Evolutionary history of chromosomal rearrangements linked with the mobilization of transposable elements within the Antarctic teleosts Nototheniidae : the adaptive radiation of the group “Trematomus”

• Main Author: Auvinet, Juliette
• Other Authors: Evolution Paris-Seine (EPS), Institut de Recherche pour le Développement (IRD)-Université Nice Sophia Antipolis (1965 - 2019) (UNS)-Université Sorbonne Paris Cité (USPC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Sorbonne Université, Dominique Higuet, Agnès Dettaï
• Format: Doctoral or Postdoctoral Thesis
• Language: French
• Published: HAL CCSD 2018
• Subjects: Chromosomal rearrangements; Antarctic teleosts Nototheniidae; Fusions; Transposable elements; DIRS1; Evolving scenario; Remaniements chromosomiques; Nototheniidae antarctiques; Éléments transposabless; Scénario évolutif; [SDV.GEN]Life Sciences [q-bio]/Genetics; Antarc*; Antarctic; Antarctique*
• Online Access: https://theses.hal.science/tel-02438851; https://theses.hal.science/tel-02438851/document; https://theses.hal.science/tel-02438851/file/These_AUVINET_Juliette_2018.pdf

In the last 20 My, multiple glacial-interglacial cycles led to strong and repeated environmental changes on the Antarctic continental shelf. In this changing environment, nototheniid fishes diversified through several rounds of species radiation (one of which within Trematominae), and now constitute the dominant group in Antarctic teleosts. Among Nototheniidae, the group « Trematomus » (genera Cryothenia, Pagothenia, Trematomus and Indonotothenia) exhibits the highest chromosomal diversity, with diploid chromosome numbers ranging between 24 and 58, involving many rearrangements probably linked to speciation. We characterized the nature of these chromosomal repatternings. With an inferred ancestral state of 2n = 48 acrocentric chromosomes, a conserved number of chromosomal structural units, and a constancy of the genomes sizes we measured; the hypothesis of structural modifications is favored rather than a whole genome duplication associated to drastic reductions. In order to reconstruct an evolutionary scenario of such chromosomal rearrangements accompanying the trematomine diversification, we identified interspecific chromosomal homologies. This allowed us to reconstruct the rearrangements events (mostly centric and tandem fusions). We plotted them on a phylogeny we reconstructed based on our own ddRAD-seq data. Contrary to what was reported for the Notothenia, our results are in favor of independent acquisitions. Transposable elements (TEs) can lead to chromosomal rearrangements through ectopic recombination events, hinting at a role as drivers of specific-lineage diversification. Moreover, due to their epigenetic regulation, TEs can be mobilized when thermic changes occur. We focused on three retrotransposon superfamilies (DIRS, Gypsy and Copia) in nototheniid genomes. The DIRS1 showed unexpected accumulation patterns of insertion in the centromeric and pericentromeric regions. Given the mechanism of DIRS1 transposition and their tendency to sometimes insert on pre-existing copies (homing), we suggest a role ...