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Evolution of duplicated genomes under environmental constraints

English title Evolution of duplicated genomes under environmental constraints
Applicant Parisod Christian
Number 178938
Funding scheme Project funding (Div. I-III)
Research institution Institut für Pflanzenwissenschaften Universität Bern
Institution of higher education University of Berne - BE
Main discipline Botany
Start/End 01.09.2018 - 31.08.2022
Approved amount 619'709.00
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All Disciplines (2)

Discipline
Botany
Ecology

Keywords (6)

genome fractionation; whole genome duplication; transcriptional plasticity; polyploidy; transposable elements; phenotypic plasticity

Lay Summary (French)

Lead
De nombreux organismes ont évolué par duplication de leur génome, mais les conséquences moléculaires et écologiques de ce changement restent controversées. Cette recherche utilise les dernières avancées technologiques pour aborder ces questions et comprendre comment l’évolution façonne la diversification des genomes et des organismes.
Lay summary

De nombreux organismes ont évolué par duplication de leur génome (ou polyploïdie), mais les conséquences moléculaires et écologiques de ce changement restent controversées. Les plantes pratiquent fréquemment la duplication du génome et représentent donc d’excellents modèles pour en étudier l’importance fondamentale. Les recherches récentes ont déjà démontré que les génomes dupliqués se réorganisaient rapidement, bien que les modalités et les mécanismes moléculaires impliqués –particulièrement le rôle des transposons - restent largement à préciser. Plus généralement, dans quelle mesure une telle dynamique du génome facilite ou entrave l’adaptation des plantes à leur environnement reste à évaluer. Les avancées technologiques permettent aujourd’hui d’aborder ces questions afin de comprendre comment l’évolution du génome façonne la diversification des organismes.

Cette recherche utilise une plante ayant colonisé les Alpes à la suite de duplications de son génome comme modèle pour étudier les interactions entre processus moléculaires et écologiques. L’espèce Biscutella laevigata (Brassicaceae) comprend en effet des populations diploïdes (avec 18 chromosomes) et polyploïdes (avec 36 chromosomes) à travers les étages altitudinaux et permet donc de comparer leurs caractéristiques dans des habitats contrastés. Le séquençage du génome de cette espèce va permettre d’identifier les mécanismes moléculaires gouvernant l’évolution des gènes dupliqués et de caractériser précisément la variation retenue dans différents habitats. Parallèlement, des populations provenant d’habitats de basses et de hautes altitudes vont être expérimentalement transplantées dans ces conditions afin de mesurer leurs performances et d’évaluer la plasticité de leurs réponses morphologiques, physiologiques et transcriptionelles face aux changements environnementaux. L’intégration de ces données permettra d’évaluer le rôle des contraintes environnementales sur l’évolution des populations et de leurs génomes.

Unifiant les composantes génomiques et écologiques de l’évolution, ces travaux vont offrir de nouvelles perspectives sur l’influence du dosage des gènes lors de changements environnementaux et ainsi contribuer significativement au débat décennal sur les conséquences de la duplication des génomes.

Direct link to Lay Summary Last update: 28.05.2018

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Associated projects

Number Title Start Funding scheme
149741 GENESCALE: Very high-resolution digital elevation models for multi-scale analysis in landscape genomics 01.04.2014 Interdisciplinary projects
131950 Impact of transposable elements on genome dynamics and reproductive isolation 01.06.2011 Ambizione

Abstract

Background: Whole-genome duplication (WGD) is pervasive among eukaryotes but still remains enigmatic. Available evidence indicates that evolution through WGD may integrate genome reorganization and ecological changes, but underlying mechanisms are elusive. In particular, processes driving the stable retention of duplicated genes in the face of genome fractionation (i.e. how they escape deletion or pseudogenization) must be further addressed. Long-held hypotheses related to change-of-function (i.e. neo- or sub-functionalization leading to new or partitioned tasks) hardly match the large-scale retention of duplicates typically reported by current genomic data. Accordingly, currently favored hypotheses postulate selection for unaltered stochiometry among interacting gene products. Such models predict the preferential retention of highly expressed duplicates as triggered by endogenous genetic factors, but neglect the impact of exogenous constraints imposed by the ecological context in which evolution takes place after WGD events.General objectives: This project addresses genomic and ecological factors driving the evolution of duplicated genomes using Buckler Mustards (Biscutella laevigata; Brassicaceae) that have colonized alpine ecosystems following recurrent WGD events. Prior data indeed highlighted an ancient Bl-m-WGD having resulted in the preferential retention of duplicated genes responding to abiotic stressors in current diploids. It was followed by a recent Bl-n-WGD that further promoted adaptive radiation across diverse alpine habitats. Such evidence is suggestive of a link between WGD events and ecological diversification, but processes relating genome evolution to endogenous and exogenous factors must be elucidated to understand the significance of WGD for biodiversity.Specific aims and approaches: Recurrent WGD events in Buckler Mustards offer an ideal framework to address the interplay between duplicated genes and environmental stressors in driving genome evolution at complementary timescales. This project will thus rely on genome sequencing and experimental characterization of transcriptional plasticity in response to environmental changes in order to understand the factors affecting the conservation of specific loci and the genomic turnover of intervening regions. The first subproject will assemble the diploid genome of B. laevigata to infer processes ruling long-term genome fractionation after the Bl-m-WGD event. In particular, patterns of duplicate retention will evaluate predictions raised by hypotheses postulating a central role of transposable elements on gene expression as the main endogenous trigger of fractionation. Another subproject will address the impact of exogenous factors imposed by environmental constraints on the expression of duplicated genes originating from both the ancient Bl-m-WGD and the recent Bl-n-WGD events. In particular, RNAseq in reciprocally transplanted diploid and autotetraploid individuals from both lowland and alpine habitats will infer the dosage and transcriptional plasticity of duplicates in response to WGD, to environmental changes and their interaction. Based on such assessment of the role of endogenous vs exogenous factors, comparison of patterns across WGD events will infer the possible chain of events linking environmental constraints and genome evolution.Significance of the proposed project: Bridging the disconnection between genomic and ecological research, the proposed integration of processes across time scales will have significant implications for the long-held debate on the evolutionary consequences of WGD. Furthermore, new insights on the impact of gene dosage for evolution under changing environments will be of wide interest to molecular biologists as well as ecologists.
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