Year: 2026
Type: preprint
Abstract: The order Thermococcales is unusual among Archaea in being known primarily from hundreds of lab-cultured isolates rather than metagenome-assembled genomes. Such cultivation is powerful for comparative genomics, allowing access to complete closed genomes rather than fragmented assemblies. We analysed 122 complete genomes, comprising all publicly available type species plus 67 new isolates, as a single pangenome. A combination of genome-scale metrics resolved 70 species across five genus-level clades, two proposed here as the new genera Oleococcus and Piezococcus , in addition to the canonical Pyrococcus, Palaeococcus, and Thermococcus. Only 6.1% of the 21,490 gene families are persistent, yet these contribute over half the genes in any genome. We observe that accessory functions, such as amino-acid biosynthesis, often behave modularly, being gained and lost as intact cassettes from genus-specific chromosomal loci. Combined with 114 mobile genetic elements, 72 integrated into the chromosome at conserved tRNA genes, and 42 extrachromosomal, we find that Thermococcales genomes accommodate rapid horizontal turnover through a constrained chromosomal architecture.
Authors: Ryan Catchpole, Clémence Lauden, Damien Courtine, Evelyne Marguet, Stéphanie Fouteau, Catherine Badel, Michalis-Daniel Lazar, Vladislav Shutko, Ghislaine Magdelenat, Valérie Barbe, Jean Weissenbach, Anthony Woo, Philippe M Oger, Gaël Erauso, Loïs Maignien, Mohamed Jebbar, Patrick Forterre, Jacques Oberto, Violette Da Cunha
Institutions: Centre National de la Recherche Scientifique, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Université Paris-Saclay, Institut de Biologie Intégrative de la Cellule, Génomique Métabolique du Genoscope, Genoscope, Ifremer, Biologie et Ecologie des Ecosystèmes Marins Profonds, Génétique Moléculaire Génomique Microbiologie, Université de Strasbourg, Lyon 1 Université, Laboratoire de Microbiologie, Adaptation et Pathogénie, Institut National des Sciences Appliquées de Lyon, Aix-Marseille Université, Institut Méditerranéen d’Océanologie, Institut de Recherche pour le Développement, Institut Pasteur
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7215727768