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Le Modèle Algue Brune Pour L'analyse Fonctionnelle Et Évolutive Du

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Le Modèle Algue Brune Pour L'analyse Fonctionnelle Et Évolutive Du Le modèle algue brune pour l’analyse fonctionnelle et évolutive du déterminisme sexuel Alexandre Cormier To cite this version: Alexandre Cormier. Le modèle algue brune pour l’analyse fonctionnelle et évolutive du déterminisme sexuel. Bio-informatique [q-bio.QM]. Université Pierre et Marie Curie - Paris VI, 2015. Français. NNT : 2015PA066646. tel-01360550 HAL Id: tel-01360550 https://tel.archives-ouvertes.fr/tel-01360550 Submitted on 6 Sep 2016 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Université Pierre et Marie Curie Ecole doctorale Complexité du vivant (ED 515) Laboratoire de Biologie Intégrative des Modèles Marins UMR 8227 Equipe de Génétique des algues, Station Biologique de Roscoff Le modèle algue brune pour l’analyse fonctionnelle et évolutive du déterminisme sexuel Par Alexandre Cormier Thèse de doctorat en Bio-informatique Dirigée par Susana Coelho et Mark Cock Présentée et soutenue publiquement le 16 novembre 2015 Devant le jury composé de : Dr. Leroy Philipe (INRA, Clermont-Ferrand) Rapporteur Dr. Renou Jean-Pierre (INRA, Angers) : Rapporteur Pr. Carbone Alessandra (UPMC, Paris) : Examinatrice Dr. Brunaud Véronique (INRA, Orsay) : Examinatrice Dr. Le Roux Frédérique (Ifremer, Roscoff) : Représentante ED 515 Dr. Coelho Susana (CNRS-UPMC, Roscoff): Directrice de thèse Dr. Cock Mark (CNRS-UPMC, Roscoff) : Directeur de thèse Dr. Corre Erwan (CNRS-UPMC, Roscoff) : Encadrant de thèse Remerciements Je tiens en premier lieu tout particulièrement à remercier mes encadrants de thèse, Susana Coelho, Mark Cock et Erwan Corre qui m’ont permis de réaliser ma thèse, pour leur encadrement et leur soutien pour mener à bien ce projet. Je remercie également les membres de mon comité de thèse, Angela Falciatore, Armel Salmon et Lieven Sterck pour m’avoir suivie durant ces trois années, pour leurs conseils et leur intérêt à l’égard de mon sujet de thèse. Je tiens à remercier Philipe Leroy, Jean-Pierre Renou, Alessandra Carbone et Véronique Brunaud d’avoir accepté de faire partie de mon jury de thèse et pour le temps consacré à la lecture de mon manuscrit. Je remercie aussi les personnes de mon équipe, présentes et passées, Nicolas Macaisne, Olivier Godfroy, Sophia Ahmed, Komlan Avia, Rémy Luthringer, Fiona Lerck, Martina Strittmatter, Alok Arun, Delphine Scornet, Agnieszka Lipinska, Marie-Mathilde Perrineau, Simon Bourdareau et Laure Mignerot avec que j’ai eu plaisir à travailler et échanger, mais aussi les personnes de l’UMR 8227, Simon Dittami, Ludovic Delage, Catherine Leblanc, Thierry Thonon, Catherine Boyen, Lionel Cladière et bien d’autres. Egalement, un grand merci aux membres de la plateforme ABiMS, Gildas Le Corguillé, Misharl Monsoor, Xi Liu, Loraine Guéguen, Camille Vacquié, Julien Wollbret, Wilfrid Carré, Gwendoline Andrès, Eric Duvignac, Jean-Michel Aroumougom, Joseph Kervellec, Antoine Bisch, Nolwenn Dantec, Mark Hoebeke, Olivier Quenez et Ludovic Legrand pour m’avoir accueillis et soutenu pendant ces trois ans. Je tiens tout particulièrement à remercier le responsable de la plateforme, Christophe Caron, pour son soutien et son aide tout au long de ma thèse, mais aussi lors de mes différents séjours à la Station. Ik wil mijn dank uitspreken aan het hele Bioinformatics & Evolutionary Genomics team van de Gentse VIB. Vooral aan Lieven Sterck, Yves van de Peer, Pierre Rouzé, Li Zhen en Stéphane Rombouts. Bedankt voor de twee maanden die ik in het team heb kunnen doorbrengen om een deel van mijn thesis projekt te voltooien, en voor de voortreffelijke momenten tijdens de Brainstorming. Een grote dank aan Lieven Sterck voor de hulp, de steun, het advies die hij me gedurende deze drie jaar heeft gegeven. Merci à tous mes amis, Océane, Ronflex, Manide, Obivalion, Maxime, Paulo, Thibaut, Lucas et bien d’autres pour m’avoir soutenu et encouragé. Un grand merci à Laurence Cladière pour son soutien, son intérêt pour ma thèse et ses conseils. Je remercie spécialement Léa Cabioch, pour m’avoir soutenu, supportée et qui a adoucit les derniers jours de ma thèse. Enfin merci à ma famille pour m’avoir permis d’arriver jusque-là et qui m’a toujours soutenu dans ce que j’entreprenais et pour m’avoir donné les moyens d’y arriver. Table des matières Préambule ............................................................................................................................................... 1 Objectifs .................................................................................................................................................. 4 Chapitre 1 : Evolution et analyse fonctionnelle de la détermination du sexe chez les algues brunes ..... 5 Introduction ........................................................................................................................................ 5 La détermination des sexes chez les Eucaryotes ............................................................................. 5 Détermination épigénétique du sexe ........................................................................................... 6 Détermination génétique du sexe ............................................................................................... 7 Les différents cycles de vie sexués chez les Eucaryotes ............................................................... 9 Les chromosomes sexuels : origine et évolution ........................................................................... 10 Les différents types de chromosomes sexuels ........................................................................... 10 Formation et évolution des chromosomes sexuels .................................................................... 12 Structure des chromosomes sexuels .......................................................................................... 15 Expression des gènes biaisés par le sexe ........................................................................................ 18 Origines des GBS ..................................................................................................................... 18 Expression et évolution des gènes biaisés par le sexe ................................................................ 20 Les algues brunes et l’étude de l’évolution des sexes ..................................................................... 22 Apport de la bio-informatique pour l’étude du déterminisme du sexe ......................................... 25 DNA-seq .................................................................................................................................. 25 RNA-seq ................................................................................................................................... 26 Article 1 - A Haploid System of Sex Determination in the Brown Alga Ectocarpus sp. .................. 35 Introduction .................................................................................................................................. 35 Article ........................................................................................................................................... 37 Discussion et perspectives ............................................................................................................. 52 Article 2 - The Pseudoautosomal Region of the U/V Sex Chromosomes of the Brown Alga Ectocarpus Exhibit Unusual Features ................................................................................................ 54 Introduction .................................................................................................................................. 54 Article ........................................................................................................................................... 56 Discussion et perspectives ............................................................................................................. 72 Article 3 - Sexual Dimorphism and the Evolution of Sex-Biased Gene Expression in the Brown Alga Ectocarpus .................................................................................................................................. 74 Introduction .................................................................................................................................. 74 Article ........................................................................................................................................... 76 Discussion et perspectives ............................................................................................................. 97 Conclusions générales et perspectives ............................................................................................... 99 Chapitre 2 : Annotation structurale et fonctionnelle chez l’algue brune modèle Ectocarpus sp. ......... 101 Introduction .................................................................................................................................... 101 Définition et caractéristiques d’un modèle biologique ...............................................................
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