Oberto, J. | Search bioRxiv

bioRxiv2026

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 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.

genomics↗

bioRxiv2021

Role of Ori in Thermococcus barophilus

The mechanisms underpinning replication of genomic DNA in Archaea have recently been challenged. Species belonging to two different taxonomic orders grow well in the absence of an origin of replication, challenging the role of the replication origin in these organisms. Here, we pursue the investigation of the particular way some archaea manage their DNA replication with Thermococcus barophilus and the role of Ori in this Archaea. Surprisingly we discovered that T. barophilus uses its Ori all along the growth curve with marked increase at the end of exponential phase. Through gene deletion, we show that Ori utilization requires Cdc6, and that origin deletion results in increased time in lag phase and a moderate decrease of growth rate in mutants. The number of chromosomes are quite similar between both strains during exponential and early stationary phases but differs after 24h of growth where {Delta}TbOriC has only 6 chromosomes/cell compared to 10 for the reference strain (WT). Following 1hr of growth in fresh media, {Delta}TbOriC strains contains 3 chromosome copies/cell, whereas the WT contains only 1. We hypothesize that the T. barophilus might degrade DNA to obtain energy to start replication and cell division, whereas the {Delta}TbOriC must maintain more chromosomal copies in order to initiate DNA replication in the absence of an origin or replication. Finally, we analyzed the role of Ori at temperatures above or below the optimal temperature, revealing that Ori is important to start growth at those temperatures, suggesting that replication origins may be involved in stress response.

microbiology↗