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Sex Chromosome Evolution in Plants : Methodological Developments and NGS Data Analysis in the Silene Genus Aline Muyle

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Sex Chromosome Evolution in Plants : Methodological Developments and NGS Data Analysis in the Silene Genus Aline Muyle Sex chromosome evolution in plants : methodological developments and NGS data analysis in the Silene genus Aline Muyle To cite this version: Aline Muyle. Sex chromosome evolution in plants : methodological developments and NGS data analysis in the Silene genus. Plants genetics. Universit´eClaude Bernard - Lyon I, 2015. English. <NNT : 2015LYO10109>. <tel-01223745> HAL Id: tel-01223745 https://tel.archives-ouvertes.fr/tel-01223745 Submitted on 3 Nov 2015 HAL is a multi-disciplinary open access L'archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destin´eeau d´ep^otet `ala diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publi´esou non, lished or not. The documents may come from ´emanant des ´etablissements d'enseignement et de teaching and research institutions in France or recherche fran¸caisou ´etrangers,des laboratoires abroad, or from public or private research centers. publics ou priv´es. Université Claude Bernard Lyon 1 - UCBL Ecole doctorale Évolution Écosystèmes Microbiologie Modélisation - E2M2 Évolution des chromosomes sexuels chez les plantes: développements méthodologiques et analyses de données NGS de Silènes. Aline MUYLE Doctorat en Biologie, sous la direction de Gabriel MARAIS Date de soutenance: 3 septembre 2015 Numéro d’ordre: 109 - 2015 Membres du Jury: Rapporteurs: John Pannell, Nicolas Galtier. Examinateurs: Xavier Vekemans, Maud Tenaillon. Professeur Université Lyon 1: Dominique Mouchiroud i test Sex chromosome evolution in plants: methodological developments and NGS data analysis in the Silene genus. Laboratoire de rattachement: UMR CNRS 5558 - LBBE “Biométrie et Biologie Évolutive” UCB Lyon 1 - Bât. Grégor Mendel 43 bd du 11 novembre 1918 69622 VILLEURBANNE cedex iii UNIVERSITE CLAUDE BERNARD - LYON 1 Président de l’Université M. François-Noël GILLY Vice-président du Conseil d’Administration M. le Professeur Hamda BEN HADID Vice-président du Conseil des Etudes et de la Vie Universitaire M. le Professeur Philippe LALLE Vice-président du Conseil Scientifique M. le Professeur Germain GILLET Directeur Général des Services M. Alain HELLEU COMPOSANTES SANTE Faculté de Médecine Lyon Est - Claude Bernard Directeur : M. le Professeur J. ETIENNE Faculté de Médecine et de Maïeutique Lyon Sud - Charles Mérieux Directeur : Mme la Professeure C. BURILLON Faculté d’Odontologie Directeur : M. le Professeur D. BOURGEOIS Institut des Sciences Pharmaceutiques et Biologiques Directeur : Mme la Professeure C. VINCIGUERRA Institut des Sciences et Techniques de la Réadaptation Directeur : M. le Professeur Y. MATILLON Département de formation et Centre de Recherche en Biologie Humaine Directeur : Mme. la Professeure A-M. SCHOTT COMPOSANTES ET DEPARTEMENTS DE SCIENCES ET TECHNOLOGIE Faculté des Sciences et Technologies Directeur : M. F.DE MARCHI Département Biologie Directeur : M. le Professeur F.FLEURY Département Chimie Biochimie Directeur : Mme Caroline FELIX Département GEP Directeur : M. Hassan HAMMOURI Département Informatique Directeur : M. le Professeur S. AKKOUCHE Département Mathématiques Directeur : M. le Professeur Georges TOMANOV Département Mécanique Directeur : M. le Professeur H. BEN HADID Département Physique Directeur : M. Jean-Claude PLENET UFR Sciences et Techniques des Activités Physiques et Sportives Directeur : M. Y.VANPOULLE Observatoire des Sciences de l’Univers de Lyon Directeur : M. B. GUIDERDONI Polytech Lyon Directeur : M. P.FOURNIER Ecole Supérieure de Chimie Physique Electronique Directeur : M. G. PIGNAULT Institut Universitaire de Technologie de Lyon 1 Directeur : M. le Professeur C. VITON Ecole Supérieure du Professorat et de l’Education Directeur : M. le Professeur A. MOUGNIOTTE Institut de Science Financière et d’Assurances Directeur : M. N. LEBOISNE Acknowledgements Cette thèse est le fruit d’un travail collaboratif, aussi je remercie toutes les personnes im- pliquées dans le contenu de ces pages. En particulier mon directeur de thèse Gabriel Marais qui a orchestré mon travail et m’a donné beaucoup de liberté, Franck Picard qui m’a guidée jusqu’à convergence et au delà et Niklaus Zemp et Alex Widmer sans qui je n’aurais eu que très peu de données à analyser, et avec qui il est toujours palpitant d’étudier le monde vivant. Merci à Rylan qui a transformé ma vie. Je remercie ma mère, mon père, mon frère, mes tantes Monique et Clotilde et ma cousine Lara pour le soutien qu’ils et elles m’ont apporté ainsi que les bons moments, Kerry et Robert pour leur gentillesse et Stéphanie pour la détente ! v CV Training April 2013: Wellcome Trust-EMBL-EBI Advanced Course on Computational Molecular Evolu- tion, Sanger Centre, Hinxton, Britain. 2011-2012: Agrégation in Biology and Geology at ENS Lyon, France (national rank : 2nd). 2009-2011: Master’s degree in Biosciences at ENS Lyon, France (rank : 1st). 2008-2009: Bachelor of science in fundamental Biology at ENS Lyon, France. 2006-2008: Preparatory classes in Science at Lycée du Parc, Lyon, France. Equivalent to the first and second year of a Bachelor of Science with a national competition at the end. 2005-2006: A-levels in Science at Lycée de Die, France. Research experiences 09/2012–present: PhD under the supervision of Dr Gabriel Marais on the joint evolution of dioecy and sex chromosomes in Silene. 02/2011–05/2011: Second year master’s internship under the supervision of Gabriel Marais (LBBE, Lyon, France). Search of new sex-linked genes in the dioecious plant Silene latifolia using New Sequencing Technologies and study of the evolution of the sex- chro- mosomes. 09/2010–12/2010: Second year master’s internship under the supervision of Sylvain Glémin (ISEM, Montpellier, France). Study of the effect of mating systems on the efficacy of selec- tion in Angiosperms. 02/2010–05/2010: First year master’sinternship under the supervision of Sylvain Glémin (ISEM, Mont- pellier, France). Study of the role of biased gene conversion and selection on the evolution of GC-content in the Oryza genus (rice). 05/2009–07/2009: Bachelor internship under the supervision of Mathilde Dufay (GEPV, Lille, France). Empirical study of gynodioecy maintenance in Beta vulgaris (beet). University teaching (64h/year during the PhD) Licence 1 Practicals on mathematics and statistics for Biology (TDs MATHSV). Licence 2 Students’ professional projects interviews (PEL4). Practicals on population genet- ics (TPs Génétique 2). Licence 3 Practicals on molecular evolution (at UCBL and ENS), creation of new topics. Master 1 Practicals on molecular evolution (at ENS). Master 2 Lecture on host-parasite coevolution (Préparation à l’Agrégation, ENS). Oral com- petition trainings (Leçons d’Agrégation). Botany field trips. vii viii CV Conferences Posters • SEX-DETector : A model-based method for detecting sex chromosomes and study- ing sex determination in non-model organisms using NGS data. 11th RECOMB - Comparative Genomics, Lyon, October 2013. • SEX-DETector : A model-based method for detecting sex chromosomes and study- ing sex determination in non-model organisms using NGS data. Recent advances on the evolution of sex and genetic systems, Roscoff, May 2013. • Dosage compensation in the XY chromosomes of Silene latifolia. Genetics, Epige- netics and Evolution of Sex Chromosomes Conference, Paris, Juin 2011. Talks • Evolution of dosage compensation in the dioecious plant Silene latifolia. SMBE, Fitch Symposium. Vienna, Austria, July 2015. • SEX-DETector : A framework for identifying sex-linked genes using RNAseq data. BGE (Bioinformatique pour la Génomique Environnementale), Lyon, May 2014. • SEX-DETector : A cheap and efficient approach to identify sex-linked genes in non- model organisms using NGS data. PAG XXII (Plant and Animal Genomes), San Diego, January 2014. • Estimating gene loss in the Y chromosome of the dioecious plant Silene latifolia. Plant Genome Evolution, Amsterdam, September 2013. • Rapid de novo evolution of X chromosome dosage compensation in Silene latifo- lia, a plant with young sex chromosomes. GDRE Comparative Genomics meeting, November 2012. • GC-biased gene conversion and selection affect GC content in the Oryza genus (rice). GDR génomique des populations, Toulouse, November 2010. Other scientific experiences 09/2013–07/2014 Weekly organisation of the Journal Club of the department in LBBE (Lyon) 09/2013–12/2013 Co-supervision of Cécile Fruchard’s Master internship. 06/2014–12/2014 Co-supervision of Paul Jay’s Master internship. Résumé (French) Mots clés: Silene latifolia, chromosomes sexuels, RNA-seq, BACs, gènes liés au sexe, com- pensation de dosage, perte de gènes Y, expression biaisée pour le sexe. Malgré leur importance dans le déterminisme du sexe chez de nombreux organismes, les chromosomes sexuels ont été étudiés chez quelques espèces seulement du fait du manque de séquences disponibles. En effet, le séquençage et l’assemblage des chro- mosomes sexuels est rendu très difficile par leurs abondantes séquences répétées. Du- rant cette thèse, une méthode probabiliste a été développée pour inférer les gènes liés au sexe à partir de données RNA-seq chez une famille. Des tests de cette méthode ap- pelée SEX-DETector sur des données réelles et simulées suggèrent qu’elle fonctionnera sur une grande variété de systèmes. La méthode a inféré ∼1300 gènes liés au sexe chez Si- lene latifolia, une plante dioïque qui possède des chromosomes sexuels XY pour lesquels quelques données de séquences sont disponibles (dont certaines obtenues lors de cette thèse par séquençage de BACs).
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