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Étude Du Génome Chloroplastique Des Algues Vertes De La Classe Chlorophyceae

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Étude Du Génome Chloroplastique Des Algues Vertes De La Classe Chlorophyceae Étude du génome chloroplastique des algues vertes de la classe Chlorophyceae Mémoire Antony Vincent Maîtrise en biochimie Maître ès sciences (M. Sc.) Québec, Canada © Antony Vincent, 2014 Résumé Les algues unicellulaires de la classe Chlorophyceae sont particulièrement étudiées pour leur potentiel économique dans la production de biocarburant. La première taxonomie de cette classe a été faite avec l'avènement de la microscopie électronique et par la suite avec des phylogénies moléculaires. Cette lignée se divise en deux groupes : OCC (Oedogoniales + Chaetophorales + Chaetopeltidales) et CS (Chlamydomonadales + Sphaeropleales). Il existe de profondes incertitudes sur les positions phylogénétiques des organismes à la base du groupe CS. Afin de renforcer la phylogénie de ces organismes, les génomes chloroplastiques de cinq algues basales ont été séquencés à l'aide de la technologie de nouvelle génération 454 et assemblés de novo. Une analyse phylogénétique de 69 séquences de protéines a permis de montrer que trois des cinq organismes classés dans l'ordre Chlamydomonadales par la littérature actuelle sont en fait basaux dans l'ordre Sphaeropleales. Ce reclassement phylogénétique implique de nouvelles hypothèses sur l'évolution des corps flagellaires. iii Abstract The unicellular algae class Chlorophyceae is notably studied for its economic potential for biofuel production. The first taxonomy of this class was made with the advent of electron microscopy and subsequently with molecular phylogenies. This lineage is divided into two groups: OCC (Oedogoniales + Chaetophorales + Chaetopeltidales) and CS (Chlamydomonadales + Sphaeropleales). There are deep uncertainties about the phylogenetic positions of the organisms at the base of the CS group. To strengthen the phylogeny of these organisms, the chloroplast genomes sequences of five basal algae were obtained by Roche 454 pyrosequencing . A phylogenetic analysis of sixty-nine chloroplast protein sequences revealed that three of these five organisms, listed in the order Chlamydomonadales by the current literature, are in fact basal in the order Sphaeropleales. This phylogenetic reclassification involves a new hypothesis on the evolution of flagellar bodies. v Table des matières Résumé ............................................................................................................................................................... iii Abstract ............................................................................................................................................................... v Table des matières ............................................................................................................................................. vii Liste des tableaux .............................................................................................................................................. xi Listes des figures .............................................................................................................................................. xiii Liste des annexes ............................................................................................................................................. xv Liste des abréviations....................................................................................................................................... xvii Organismes ................................................................................................................................................. xvii Autres .......................................................................................................................................................... xvii Remerciements ................................................................................................................................................. xxi Avant-propos ................................................................................................................................................... xxiii Introduction ......................................................................................................................................................... 1 Les plantes vertes ........................................................................................................................................... 1 La classe Chlorophyceae ........................................................................................................................... 4 Les organites .................................................................................................................................................. 5 L'origine de la mitochondrie ........................................................................................................................ 5 L'origine du chloroplaste ............................................................................................................................. 8 Les génomes d'organites............................................................................................................................ 9 La conformation circulaire et linéaire ........................................................................................................ 11 L'architecture du génome chloroplastique ................................................................................................ 12 Les gènes ..................................................................................................................................................... 12 Le partitionnement des gènes .................................................................................................................. 15 L'ordre des gènes ..................................................................................................................................... 15 La déviation en G+C ..................................................................................................................................... 17 Les introns .................................................................................................................................................... 17 Les introns du groupe I ............................................................................................................................. 18 Les introns du groupe II ............................................................................................................................ 18 Les introns trans-épissés .......................................................................................................................... 22 La réinsertion des introns ......................................................................................................................... 22 Les séquences répétées ............................................................................................................................... 23 Les études sur le génome chloroplastique des algues de la classe Chlorophyceae .................................... 25 vii La problématique .......................................................................................................................................... 28 Objectifs ........................................................................................................................................................ 29 Les organismes à l’étude .............................................................................................................................. 30 Hafniomonas laevis .................................................................................................................................. 30 Carteria cerasiformis ................................................................................................................................. 31 Treubaria triappendiculata ........................................................................................................................ 31 Golenkinia longispicula ............................................................................................................................. 31 Jenufa minuta ........................................................................................................................................... 31 Matériels et méthodes ....................................................................................................................................... 35 Culture cellulaire ........................................................................................................................................... 35 Extraction et purification de l’ADN chloroplastique ........................................................................................ 35 Séquençage et analyse de l’ADNcp .............................................................................................................. 36 Analyses de l'ordre de gènes ........................................................................................................................ 40 Le partitionnement des gènes ....................................................................................................................... 42 Les séquences répétées ............................................................................................................................... 42 La déviation en GC et l'indice de distribution ...............................................................................................
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