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Impact of transposable elements on genome dynamics and reproductive isolation

Titel Englisch Impact of transposable elements on genome dynamics and reproductive isolation
Gesuchsteller/in Parisod Christian
Nummer 131950
Förderungsinstrument Ambizione
Forschungseinrichtung Laboratoire de Botanique Évolutive Institut de Biologie Université de Neuchâtel
Hochschule Universität Neuenburg - NE
Hauptdisziplin Botanik
Beginn/Ende 01.06.2011 - 31.05.2014
Bewilligter Betrag 625'870.00
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Alle Disziplinen (3)

Disziplin
Botanik
Genetik
Oekologie

Lay Summary (Englisch)

Lead
Lay summary
Associating genome reorganization with evolutionary diversification remains an enduring challenge of evolutionary biology. Transposable Elements (TEs) - also called jumping genes - are postulated to play a pivotal role in shaping genome architecture, triggering restructuring and functional changes, and producing abundant raw material for evolution. As divergent chromosomal structure contributes to hybrid infertility, reducing the level of recombination around rearranged segments and thereby restricting gene exchange, TEs may be important in promoting reproductive isolation.

As chromosome doubling specifically restores the fertility of hybrids between structurally divergent genomes, we choose to investigate the role of TEs in chromosomal speciation among diploid taxa of the young autopolyploid complex Biscutella laevigata (Brassicaceae). Producing low genome snapshots by 454 sequencing, we unravel TE families contributing to genome organization in divergent populations of B. laevigata. Then, producing hybrids between naturally occurring diploids as well as synthetic polyploids, we assess whether intraspecific divergence in genome structure results in reproductive isolation. Using complementary molecular tools, we track immediate reorganization (restructuring vs. methylation changes) in contrasted genome fractions (TEs vs. random sequences) to reveal the mechanisms underlying reproductive isolation.

In a complementary sub-project, we investigate how genome reorganization is related to ecological differentiation and local adaptation, making use of landscape genetics approaches to infer spatial genetic structure and identify patterns of local adaptation. Setting up a reciprocal transplant experiment among selected sites, we will detect patterns of local adaptation to environmental heterogeneity. In autopolyploids, local adaptation is predicted to evolve with genome restructuring that decreases polysomic inheritance. Accordingly, experimental crossing of selected accessions will assess whether locally adapted populations present increased levels of disomic inheritance as compared to populations showing signature of recent expansion.

Direktlink auf Lay Summary Letzte Aktualisierung: 21.02.2013

Verantw. Gesuchsteller/in und weitere Gesuchstellende

Mitarbeitende

Publikationen

Publikation
Current plant speciation research: unraveling the processes and mechanisms behind the evolution of reproductive isolation barriers.
Lafon-Placette Clément, Vallejo-Marin Mario, Parisod Christian, Abbott Richard, Köhler Claudia (2016), Current plant speciation research: unraveling the processes and mechanisms behind the evolution of reproductive isolation barriers., in New Phytologist, 209, 29-33.
Differential introgression and reorganization of retrotransposons in hybrid zones between wild wheats.
Senerchia Natacha, Felber François, North Béatrice, Sarr Anouk, Guadagnolo Roberto, Parisod Christian (2016), Differential introgression and reorganization of retrotransposons in hybrid zones between wild wheats., in Molecular Ecology, 25, 2518-2528.
Repeated whole-genome duplication, karyotype reshuffling and biased retention of stress-responding genes in Buckler Mustards.
Geiser Céline, Mandakova Teresie, Arrigo Nils, Lysak Martin, Parisod Christian (2016), Repeated whole-genome duplication, karyotype reshuffling and biased retention of stress-responding genes in Buckler Mustards., in The Plant Cell, 28, 17-27.
Towards unified hypotheses of the impact of polyploidy on ecological niches
Parisod Christian, Broennimann Olivier (2016), Towards unified hypotheses of the impact of polyploidy on ecological niches, in New Phytologist, 212, 540-542.
Evolutionary dynamics of retrotransposons following autopolyploidy in the Buckler Mustard species complex
Bardil Amélie, Tayalé Alexandre, Parisod Christian (2015), Evolutionary dynamics of retrotransposons following autopolyploidy in the Buckler Mustard species complex, in The Plant Journal, 82, 621-631.
Genome reorganization in F1 hybrids uncovers the role of retrotransposons in reproductive isolation
Senerchia Natacha, Felber François, Parisod Christian (2015), Genome reorganization in F1 hybrids uncovers the role of retrotransposons in reproductive isolation, in Proceedings of the Royal Society B-Biological Sciences, 282, 20142874.
Very high resolution digital elevation models: are multi-scale derived variables ecologically relevant?
Leempoel Kévin, Parisod Christian, Geiser Céline, Daprà Luca, Vittoz Pascal, Joost Stéphane (2015), Very high resolution digital elevation models: are multi-scale derived variables ecologically relevant?, in Methods in Ecology and Evolution , 6, 1373-1383.
Contrasting evolutionary dynamics of multiple retrotransposons after independent polyploidy events in wild wheats
Senerchia Natacha, Felber François, Parisod Christian (2014), Contrasting evolutionary dynamics of multiple retrotransposons after independent polyploidy events in wild wheats, in New Phytologist, 202, 975-985.
Detecting epigenetic effects of transposable elements in plants
Parisod Christian, Salmon Armel, Ainouche Malika, Grandbastien Marie-Angèle (2014), Detecting epigenetic effects of transposable elements in plants, in Methods in Molecular Biology, 112, 211-217.
Genetics of cryptic speciation within an arctic mustard, Draba nivalis
Gustaffsson Lovisa, Skrede Inger, Gussarova Galina, Borgen Liv, Rowe Heather, Rieseberg Loren, Brochmann Christian, Parisod Christian (2014), Genetics of cryptic speciation within an arctic mustard, Draba nivalis, in PLoS ONE, 9, e93834.
Patterns of genetic divergence among populations of the pseudometallophyte Biscutella laevigata from southern Poland
Babst-Kostecka Alicja, Parisod Christian, Godé Cécile, Vollenweider Pierre, Pauwels Maxime (2014), Patterns of genetic divergence among populations of the pseudometallophyte Biscutella laevigata from southern Poland, in Plant and Soil, 383, 245-256.
Evolutionary dynamics of LTR retrotransposons in wild wheats assessed with high throughput sequencing
Senerchia Natacha, Wicker Thomas, Felber François, Parisod Christian (2013), Evolutionary dynamics of LTR retrotransposons in wild wheats assessed with high throughput sequencing, in Genome Biology and Evolution, 5, 1010-1020.
Gènes et environnement: la lunetière lisse pour comprendre l’origine de la biodiversité.
Geiser Céline, Tayalé Alexandre, Parisod Christian (2013), Gènes et environnement: la lunetière lisse pour comprendre l’origine de la biodiversité., in L'Ermite Herbu, Journal de l’Association Des Amis du Jardin botanique de l'Ermitage , 46, 13-17.
Genome-specific introgression between wheat and its wild relative Aegilops triuncialis
Parisod Christian, Definod Céline, Sarr Anouk, Arrigo Nils, Felber François (2013), Genome-specific introgression between wheat and its wild relative Aegilops triuncialis, in Journal of Evolutionary Biology, 26, 223-228.
Hybridization and speciation
Abbott et al. (39 authors incl. Parisod as discussion leader) (2013), Hybridization and speciation, in Journal of Evolutionary Biology, 26, 229-246.
Natural pathways to polyploidy and consequences for genome organization and genome size
Tayalé Alexandre, Parisod Christian (2013), Natural pathways to polyploidy and consequences for genome organization and genome size, in Cytogenetics and Genome Research, 140, 79-96.
Transposable elements and microevolutionary changes in natural populations
Bonchev Georgi, Parisod Christian (2013), Transposable elements and microevolutionary changes in natural populations, in Molecular Ecology Resources, 13, 765-775.
Adaptive landscape genetics: pitfalls and benefits
Parisod Christian, Holderegger Rolf (2012), Adaptive landscape genetics: pitfalls and benefits, in Molecular Ecology, 21, 3644-3646.
Differential impact of Transposable Elements on long-term genome diploidization in the allopolyploid Nicotiana section Repandae
Parisod Christian, Mihri Corinne, Clarkson James, Lim Yoong, Chase Mark, Leitch Andrew, Grandbastien Marie-Angèle (2012), Differential impact of Transposable Elements on long-term genome diploidization in the allopolyploid Nicotiana section Repandae, in PLoS ONE, 7, e50352.
Polyploids integrate genomic changes and ecological shifts
Parisod C (2012), Polyploids integrate genomic changes and ecological shifts, in New Phytologist, 193, 297-300.
Responses of transposable elements to polyploidy
Parisod Christian, Senerchia Natacha (2012), Responses of transposable elements to polyploidy, in M-A Grandbastien & J Casacuberta (ed.), Springer, Heidelberg, 147-168.
Very high resolution digital elevation model (VHR DEMs) and multiscale landscape genomics applied to an alpine plant species
Leempoel Kevin, Stucki Sylvie, Parisod Christian, Joost Stéphane (2011), Very high resolution digital elevation model (VHR DEMs) and multiscale landscape genomics applied to an alpine plant species, in SIGSPATIAL, 3, 10-14.
Benefits from living together? Clades whose species use similar habitats decline less.
Prinzing Andrea, Benefits from living together? Clades whose species use similar habitats decline less., in New Phytologist.

Zusammenarbeit

Gruppe / Person Land
Formen der Zusammenarbeit
Department of Plant Sciences, Weizmann Institute of Science Israel (Asien)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Austausch von Mitarbeitern
Masaryk University of Brno Tschechische Republik (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Publikation
- Austausch von Mitarbeitern
Natural History Museum, University of Oslo Norwegen (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Publikation
- Austausch von Mitarbeitern
Department of Ecology and Evolution, University of Lausanne Schweiz (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Publikation
Hydrogéologie, University of Neuchâtel Schweiz (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
Ecole Polytechnique Fédérale de Lausanne Schweiz (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Publikation
- Forschungsinfrastrukturen
- Austausch von Mitarbeitern
- Industrie/Wirtschaft/weitere anwendungs-orientierte Zusammenarbeit
Department of Botany, University of British Columbia Kanada (Nordamerika)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Publikation
Musée et Jardins botanique de Lausanne Schweiz (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Publikation
- Forschungsinfrastrukturen
- Austausch von Mitarbeitern
Institute of Plant Biology, University of Zürich Schweiz (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Publikation
- Austausch von Mitarbeitern
WSL Schweiz (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Publikation
- Forschungsinfrastrukturen
- Austausch von Mitarbeitern

Wissenschaftliche Veranstaltungen

Aktiver Beitrag

Titel Art des Beitrags Titel des Artikels oder Beitrages Datum Ort Beteiligte Personen
Workshop of the Molecular Bioinformatics Research Group ‘ALPHY16’ Vortrag im Rahmen einer Tagung Whole genome duplications and recruitment of ecological genes in alpine Mustards 03.03.2016 Lille, Frankreich Parisod Christian;
Ecology and Evolution of the Living World Vortrag im Rahmen einer Tagung Retrotransposons and reproductive isolation in widl wheats 12.10.2015 Gif-sur-Yvette, Frankreich Parisod Christian;
Congress of the European Society for Evolutionary Biology Vortrag im Rahmen einer Tagung Whole genome duplications and recruitment of ecological genes in alpine Mustards 10.08.2015 Lausanne, Schweiz Parisod Christian;
Workshop of the European Molecular Biology Organization ‘Mechanisms of plant speciation’ Vortrag im Rahmen einer Tagung The role of retrotransposons in reproductive isolation 09.06.2015 Norrtälje, Schweden Parisod Christian;
SWISSPLANT 2015 Vortrag im Rahmen einer Tagung The role of retrotransposons in reproductive isolation 15.01.2015 Leukerbad, Schweiz Parisod Christian;
Réunion du groupe Polyploïdie et Cytogénétique Vortrag im Rahmen einer Tagung Evolutionary dynamics of retrotransposons in the Biscutella laevigata autopolyploid complex 22.05.2014 Clermont-Ferrand, Frankreich Parisod Christian;
SWISSPLANT 2014, Einzelvortrag Causes and consequences of plant genome dynamics 29.01.2014 Meiringen, Schweiz Parisod Christian;
SWISSPLANT 2014 Vortrag im Rahmen einer Tagung Causes and consequences of plant genome dynamics 16.01.2014 Meiringen, Schweiz Parisod Christian;
EvoGen Einzelvortrag The dynamic evolution of plants and their genomes 21.05.2013 Mazaryk University, Brno, Tschechische Republik Parisod Christian;
Biology 13 Poster Patterns and processes underlying reproductive isolation among ecotypes of the tetraploid Biscutella laevigata 07.02.2013 Univ. Basel, Schweiz Geiser Céline;
PhD students meeting Poster reproductive isolation in an hybrid zone between ecotypes of Biscutella laevigata 25.05.2012 Neuchatel, Switzerland, Schweiz Geiser Céline;
International Congress on Polyploidy, Hybridization and Biodiversity Einzelvortrag Merging genomes with increasingly divergent transposable elements: diverge, merge and diverge (again) 07.05.2012 Pruhonice, Czech Republic, Tschechische Republik Parisod Christian; Geiser Céline;
Next generation SNP data: experimental design and analysis Vortrag im Rahmen einer Tagung Using transcriptome data to design candidate SNPs 26.03.2012 Neuchatel, Switzerland, Schweiz Geiser Céline;
Méthodologies et statistiques spatiales appliquées à la génétique environnementale Einzelvortrag Association between genetic variation and environmental heterogeneity - what does it (may) mean ? 09.12.2011 Lausanne, Switzerland, Schweiz Parisod Christian; Geiser Céline;
Hybyridization and speciation - Frontiers in Speciation Research Vortrag im Rahmen einer Tagung The impact of transposable elements on hybridization-induced genome reorganization 23.10.2011 Gregynog, UK, Grossbritannien und Nordirland Parisod Christian;
Plant Light Response Poster Adaptation to solar radiation in the wild 25.08.2011 Neuchatel, Switzerland, Schweiz Geiser Céline;


Selber organisiert

Titel Datum Ort
Phylogenomics: pitfalls and benefits 09.03.2015 Neuchâtel, Schweiz
Adaptive Landscape Genetics: current insights and future directions 07.02.2012 Neuchatel, Switzerland, Schweiz
Polyploid Ecological Genomics 20.08.2011 Tuebingen, Germany, Deutschland

Veranstaltungen zum Wissenstransfer

Aktiver Beitrag

Titel Art des Beitrags Titel des Artikels oder Beitrages Datum Ort Beteiligte Personen
Recherches universitaires au Jardin Botanique de Neuchâtel Vortrag 09.04.2013 Neuchâtel, Schweiz


Kommunikation mit der Öffentlichkeit

Kommunikation Titel Medien Ort Jahr
Medienarbeit: Radio, Fernsehen ADN poubelle et origine des espèces RTS Westschweiz 2015
Referate/Veranstaltungen/Ausstellungen Symposium of the Société vaudoise des Sciences Naturelles Westschweiz 2015
Medienarbeit: Printmedien, Online-Medien Le réchauffement climatique pourrait enrichir la biodiversité Agence Télégraphique Suisse, repris par divers media Italienische Schweiz Romanische Schweiz International Deutschschweiz Westschweiz 2014
Medienarbeit: Radio, Fernsehen Un effet positif du réchauffement climatique RTS Westschweiz 2014
Medienarbeit: Printmedien, Online-Medien Gènes et environnement: la lunetière lisse pour comprendre l'origine de la biodiversité L'Ermite Herbu - Journal de l'Association des Amis du Jardin Botanique de l'Ermitage Westschweiz 2013

Verbundene Projekte

Nummer Titel Start Förderungsinstrument
178938 Evolution of duplicated genomes under environmental constraints 01.09.2018 Projektförderung (Abt. I-III)
149741 GENESCALE: Very high-resolution digital elevation models for multi-scale analysis in landscape genomics 01.04.2014 Interdisziplinäre Projekte

Abstract

Background. Genomes are highly variable in their organization, but we are far from understanding the forces driving this diversity and its evolutionary consequences. Accordingly, associating genome reorganization with evolutionary diversification remains an enduring challenge of evolutionary biology. Recent advances in molecular genetics and sequencing of diverse genomes have revealed that Transposable Elements (TEs) are playing a pivotal role in shaping genome architecture, triggering restructuring and functional changes, and producing abundant raw material for evolution. Very few empirical studies have investigated genome dynamics in naturally occurring populations and the impact of TEs on speciation and local adaptation is still elusive. General objectives. Divergent chromosomal structure contributes to hybrid infertility and reduces the level of recombination around rearranged segments, thereby restricting gene exchange. Such reproductive isolation is predicted to facilitate the accumulation of genetic differences between lineages and to permit adaptive traits to become established. However, the importance of chromosomal speciation has been questioned, because of insufficient evidence that chromosomal rearrangements indeed restrict realized gene flow. Recent advances in the study of TEs suggest that they may be important in enhancing reproductive isolation. In this project, I propose to investigate the role of TEs in chromosomal speciation. As chromosome doubling specifically restores the fertility of hybrids between structurally divergent genomes, a promising approach is to investigate a system that has recently undergone genome doubling (i.e. a young autopolyploid complex where both diploids and polyploids still occur). In addition, autopolyploidy is unlikely to immediately induce the expression of new traits, thus offering the opportunity to assess the genomic processes supporting ecological differentiation through local adaptation. Studying genome dynamics in wild species will contribute to elucidate how genomic and evolutionary processes interact in shaping biodiversity.Specific aims. The proposed project combines genomic and ecological methods to associate the main processes driving plant genome evolution - polyploidy, retrotransposition and genome silencing - with the evolutionary processes of speciation and ecological diversification. I suggest working with Biscutella laevigata (Brassicaceae) because it is formed of divergent diploid populations and recent autopolyploid lineages. In particular, the following questions will be addressed: Is chromosomal restructuring driving incipient speciation? Is differential TE accumulation between lineages involved in reproductive isolation? What are the mechanisms and the timing of genome reorganization during speciation? Is autopolyploidy advantageous under environmental change as it might increase the ability to both shift the distribution range and adapt to environmental heterogeneity? To what extent is genome dynamics sustaining local adaptation? Experimental design and approaches. I suggest comparing changes in recently active TE families between genomes of diploid and polyploid populations of B. laevigata. I will thus first produce low coverage Genome Survey Sequences by 454 pyrosequencing to unravel TE families contributing to genome organization. In a first set of experiments, I will establish hybrids between naturally occurring diploids of B. laevigata as well as synthetic polyploids to assess whether intraspecific divergence in genome structure results in immediate reproductive isolation. These experimental accessions will be characterized with complementary molecular tools tracking immediate reorganization in contrasted genome fractions. I will make use of the following techniques: AFLPs marking random sequences, SSAPs marking TE insertions and their Methyl-Sensitive counterparts, as well as comparative chromosome painting. This part of the study will reveal to what extent TEs are involved in incipient speciation and the mechanisms underlying reproductive isolation. I further suggest comparing experimental and naturally occurring polyploids with a similar approach to estimate the timing of genome reorganization after polyploidization. In a complementary sub-project, a PhD student will investigate how genome reorganization is related to ecological differentiation and local adaptation. We will make use of landscape genetics approaches to infer spatial genetic structure and identify patterns of local adaptation in three pairs of marginal populations located at the trailing edge versus the leading edge of the species distribution range. The PhD student will set up a reciprocal transplant experiment among selected sites, which will allow the detection of local adaptation. Local adaptation is predicted to evolve with genome reorganization and decreasing polysomic inheritance. Accordingly, experimental crossing of polyploid accessions will further assess whether populations showing signature of adaptation to environmental heterogeneity present increased levels of disomic inheritance as compared to populations showing signature of recent expansion. Value of the proposed project. This project tackles several important questions in our understanding of plant speciation and the role of genome dynamics in driving evolutionary diversification. In particular, this research will bridge insights offered by molecular and ecological genetics to highlight the impact of TEs on the evolutionary diversification of natural populations. The outcomes will thus be of wide interest for evolutionary and molecular biologists as well as ecologists.
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