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Legrand S, Caron T, Maumus F, Schvartzman S, Quadrana L, Durand E, Gallina S, Pauwels M, Mazoyer C, Huyghe L, Colot V, Hanikenne M, Castric V. Differential retention of transposable element-derived sequences in outcrossing Arabidopsis genomes. Mob DNA 2019; 10:30. [PMID: 31346350 PMCID: PMC6636163 DOI: 10.1186/s13100-019-0171-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 06/28/2019] [Indexed: 12/20/2022] Open
Abstract
Background Transposable elements (TEs) are genomic parasites with major impacts on host genome architecture and host adaptation. A proper evaluation of their evolutionary significance has been hampered by the paucity of short scale phylogenetic comparisons between closely related species. Here, we characterized the dynamics of TE accumulation at the micro-evolutionary scale by comparing two closely related plant species, Arabidopsis lyrata and A. halleri. Results Joint genome annotation in these two outcrossing species confirmed that both contain two distinct populations of TEs with either 'recent' or 'old' insertion histories. Identification of rare segregating insertions suggests that diverse TE families contribute to the ongoing dynamics of TE accumulation in the two species. Orthologous TE fragments (i.e. those that have been maintained in both species), tend to be located closer to genes than those that are retained in one species only. Compared to non-orthologous TE insertions, those that are orthologous tend to produce fewer short interfering RNAs, are less heavily methylated when found within or adjacent to genes and these tend to have lower expression levels. These findings suggest that long-term retention of TE insertions reflects their frequent acquisition of adaptive roles and/or the deleterious effects of removing nearly neutral TE insertions when they are close to genes. Conclusion Our results indicate a rapid evolutionary dynamics of the TE landscape in these two outcrossing species, with an important input of a diverse set of new insertions with variable propensity to resist deletion.
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Affiliation(s)
- Sylvain Legrand
- 1Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | - Thibault Caron
- 1Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | - Florian Maumus
- 2URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - Sol Schvartzman
- 3InBioS - PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000 Liège, Belgium
| | - Leandro Quadrana
- 4IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France
| | - Eléonore Durand
- 1Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | - Sophie Gallina
- 1Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | - Maxime Pauwels
- 1Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | - Clément Mazoyer
- 1Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | - Lucie Huyghe
- 1Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | - Vincent Colot
- 4IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France
| | - Marc Hanikenne
- 3InBioS - PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000 Liège, Belgium
| | - Vincent Castric
- 1Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
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Bennetzen JL, Wang X. Relationships between Gene Structure and Genome Instability in Flowering Plants. MOLECULAR PLANT 2018; 11:407-413. [PMID: 29462722 DOI: 10.1016/j.molp.2018.02.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/11/2018] [Accepted: 02/13/2018] [Indexed: 06/08/2023]
Abstract
Flowering plant (angiosperm) genomes are exceptional in their variability with respect to genome size, ploidy, chromosome number, gene content, and gene arrangement. Gene movement, although observed in some of the earliest plant genome comparisons, has been relatively underinvestigated. We present herein a description of several interesting properties of plant gene and genome structure that are pertinent to the successful movement of a gene to a new location. These considerations lead us to propose a model that can explain the frequent success of plant gene mobility, namely that Small Insulated Genes Move Around (SIGMAR). The SIGMAR model is then compared with known processes for gene mobilization, and predictions of the SIGMAR model are formulated to encourage future experimentation. The overall results indicate that the frequent gene movement in angiosperm genomes is partly an outcome of the unusual properties of angiosperm genes, especially their small size and insulation from epigenetic silencing.
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Affiliation(s)
- Jeffrey L Bennetzen
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, Hefei, Anhui 230036, People's Republic of China; Department of Genetics, University of Georgia, Athens, GA 30602, USA.
| | - Xuewen Wang
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, Hefei, Anhui 230036, People's Republic of China; Department of Genetics, University of Georgia, Athens, GA 30602, USA
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Renaut S, Rowe HC, Ungerer MC, Rieseberg LH. Genomics of homoploid hybrid speciation: diversity and transcriptional activity of long terminal repeat retrotransposons in hybrid sunflowers. Philos Trans R Soc Lond B Biol Sci 2015; 369:rstb.2013.0345. [PMID: 24958919 DOI: 10.1098/rstb.2013.0345] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Hybridization is thought to play an important role in plant evolution by introducing novel genetic combinations and promoting genome restructuring. However, surprisingly little is known about the impact of hybridization on transposable element (TE) proliferation and the genomic response to TE activity. In this paper, we first review the mechanisms by which homoploid hybrid species may arise in nature. We then present hybrid sunflowers as a case study to examine transcriptional activity of long terminal repeat retrotransposons in the annual sunflowers Helianthus annuus, Helianthus petiolaris and their homoploid hybrid derivatives (H. paradoxus, H. anomalus and H. deserticola) using high-throughput transcriptome sequencing technologies (RNAseq). Sampling homoploid hybrid sunflower taxa revealed abundant variation in TE transcript accumulation. In addition, genetic diversity for several candidate genes hypothesized to regulate TE activity was characterized. Specifically, we highlight one candidate chromatin remodelling factor gene with a direct role in repressing TE activity in a hybrid species. This paper shows that TE amplification in hybrid lineages is more idiosyncratic than previously believed and provides a first step towards identifying the mechanisms responsible for regulating and repressing TE expansions.
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Affiliation(s)
- Sebastien Renaut
- Biodiversity Research Centre and Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Heather C Rowe
- Biodiversity Research Centre and Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Mark C Ungerer
- Division of Biology, Kansas State University, 426 Ackert Hall, Manhattan, KS 66506, USA
| | - Loren H Rieseberg
- Biodiversity Research Centre and Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4 Department of Biology, Indiana University, 1001 East Third St., Bloomington, IN 47405, USA
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Bennetzen JL, Wang H. The contributions of transposable elements to the structure, function, and evolution of plant genomes. ANNUAL REVIEW OF PLANT BIOLOGY 2014; 65:505-30. [PMID: 24579996 DOI: 10.1146/annurev-arplant-050213-035811] [Citation(s) in RCA: 304] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Transposable elements (TEs) are the key players in generating genomic novelty by a combination of the chromosome rearrangements they cause and the genes that come under their regulatory sway. Genome size, gene content, gene order, centromere function, and numerous other aspects of nuclear biology are driven by TE activity. Although the origins and attitudes of TEs have the hallmarks of selfish DNA, there are numerous cases where TE components have been co-opted by the host to create new genes or modify gene regulation. In particular, epigenetic regulation has been transformed from a process to silence invading TEs and viruses into a key strategy for regulating plant genes. Most, perhaps all, of this epigenetic regulation is derived from TE insertions near genes or TE-encoded factors that act in trans. Enormous pools of genome data and new technologies for reverse genetics will lead to a powerful new era of TE analysis in plants.
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Affiliation(s)
- Jeffrey L Bennetzen
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
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Pecinka A, Abdelsamad A, Vu GTH. Hidden genetic nature of epigenetic natural variation in plants. TRENDS IN PLANT SCIENCE 2013; 18:625-32. [PMID: 23953885 DOI: 10.1016/j.tplants.2013.07.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 07/08/2013] [Accepted: 07/11/2013] [Indexed: 05/22/2023]
Abstract
Transcriptional gene silencing (TGS) is an epigenetic mechanism that suppresses the activity of repetitive DNA elements via accumulation of repressive chromatin marks. We discuss natural variation in TGS, with a particular focus on cases that affect the function of protein-coding genes and lead to developmental or physiological changes. Comparison of the examples described has revealed that most natural variation is associated with genetic determinants, such as gene rearrangements, inverted repeats, and transposon insertions that triggered TGS. Recent technical advances have enabled the study of epigenetic natural variation at a whole-genome scale and revealed patterns of inter- and intraspecific epigenetic variation. Future studies exploring non-model species may reveal species-specific evolutionary adaptations at the level of chromatin configuration.
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Affiliation(s)
- Ales Pecinka
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany.
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Paape T, Bataillon T, Zhou P, J Y Kono T, Briskine R, Young ND, Tiffin P. Selection, genome-wide fitness effects and evolutionary rates in the model legume Medicago truncatula. Mol Ecol 2013; 22:3525-38. [PMID: 23773281 DOI: 10.1111/mec.12329] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 02/22/2013] [Accepted: 03/12/2013] [Indexed: 12/15/2022]
Abstract
Sequence data for >20 000 annotated genes from 56 accessions of Medicago truncatula were used to identify potential targets of positive selection, the determinants of evolutionary rate variation and the relative importance of positive and purifying selection in shaping nucleotide diversity. Based upon patterns of intraspecific diversity and interspecific divergence, c. 50-75% of nonsynonymous polymorphisms are subject to strong purifying selection and 1% of the sampled genes harbour a signature of positive selection. Combining polymorphism with expression data, we estimated the distribution of fitness effects and found that the proportion of deleterious mutations is significantly greater for expressed genes than for genes with undetected transcripts (nonexpressed) in a previous RNA-seq experiment and greater for broadly expressed genes than those expressed in only a single tissue. Expression level is the strongest correlate of evolutionary rates at nonsynonymous sites, and despite multiple genomic features being significantly correlated with evolutionary rates, they explain less than 20% of the variation in nonsynonymous rates (dN) and <15% of the variation in either synonymous rates (dS) or dN:dS. Among putative targets of selection were genes involved in defence against pathogens and herbivores, genes with roles in mediating the relationship with rhizobial symbionts and one-third of annotated histone-lysine methyltransferases. Adaptive evolution of the methyltransferases suggests that positive selection in gene expression may have occurred through evolution of enzymes involved in epigenetic modification.
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Affiliation(s)
- Timothy Paape
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, 8057, Switzerland
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