Thermococcales pangenome uncovers new genera and modular evolution.
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…
The Thermococcales order, predominantly known from laboratory-cultured isolates, has revealed new insights into its evolutionary structure. By analyzing 122 complete genomes, including 67 newly discovered isolates and all publicly available type species, researchers have identified 70 species across five clades, two of which are proposed as new genera: Oleococcus and Piezococcus.
This analysis, which combined genome-scale metrics, unveiled the presence of two additional genera alongside the well-known Pyrococcus, Palaeococcus, and Thermococcus.
Despite the relatively small proportion of persistent gene families, accounting for just 6.1% of the 21,490 gene families, these genes contribute over half of the genes within each genome. The study highlights the modular nature of accessory functions, such as amino-acid biosynthesis, which can be gained or lost as cohesive cassettes from genus-specific chromosomal locations.
This modular evolution, coupled with 114 mobile genetic elements, of which 72 are integrated into the chromosome near conserved tRNA genes, elucidates Thermococcales' capacity for rapid horizontal gene transfer through a genetically constrained chromosomal framework.
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