Empirical analyses of first and last steps of sex chromosome evolution in plants with Silene acaulis, Cannabis sativa et Humulus lupulus

• Main Author: Prentout, Djivan
• Other Authors: Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon, Gabriel Marais, Jos Käfer
• Format: Doctoral or Postdoctoral Thesis
• Language: French
• Published: HAL CCSD 2021
• Subjects: Sex chromosomes; Silene acaulis; Dioecy; Cannabis sativa; Humulus lupulus; Y degeneration; Arrest of recombination; Chromosomes sexuels; Dioécie; Arrêt de recombinaison; Dégénérescence du Y; [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry; Molecular Biology/Genomics [q-bio.GN]; The ''Y''
• Online Access: https://theses.hal.science/tel-03708847; https://theses.hal.science/tel-03708847/document; https://theses.hal.science/tel-03708847/file/TH2021PRENTOUTDJIVAN.pdf

There is currently a main view describing the steps in the evolution of sex chromosomes in plants in the literature, although alternative views have recently been put forward. First, a non-recombining region (XY or ZW) should emerge. Then, this region is predicted to expand, and at the same time, the local loss of recombination between the sex chromosomes should induce a degeneration of the Y (or W) chromosome. This degeneration is then expected to progress, and after a certain amount of time, the Y (or W) chromosome should become smaller than the X (or Z) chromosome, or even disappear. A main issue of this view is that it is based on the genomic study of only about thirty plant sex chromosome systems, while there are more than 15,000 dioecious species (i.e., plants with separate sexes). As a consequence, while some of these steps are well characterized, others are clearly lacking empirical support. In particular, theformation of a non-recombining region has only been studied theoretically and a strongly degenerated system with a Y (or W) chromosome smaller than the X (or Z) has only been genomically studied in animals. In order to better understand the first step of this view, i.e. the emergence of a non-recombining region, the first part of this thesis focuses on Silene acaulis ssp exscapa, the only subspecies in the Silene acaulis complex that is dioecious. This pattern suggests that dioecy is a recently derived character in this subspecies. Since the sex determination mechanism was unknown in this subspecies, I sought to identify a non-recombining region typical of a pair of sex chromosomes. In order to do so, RNA-seq data was generated from two different populations, to which I applied a new probabilistic tool based on the analysis of genotyping and phenotyping frequencies. This approach allowed me to identify 27 potential XY genes and to propose that they belong to a young sex chromosome system. However, complementary analyses will be required to validate this hypothesis. In order to test whether plants ...