions to genome size variation were much smaller (up to 6%). Repeat analysis within a phylogenetic framework also revealed profound differences in the extent of sequence conservation between different repeat types across Fabeae. In addition to these findings, the study has provided a proof of concept for the approach combining recent developments in sequencing and bioinformatics to perform comparative analyses of repetitive DNAs in a large number of non-model species without the need to assemble their genomes.
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Affiliation(s)
- Jiří Macas
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
- * E-mail:
| | - Petr Novák
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
| | - Jaume Pellicer
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom
| | - Jana Čížková
- Institute of Experimental Botany, Olomouc, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Andrea Koblížková
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
| | - Pavel Neumann
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
| | - Iva Fuková
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany, Olomouc, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Laura J. Kelly
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Ilia J. Leitch
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom
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25
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Ågren JA, Greiner S, Johnson MTJ, Wright SI. No evidence that sex and transposable elements drive genome size variation in evening primroses. Evolution 2015; 69:1053-62. [PMID: 25690700 DOI: 10.1111/evo.12627] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 01/13/2015] [Indexed: 01/05/2023]
Abstract
Genome size varies dramatically across species, but despite an abundance of attention there is little agreement on the relative contributions of selective and neutral processes in governing this variation. The rate of sex can potentially play an important role in genome size evolution because of its effect on the efficacy of selection and transmission of transposable elements (TEs). Here, we used a phylogenetic comparative approach and whole genome sequencing to investigate the contribution of sex and TE content to genome size variation in the evening primrose (Oenothera) genus. We determined genome size using flow cytometry for 30 species that vary in genetic system and find that variation in sexual/asexual reproduction cannot explain the almost twofold variation in genome size. Moreover, using whole genome sequences of three species of varying genome sizes and reproductive system, we found that genome size was not associated with TE abundance; instead the larger genomes had a higher abundance of simple sequence repeats. Although it has long been clear that sexual reproduction may affect various aspects of genome evolution in general and TE evolution in particular, it does not appear to have played a major role in genome size evolution in the evening primroses.
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Affiliation(s)
- J Arvid Ågren
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, M5S 3B2, Canada.
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26
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Schwander T, Marais G, Roze D. Sex uncovered: the evolutionary biology of reproductive systems. J Evol Biol 2015; 27:1287-91. [PMID: 24975885 DOI: 10.1111/jeb.12424] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- T Schwander
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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27
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Bonandin L, Scavariello C, Luchetti A, Mantovani B. Evolutionary dynamics of R2 retroelement and insertion inheritance in the genome of bisexual and parthenogenetic Bacillus rossius populations (Insecta Phasmida). INSECT MOLECULAR BIOLOGY 2014; 23:808-820. [PMID: 25134735 DOI: 10.1111/imb.12126] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Theoretical and empirical studies have shown differential management of transposable elements in organisms with different reproductive strategies. To investigate this issue, we analysed the R2 retroelement structure and variability in parthenogenetic and bisexual populations of Bacillus rossius stick insects, as well as insertions inheritance in the offspring of parthenogenetic isolates and of crosses. The B. rossius genome hosts a functional (R2Br(fun) ) and a degenerate (R2Br(deg) ) element, their presence correlating with neither reproductive strategies nor population distribution. The median-joining network method indicated that R2Br(fun) duplicates through a multiple source model, while R2Br(deg) is apparently still duplicating via a master gene model. Offspring analyses showed that unisexual and bisexual offspring have a similar number of R2Br-occupied sites. Multiple or recent shifts from gonochoric to parthenogenetic reproduction may explain the observed data. Moreover, insertion frequency spectra show that higher-frequency insertions in unisexual offspring significantly outnumber those in bisexual offspring. This suggests that unisexual offspring eliminate insertions with lower efficiency. A comparison with simulated insertion frequencies shows that inherited insertions in unisexual and bisexual offspring are significantly different from the expectation. On the whole, different mechanisms of R2 elimination in unisexual vs bisexual offspring and a complex interplay between recombination effectiveness, natural selection and time can explain the observed data.
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Affiliation(s)
- L Bonandin
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
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de Meaux J, Pecinka A. The Arabidopsis genus: An emerging model to elucidate the molecular basis of interspecific differences in transposable element activity. Mob Genet Elements 2014; 2:142-144. [PMID: 23061020 PMCID: PMC3463470 DOI: 10.4161/mge.21111] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Arabidopsis thaliana is a model plant species and its molecular dissection has greatly contributed to our understanding of the systems preventing genome invasion by transposable elements (TE). Recent advances suggest that A. thaliana may be more efficient than its congener A. lyrata at controlling TE expression and proliferation. The comparative analysis of TE transcription in A. thaliana and A. lyrata, which differ by 40% in genome size, may help understand how silencing mechanisms contribute to the evolution of transposition rate, an important factor controlling genome size variation in plants and animals.
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Affiliation(s)
- Juliette de Meaux
- Institute for Evolution and Biodiversity; University of Münster; Münster, Germany
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Agren JÅ, Wang W, Koenig D, Neuffer B, Weigel D, Wright SI. Mating system shifts and transposable element evolution in the plant genus Capsella. BMC Genomics 2014; 15:602. [PMID: 25030755 PMCID: PMC4112209 DOI: 10.1186/1471-2164-15-602] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 07/10/2014] [Indexed: 11/11/2022] Open
Abstract
Background Despite having predominately deleterious fitness effects, transposable elements (TEs) are major constituents of eukaryote genomes in general and of plant genomes in particular. Although the proportion of the genome made up of TEs varies at least four-fold across plants, the relative importance of the evolutionary forces shaping variation in TE abundance and distributions across taxa remains unclear. Under several theoretical models, mating system plays an important role in governing the evolutionary dynamics of TEs. Here, we use the recently sequenced Capsella rubella reference genome and short-read whole genome sequencing of multiple individuals to quantify abundance, genome distributions, and population frequencies of TEs in three recently diverged species of differing mating system, two self-compatible species (C. rubella and C. orientalis) and their self-incompatible outcrossing relative, C. grandiflora. Results We detect different dynamics of TE evolution in our two self-compatible species; C. rubella shows a small increase in transposon copy number, while C. orientalis shows a substantial decrease relative to C. grandiflora. The direction of this change in copy number is genome wide and consistent across transposon classes. For insertions near genes, however, we detect the highest abundances in C. grandiflora. Finally, we also find differences in the population frequency distributions across the three species. Conclusion Overall, our results suggest that the evolution of selfing may have different effects on TE evolution on a short and on a long timescale. Moreover, cross-species comparisons of transposon abundance are sensitive to reference genome bias, and efforts to control for this bias are key when making comparisons across species. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-602) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- J Ågren Agren
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada.
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Castric V, Billiard S, Vekemans X. Trait transitions in explicit ecological and genomic contexts: plant mating systems as case studies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 781:7-36. [PMID: 24277293 DOI: 10.1007/978-94-007-7347-9_2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Plants are astonishingly diverse in how they reproduce sexually, and the study of plant mating systems provides some of the most compelling cases of parallel and independent evolutionary transitions. In this chapter, we review how the massive amount of genomic data being produced is allowing long-standing predictions from ecological and evolutionary theory to be put to test. After a review of theoretical predictions about the importance of considering the genomic architecture of the mating system, we focus on a set of recent discoveries on how the mating system is controlled in a variety of model and non-model species. In parallel, genomic approaches have revealed the complex interaction between the evolution of genes controlling mating systems and genome evolution, both genome-wide and in the mating system control region. In several cases, major transitions in the mating system can be clearly associated with important ecological changes, hence illuminating an important interplay between ecological and genomic approaches. We also list a number of major unsolved questions that remain for the field, and highlight foreseeable conceptual developments that are likely to play a major role in our understanding of how plant mating systems evolve in Nature.
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Affiliation(s)
- Vincent Castric
- Laboratoire de Génétique et Evolution des Populations Végétales (GEPV), UMR 8198; CNRS, Université Lille 1, Sciences et Technologies, Cité Scientifique, Villeneuve d'Ascq, France,
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31
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Vitte C, Fustier MA, Alix K, Tenaillon MI. The bright side of transposons in crop evolution. Brief Funct Genomics 2014; 13:276-95. [PMID: 24681749 DOI: 10.1093/bfgp/elu002] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The past decades have revealed an unexpected yet prominent role of so-called 'junk DNA' in the regulation of gene expression, thereby challenging our view of the mechanisms underlying phenotypic evolution. In particular, several mechanisms through which transposable elements (TEs) participate in functional genome diversity have been depicted, bringing to light the 'TEs bright side'. However, the relative contribution of those mechanisms and, more generally, the importance of TE-based polymorphisms on past and present phenotypic variation in crops species remain poorly understood. Here, we review current knowledge on both issues, and discuss how analyses of massively parallel sequencing data combined with statistical methodologies and functional validations will help unravelling the impact of TEs on crop evolution in a near future.
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Zhao D, Jiang N. Nested insertions and accumulation of indels are negatively correlated with abundance of mutator-like transposable elements in maize and rice. PLoS One 2014; 9:e87069. [PMID: 24475224 PMCID: PMC3903597 DOI: 10.1371/journal.pone.0087069] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 12/23/2013] [Indexed: 11/29/2022] Open
Abstract
Mutator-like transposable elements (MULEs) are widespread in plants and were first discovered in maize where there are a total of 12,900 MULEs. In comparison, rice, with a much smaller genome, harbors over 30,000 MULEs. Since maize and rice are close relatives, the differential amplification of MULEs raised an inquiry into the underlying mechanism. We hypothesize this is partly attributed to the differential copy number of autonomous MULEs with the potential to generate the transposase that is required for transposition. To this end, we mined the two genomes and detected 530 and 476 MULEs containing transposase sequences (candidate coding-MULEs) in maize and rice, respectively. Over 1/3 of the candidate coding-MULEs harbor nested insertions and the ratios are similar in the two genomes. Among the maize elements with nested insertions, 24% have insertions in coding regions and over half of them harbor two or more insertions. In contrast, only 12% of the rice elements have insertions in coding regions and 19% have multiple insertions, suggesting that nested insertions in maize are more disruptive. This is because most nested insertions in maize are from LTR retrotransposons, which are large in size and are prevalent in the maize genome. Our results suggest that the amplification of retrotransposons may limit the amplification of DNA transposons but not vice versa. In addition, more indels are detected among maize elements than rice elements whereas defects caused by point mutations are comparable between the two species. Taken together, more disruptive nested insertions combined with higher frequency of indels resulted in few (6%) coding-MULEs that may encode functional transposases in maize. In contrast, 35% of the coding-MULEs in rice retain putative intact transposase. This is in addition to the higher expression frequency of rice coding-MULEs, which may explain the higher occurrence of MULEs in rice than that in maize.
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Affiliation(s)
- Dongyan Zhao
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
| | - Ning Jiang
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
- * E-mail:
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Aliyu OM, Seifert M, Corral JM, Fuchs J, Sharbel TF. Copy number variation in transcriptionally active regions of sexual and apomictic Boechera demonstrates independently derived apomictic lineages. THE PLANT CELL 2013; 25:3808-23. [PMID: 24170129 PMCID: PMC3877827 DOI: 10.1105/tpc.113.113860] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 09/11/2013] [Accepted: 10/15/2013] [Indexed: 05/19/2023]
Abstract
In asexual (apomictic) plants, the absence of meiosis and sex is expected to lead to mutation accumulation. To compare mutation accumulation in the transcribed genomic regions of sexual and apomictic plants, we performed a double-validated analysis of copy number variation (CNV) on 10 biological replicates each of diploid sexual and diploid apomictic Boechera, using a high-density (>700 K) custom microarray. The Boechera genome demonstrated higher levels of depleted CNV, compared with enriched CNV, irrespective of reproductive mode. Genome-wide patterns of CNV revealed four divergent lineages, three of which contain both sexual and apomictic genotypes. Hence genome-wide CNV reflects at least three independent origins (i.e., expression) of apomixis from different sexual genetic backgrounds. CNV distributions for different families of transposable elements were lineage specific, and the enrichment of LINE/L1 and long term repeat/Copia elements in lineage 3 apomicts is consistent with sex and meiosis being mechanisms for purging genomic parasites. We hypothesize that significant overrepresentation of specific gene ontology classes (e.g., pollen-pistil interaction) in apomicts implies that gene enrichment could be an adaptive mechanism for genome stability in diploid apomicts by providing a polyploid-like system for buffering the effects of deleterious mutations.
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Affiliation(s)
- Olawale M. Aliyu
- Apomixis Research Group, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | - Michael Seifert
- Data Inspection Research Group, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
- Cellular Networks and Systems Biology, Biotechnology Center of the Technical University Dresden, D-01307 Dresden, Germany
- Innovative Methods of Computing, Center for Information Services and High Performance Computing, Technical University Dresden, D-01187 Dresden, Germany
| | - José M. Corral
- Apomixis Research Group, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | - Joerg Fuchs
- Karyotype Evolution Research Group, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | - Timothy F. Sharbel
- Apomixis Research Group, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
- Address correspondence to
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Startek M, Le Rouzic A, Capy P, Grzebelus D, Gambin A. Genomic parasites or symbionts? Modeling the effects of environmental pressure on transposition activity in asexual populations. Theor Popul Biol 2013; 90:145-51. [PMID: 23948701 DOI: 10.1016/j.tpb.2013.07.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 07/17/2013] [Accepted: 07/25/2013] [Indexed: 11/17/2022]
Abstract
Transposable elements are DNA segments capable of persisting in host genomes by self-replication in spite of deleterious mutagenic effects. The theoretical dynamics of these elements within genomes has been studied extensively, and population genetic models predict that they can invade and maintain as a result of both intra-genomic and inter-individual selection in sexual species. In asexuals, the success of selfish DNA is more difficult to explain. However, most theoretical work assumes constant environment. Here, we analyze the impact of environmental change on the dynamics of transposition activity when horizontal DNA exchange is absent, based on a stochastic computational model of transposable element proliferation. We argue that repeated changes in the phenotypic optimum in a multidimensional fitness landscape may induce explosive bursts of transposition activity associated with faster adaptation. However, long-term maintenance of transposition activity is unlikely. This could contribute to the significant variation in the transposable element copy number among closely related species.
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Affiliation(s)
- Michał Startek
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Poland
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35
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Nagamachi CY, Pieczarka JC, O'Brien PCM, Pinto JA, Malcher SM, Pereira AL, Rissino JDD, Mendes-Oliveira AC, Rossi RV, Ferguson-Smith MA. FISH with whole chromosome and telomeric probes demonstrates huge karyotypic reorganization with ITS between two species of Oryzomyini (Sigmodontinae, Rodentia): Hylaeamys megacephalus probes on Cerradomys langguthi karyotype. Chromosome Res 2013; 21:107-19. [PMID: 23494775 DOI: 10.1007/s10577-013-9341-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 02/14/2013] [Accepted: 02/18/2013] [Indexed: 10/27/2022]
Abstract
Rodentia comprises 42 % of living mammalian species. The taxonomic identification can be difficult, the number of species currently known probably being underestimated, since many species show only slight morphological variations. Few studies surveyed the biodiversity of species, especially in the Amazon region. Cytogenetic studies show great chromosomal variability in rodents, with diploid numbers ranging from 10 to 102, making it difficult to find chromosomal homologies by comparative G banding. Chromosome painting is useful, but only a few species of rodents have been studied by this technique. In this study, we sorted whole chromosome probes by fluorescence-activated cell sorting from two Hylaeamys megacephalus individuals, an adult female (2n = 54) and a fetus (2n = 50). We made reciprocal chromosome painting between these karyotypes and cross-species hybridization on Cerradomys langguthi (2n = 46). Both species belong to the tribe Oryzomyini (Sigmodontinae), which is restricted to South America and were collected in the Amazon region. Twenty-four chromosome-specific probes from the female and 25 from the fetus were sorted. Reciprocal chromosome painting shows that the karyotype of the fetus does not represent a new cytotype, but an unbalanced karyotype with multiple rearrangements. Cross-species hybridization of H. megacephalus probes on metaphases of C. langguthi shows that 11 chromosomes of H. megacephalus revealed conserved synteny, 10 H. megacephalus probes hybridized to two chromosomal regions and three hybridized to three regions. Associations were observed on chromosomes pairs 1-4 and 11. Fluorescence in situ hybridization with a telomeric probe revealed interstitial regions in three pairs (1, 3, and 4) of C. langguthi chromosomes. We discuss the genomic reorganization of the C. langguthi karyotype.
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36
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Wang X, Weigel D, Smith LM. Transposon variants and their effects on gene expression in Arabidopsis. PLoS Genet 2013; 9:e1003255. [PMID: 23408902 PMCID: PMC3567156 DOI: 10.1371/journal.pgen.1003255] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 12/03/2012] [Indexed: 02/01/2023] Open
Abstract
Transposable elements (TEs) make up the majority of many plant genomes. Their transcription and transposition is controlled through siRNAs and epigenetic marks including DNA methylation. To dissect the interplay of siRNA–mediated regulation and TE evolution, and to examine how TE differences affect nearby gene expression, we investigated genome-wide differences in TEs, siRNAs, and gene expression among three Arabidopsis thaliana accessions. Both TE sequence polymorphisms and presence of linked TEs are positively correlated with intraspecific variation in gene expression. The expression of genes within 2 kb of conserved TEs is more stable than that of genes next to variant TEs harboring sequence polymorphisms. Polymorphism levels of TEs and closely linked adjacent genes are positively correlated as well. We also investigated the distribution of 24-nt-long siRNAs, which mediate TE repression. TEs targeted by uniquely mapping siRNAs are on average farther from coding genes, apparently because they more strongly suppress expression of adjacent genes. Furthermore, siRNAs, and especially uniquely mapping siRNAs, are enriched in TE regions missing in other accessions. Thus, targeting by uniquely mapping siRNAs appears to promote sequence deletions in TEs. Overall, our work indicates that siRNA–targeting of TEs may influence removal of sequences from the genome and hence evolution of gene expression in plants. Transposable elements (TEs) are selfish DNA sequences. Together with their immobilized derivatives, they account for a large fraction of eukaryotic genomes. TEs can affect nearby gene activity, either directly by disrupting regulatory sequences or indirectly through the host mechanisms used to prevent TE proliferation. A comparison of Arabidopsis thaliana genomes reveals rapid TE degeneration. We asked what drives TE degeneration and how often TE variation affects nearby gene expression. To answer these questions, we studied the interplay between TEs, DNA sequence variation, and short interfering RNAs (siRNAs) in three A. thaliana strains. We find sequence variation in genes and adjacent TEs to be correlated, from which we conclude either that TEs insert more often near polymorphic genes or that TEs next to polymorphic genes are less efficiently purged from the genome. We also noticed that processes that cause deletions within TEs and ones that silence TEs appear to be linked, because siRNA targeting is a predictor of sequence loss in accessions. Our work provides insight into the contribution of TEs to gene expression plasticity, and it links TE silencing mechanisms to the evolution of TE variation between genomes, thereby linking TE silencing mechanisms to expression plasticity.
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Affiliation(s)
- Xi Wang
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
- * E-mail: (DW); (LMS)
| | - Lisa M. Smith
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
- * E-mail: (DW); (LMS)
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Ito H, Yoshida T, Tsukahara S, Kawabe A. Evolution of the ONSEN retrotransposon family activated upon heat stress in Brassicaceae. Gene 2013; 518:256-61. [PMID: 23370337 DOI: 10.1016/j.gene.2013.01.034] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 01/15/2013] [Accepted: 01/17/2013] [Indexed: 11/20/2022]
Abstract
A Ty1/Copia-like retrotransposon, ONSEN, is activated by heat stress in Arabidopsis thaliana, and its de novo integrations that were observed preferentially within genes implies its regulation of neighboring genes. Here we show that ONSEN related copies were found in most species of Brassicaceae, forming a cluster with each species in phylogenetic tree. Most copies were localized close to genes in Arabidopsis lyrata and Brassica rapa, suggesting conserved integration specificity of ONSEN family into genic or open chromatin. In addition, we found heat-induced transcriptional activation of ONSEN family in several species of Brassicaceae. These results suggest that ONSEN has conserved transcriptional activation promoted by environmental heat stress in some Brassicaceae species.
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Affiliation(s)
- Hidetaka Ito
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
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38
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Shen JJ, Dushoff J, Bewick AJ, Chain FJ, Evans BJ. Genomic dynamics of transposable elements in the western clawed frog (Silurana tropicalis). Genome Biol Evol 2013; 5:998-1009. [PMID: 23645600 PMCID: PMC3673623 DOI: 10.1093/gbe/evt065] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2013] [Indexed: 02/07/2023] Open
Abstract
Transposable elements (TEs) are repetitive DNA sequences that can make new copies of themselves that are inserted elsewhere in a host genome. The abundance and distributions of TEs vary considerably among phylogenetically diverse hosts. With the aim of exploring the basis of this variation, we evaluated correlations between several genomic variables and the presence of TEs and non-TE repeats in the complete genome sequence of the Western clawed frog (Silurana tropicalis). This analysis reveals patterns of TE insertion consistent with gene disruption but not with the insertional preference model. Analysis of non-TE repeats recovered unique features of their genome-wide distribution when compared with TE repeats, including no strong correlation with exons and a particularly strong negative correlation with GC content. We also collected polymorphism data from 25 TE insertion sites in 19 wild-caught S. tropicalis individuals. DNA transposon insertions were fixed at eight of nine sites and at a high frequency at one of nine, whereas insertions of long terminal repeat (LTR) and non-LTR retrotransposons were fixed at only 4 of 16 sites and at low frequency at 12 of 16. A maximum likelihood model failed to attribute these differences in insertion frequencies to variation in selection pressure on different classes of TE, opening the possibility that other phenomena such as variation in rates of replication or duration of residence in the genome could play a role. Taken together, these results identify factors that sculpt heterogeneity in TE distribution in S. tropicalis and illustrate that genomic dynamics differ markedly among TE classes and between TE and non-TE repeats.
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Affiliation(s)
- Jiangshan J. Shen
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
- Present address: Department of Pathology, The University of Hong Kong, Hong Kong, China
| | - Jonathan Dushoff
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Adam J. Bewick
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Frédéric J.J. Chain
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Ben J. Evans
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
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Käfer J, Talianová M, Bigot T, Michu E, Guéguen L, Widmer A, Žlůvová J, Glémin S, Marais GAB. Patterns of molecular evolution in dioecious and non-dioecious Silene. J Evol Biol 2012. [PMID: 23206219 DOI: 10.1111/jeb.12052] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dioecy (i.e. having separate sexes) is a rather rare breeding system in flowering plants. Such rareness may result from a high probability of extinction in dioecious species because of less efficient dispersal and the costs of sexual selection, which are expected to harm dioecious species' survival on the long term. These handicaps should decrease the effective population size (Ne) of dioecious species, which in turn should reduce the efficacy of selection. Moreover, sexual selection in dioecious species is expected to specifically affect some genes, which will evolve under positive selection. The relative contribution of these effects is currently unknown and we tried to disentangle them by comparing sequence evolution between dioecious and non-dioecious species in the Silene genus (Caryophyllaceae), where dioecy has evolved at least twice. For the dioecious species in the section Melandrium, where dioecy is the oldest, we found a global reduction of purifying selection, while on some, male-biased genes, positive selection was found. For section Otites, where dioecy evolved more recently, we found no significant differences between dioecious and non-dioecious species. Our results are consistent with the view that dioecy is an evolutionary dead end in flowering plants, although other scenarios for explaining reduced Ne cannot be ruled out. Our results also show that contrasting forces act on the genomes of dioecious plants, and suggest that some time is required before the genome of such plants bears the footprints of dioecy.
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Affiliation(s)
- J Käfer
- Univ Lyon 1, Centre National de la Recherche Scientifique, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, Villeurbanne, France.
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A comparison of transcriptome and epigenetic status between closely related species in the genus Arabidopsis. Gene 2012; 506:301-9. [PMID: 22796129 DOI: 10.1016/j.gene.2012.07.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 06/14/2012] [Accepted: 07/03/2012] [Indexed: 01/02/2023]
Abstract
Difference in the level of expression of genes is one of the factors contributing to plant phenotype. As well as being under genetic control, gene expression is regulated by epigenetic processes such as DNA methylation and histone modifications. We compared genome-wide gene expression between Arabidopsis thaliana and the related species Arabidopsis lyrata subsp. lyrata and Arabidopsis halleri subsp. gemmifera to understand which genes might contribute to species differences. Genes categorized into response to stress tended to show differential expression between species, suggesting that divergence of expression in these genes contributes to adaptation to environmental conditions following the divergence of species. Regions methylated in A. lyrata were identified from Methylated-DNA immunoprecipitation, and this DNA methylation profile together with transcriptome data revealed that gene body methylation was not associated with differential gene expression between A. thaliana and A. lyrata. The DNA methylation status of four putative imprinted genes of A. lyrata was examined and found to be conserved in vegetative tissues between A. thaliana and A. lyrata in FIS2, HDG3, and HDG9, but not in HDG8.
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Kraaijeveld K, Zwanenburg B, Hubert B, Vieira C, De Pater S, Van Alphen JJM, Den Dunnen JT, De Knijff P. Transposon proliferation in an asexual parasitoid. Mol Ecol 2012; 21:3898-906. [PMID: 22548357 DOI: 10.1111/j.1365-294x.2012.5582.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The widespread occurrence of sex is one of the most elusive problems in evolutionary biology. Theory predicts that asexual lineages can be driven to extinction by uncontrolled proliferation of vertically transmitted transposable elements (TEs), which accumulate because of the inefficiency of purifying selection in the absence of sex and recombination. To test this prediction, we compared genome-wide TE load between a sexual lineage of the parasitoid wasp Leptopilina clavipes and a lineage of the same species that is rendered asexual by Wolbachia-induced parthenogenesis. We obtained draft genome sequences at 15-20× coverage of both the sexual and the asexual lineages using next-generation sequencing. We identified transposons of most major classes in both lineages. Quantification of TE abundance using coverage depth showed that copy numbers in the asexual lineage exceeded those in the sexual lineage for DNA transposons, but not LTR and LINE-like elements. However, one or a small number of gypsy-like LTR elements exhibited a fourfold higher coverage in the asexual lineage. Quantitative PCR showed that high loads of this gypsy-like TE were characteristic for 11 genetically distinct asexual wasp lineages when compared to sexual lineages. We found no evidence for an overall increase in copy number for all TE types in asexuals as predicted by theory. Instead, we suggest that the expansions of specific TEs are best explained as side effects of (epi)genetic manipulations of the host genome by Wolbachia. Asexuality is achieved in a myriad of ways in nature, many of which could similarly result in TE proliferation.
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Affiliation(s)
- Ken Kraaijeveld
- Department of Human Genetics, Leiden University Medical Center S4-P, PO Box 9600, 2300 RC Leiden, The Netherlands.
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Boutin TS, Le Rouzic A, Capy P. How does selfing affect the dynamics of selfish transposable elements? Mob DNA 2012; 3:5. [PMID: 22394388 PMCID: PMC3395816 DOI: 10.1186/1759-8753-3-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 03/07/2012] [Indexed: 02/02/2023] Open
Abstract
Background Many theoretical models predicting the dynamics of transposable elements (TEs) in genomes, populations, and species have already been proposed. However, most of them only focus on populations of sexual diploid individuals, and TE dynamics in populations partly composed by autogamous individuals remains poorly investigated. To estimate the impact of selfing on TE dynamics, the short- and long-term evolution of TEs was simulated in outcrossing populations with various proportions of selfing individuals. Results Selfing has a deep impact on TE dynamics: the higher the selfing rate, the lower the probability of invasion. Already known non-equilibrium dynamics (complete loss, domestication, cyclical invasion of TEs) can all be described whatever the mating system. However, their pattern and their respective frequencies greatly depend on the selfing rate. For instance, in cyclical dynamics resulting from interactions between autonomous and non-autonomous copies, cycles are faster when the selfing rate increases. Interestingly, an abrupt change in the mating system from sexuality to complete asexuality leads to the loss of all the elements over a few hundred generations. In general, for intermediate selfing rates, the transposition activity remains maintained. Conclusions Our theoretical results evidence that a clear and systematic contrast in TE content according to the mating system is expected, with a smooth transition for intermediate selfing rates. Several parameters impact the TE copy number, and all dynamics described in allogamous populations can be also observed in partly autogamous species. This study thus provides new insights to understand the complex signal from empirical comparison of closely related species with different mating systems.
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Affiliation(s)
- Thibaud S Boutin
- LEGS, CNRS UPR9034, IDEEV FR3284, Avenue de la terrasse, Bat 13, 91198 Gif-sur-Yvette, France.
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de la Chaux N, Tsuchimatsu T, Shimizu KK, Wagner A. The predominantly selfing plant Arabidopsis thaliana experienced a recent reduction in transposable element abundance compared to its outcrossing relative Arabidopsis lyrata. Mob DNA 2012; 3:2. [PMID: 22313744 PMCID: PMC3292453 DOI: 10.1186/1759-8753-3-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 02/07/2012] [Indexed: 12/11/2022] Open
Abstract
Background Transposable elements (TEs) are major contributors to genome evolution. One factor that influences their evolutionary dynamics is whether their host reproduces through selfing or through outcrossing. According to the recombinational spreading hypothesis, for instance, TEs can spread more easily in outcrossing species through recombination, and should thus be less abundant in selfing species. We here studied the distribution and evolutionary dynamics of TE families in the predominantly selfing plant Arabidopsis thaliana and its close outcrossing relative Arabidopsis lyrata on a genome-wide scale. We characterized differences in TE abundance between them and asked which, if any, existing hypotheses about TE abundances may explain these differences. Results We identified 1,819 TE families representing all known classes of TEs in both species, and found three times more copies in the outcrossing A. lyrata than in the predominantly selfing A. thaliana, as well as ten times more TE families unique to A. lyrata. On average, elements in A. lyrata are younger than elements in A. thaliana. In particular, A. thaliana shows a marked decrease in element number that occurred during the most recent 10% of the time interval since A. thaliana split from A. lyrata. This most recent period in the evolution of A. thaliana started approximately 500,000 years ago, assuming a splitting time of 5 million years ago, and coincides with the time at which predominant selfing originated. Conclusions Our results indicate that the mating system may be important for determining TE copy number, and that selfing species are likely to have fewer TEs.
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Affiliation(s)
- Nicole de la Chaux
- Molecular Evolution and Evolutionary Systems Biology, Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
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Ågren JA, Wright SI. Co-evolution between transposable elements and their hosts: a major factor in genome size evolution? Chromosome Res 2012; 19:777-86. [PMID: 21850458 DOI: 10.1007/s10577-011-9229-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Most models of genome size evolution emphasize changes in relative rates of and/or the efficacy of selection on insertions and deletions. However, transposable elements (TEs) are a major contributor to genome size evolution, and since they experience their own selective pressures for expansion, genome size changes may in part be driven by the dynamics of co-evolution between TEs and their hosts. Under this perspective, predictions about the conditions that allow for genome expansion may be altered. In this review, we outline the evidence for TE-host co-evolution, discuss the conditions under which these dynamics can change, and explore the possible contribution to the evolution of genome size. Aided partly by advances in our understanding of the mechanisms of TE silencing via small RNAs, there is growing evidence that the evolution of transposition rates can be important in driving genome expansion and contraction. Shifts in genome size and transposon abundance associated with interspecific hybridization and changes in mating system are consistent with an important role for transposition rate evolution, although other possible explanations persist. More understanding of the potential for the breakdown of host silencing mechanisms and/or the potential for TEs to evade host immune responses will improve our understanding of the importance of changes in TE activity in driving genome size evolution.
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Affiliation(s)
- J Arvid Ågren
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S3B2, Canada
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Muñoz-Diez C, Vitte C, Ross-Ibarra J, Gaut BS, Tenaillon MI. Using Nextgen Sequencing to Investigate Genome Size Variation and Transposable Element Content. PLANT TRANSPOSABLE ELEMENTS 2012. [DOI: 10.1007/978-3-642-31842-9_3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Abstract
Plant genomes are unique in an intriguing feature: the range of their size variation is unprecedented among living organisms. Although polyploidization contributes to this variability, transposable elements (TEs) seem to play the pivotal role. TEs, often considered intragenomic parasites, not only affect the genome size of the host, but also interact with other genes, disrupting and creating new functions and regulatory networks. Coevolution of plant genomes and TEs has led to tight regulation of TE activity, and growing evidence suggests their relationship became mutualistic. Although the expansions of TEs represent certain costs for the host genomes, they may also bring profits for populations, helping to overcome challenging environmental (biotic/abiotic stress) or genomic (hybridization and allopolyploidization) conditions. In this paper, we discuss the possibility that the possession of inducible TEs may provide a selective advantage for various plant populations.
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He F, Zhang X, Hu JY, Turck F, Dong X, Goebel U, Borevitz JO, de Meaux J. Widespread interspecific divergence in cis-regulation of transposable elements in the Arabidopsis genus. Mol Biol Evol 2011; 29:1081-91. [PMID: 22086904 DOI: 10.1093/molbev/msr281] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Transposable elements (TEs) are so abundant and variable that they count among the most important mutational sources in genomes. Nonetheless, little is known about the genetics of their variation in activity or silencing across closely related species. Here, we demonstrate that regulation of TE genes can differ dramatically between the two closely related Arabidopsis species A. thaliana and A. lyrata. In leaf and floral tissues of F1 interspecific hybrids, about 47% of TEs show allele-specific expression, with the A. lyrata copy being generally expressed at higher level. We confirm that TEs are generally expressed in A. lyrata but not in A. thaliana. Allele-specific differences in TE expression are associated with divergence in epigenetic modifications like DNA and histone methylation between species as well as with sequence divergence. Our data demonstrate that A. thaliana silences TEs much better than A. lyrata. For long terminal repeat retrotransposons, these differences are more pronounced for younger insertions. Interspecific differences in TE silencing may have a great impact on genome size changes.
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Affiliation(s)
- Fei He
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
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