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, Nous allons utiliser ces différentes caractéristiques des transposases pour développer notre approche. Parmi les différents éléments de classe II
, Nous pourrons ainsi à chaque étape tester nos résultats par rapport à ceux déjà obtenu par Damon
Mariner? L'objectif étant de développer des outils bioinformatiques pour conduire des analyses exhaustives de génomiques comparatives, ce qui nous permettra de déterminer le répertoire complet des gènes qui sont potentiellement dérivés d'éléments de classe II dans les différentes espèces d'Oryza. Approche expérimentale : Tout d'abord, je vais rechercher tous les gènes liés aux transposases provenant des MULEs dans le génome de Nipponbare. Pour cela, j'utiliserai tblastn et PsiBlast en parallèle. Je réaliserai la caractérisation des signatures structurales de ces séquences (conservation des domaines des transposases, présence des TIRs?) puis une classification phylogénétique avec les gènes identifiés et les transposases pour remettre les événements de domestication dans leur contexte. Lors de ces analyses, Puis, lorsque notre approche sera validée sur ces éléments, nous pourrons élargir notre recherche aux autres éléments de classe II ,
, Je rechercherai les relations de synténie dans les différents génomes d'Oryza et sorghum, et je déclarerai une synténie conservée si au moins un des gènes flanquants est conservé. Quand j'aurai identifié de nouveaux candidats, Damon m'aidera à les vérifier en utilisant GeVo, un outil très puissant permettant d'identifier rapidement des d'erreurs (comme les faux positifs), Ensuite les deux gènes flanquants (le plus proches du coté 5' et 3'
, Les signatures de sélection seront ensuite étudiée avec le ratio de substitution non synonyme par substitutions synonymes (Ka/Ks). Cela permettra de voir, par exemple, s'il existe une sélection positive sur les domaines de fixation à l
, Oryza et sorghum, je pourrai les analyser pour les candidats retenus. La transcription étant une caractéristique importante des ETs domestiqués car requise dans les fonctions cellulaires de l'hôte, en regardant l'activité transcriptionnelle et en combinant avec les différentes approches, De plus, comme nous possédons les données RNAseq des différents génomes d
, Il serait aussi intéressant de pouvoir combiner des analyses de méthylomes et de petits
, De plus, j'analyserai des mutants de ces gènes afin de voir si je peux mettre en évidence des phénotypes particuliers. Ainsi, nous pourrons observer l'ensemble des mécanismes génétiques et épigénétiques intervenant dans la domestication des ETs et peut être identifier des gènes domestiqués qui seraient à l, ARNs pour obtenir une vue globale de ces éléments domestiqués. Je pourrai aussi étudier les séquences cisrégulatrices présentes dans les promoteurs de ces gènes
15 et 50 millions d'années de divergence avec O. sativa, respectivement. Avec cette échelle de temps, nous pourrons détecter des événements de domestication très récents. 2ème partie : J'appliquerai ensuite ce protocole aux éléments de classe I. En effet, quelques exemples de domestication concernant les différentes protéines des éléments de classe I ont été mis en évidence : l'intégrase chez les mammifères (Lloréns and Marín, 2001), la reverse transcriptase chez la drosophile, qui serait à l'origine des télomérases, Ces différentes étapes seront réalisées sur les espèces suivantes, représentant une divergence allant jusqu'à 50 millions d'années : Oryza glaberrima, O. meridionalis, O. punctata, O. brachyantha et sorghum avec 0.5, 2.5, vol.7, 2003. ,
, J'analyserai donc ces différents candidats dans le genre Oryza, en utilisant la même approche
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