Thermococcales pangenome uncovers new genera and modular evolution
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 of which are integrated in the chromosome at conserved tRNA genes, we find that Thermococcales genomes accommodate rapid horizontal turnover through a constrained chromosomal architecture.
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BibTeX
@misc{catchpole2026thermococcales,
title = {{Thermococcales pangenome uncovers new genera and modular evolution}},
author = {Ryan Catchpole and Clémence Lauden and Damien Courtine and Evelyne Marguet and Stéphanie Fouteau and Catherine Badel and Michalis-Daniel Lazar and Vladislav Shutko and Ghislaine Magdelenat and Valérie Barbe and Jean Weissenbach and Anthony Woo and Philippe Oger and Gaël Erauso and Loïs Maignien and Mohamed Jebbar and Patrick Forterre and Jacques Oberto and Violette Da Cunha},
howpublished = {HAL},
year = {2026},
month = sep,
doi = {10.64898/2026.09.28.752058},
url = {https://hal.science/hal-05786714v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Thermococcales pangenome uncovers new genera and modular evolution
AU - Ryan Catchpole
AU - Clémence Lauden
AU - Damien Courtine
AU - Evelyne Marguet
AU - Stéphanie Fouteau
AU - Catherine Badel
AU - Michalis-Daniel Lazar
AU - Vladislav Shutko
AU - Ghislaine Magdelenat
AU - Valérie Barbe
AU - Jean Weissenbach
AU - Anthony Woo
AU - Philippe Oger
AU - Gaël Erauso
AU - Loïs Maignien
AU - Mohamed Jebbar
AU - Patrick Forterre
AU - Jacques Oberto
AU - Violette Da Cunha
PY - 2026
DA - 2026/09/28
PB - HAL
DO - 10.64898/2026.09.28.752058
UR - https://hal.science/hal-05786714v1
AB - 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 of which are integrated in the chromosome at conserved tRNA genes, we find that Thermococcales genomes accommodate rapid horizontal turnover through a constrained chromosomal architecture.
ER -