The global distribution and evolutionary history of the pT26‐2 archaeal plasmid family

Abstract

Summary Although plasmids play an important role in biological evolution, the number of plasmid families well‐characterized in terms of geographical distribution and evolution remains limited, especially in archaea. Here, we describe the first systematic study of an archaeal plasmid family, the pT26‐2 plasmid family. The in‐depth analysis of the distribution, biogeography and host–plasmid co‐evolution patterns of 26 integrated and 3 extrachromosomal plasmids of this plasmid family shows that they are widespread in Thermococcales and Methanococcales isolated from around the globe but are restricted to these two orders. All members of the family share seven core genes but employ different integration and replication strategies. Phylogenetic analysis of the core genes and CRISPR spacer distribution suggests that plasmids of the pT26‐2 family evolved with their hosts independently in Thermococcales and Methanococcales, despite these hosts exhibiting similar geographic distribution. Remarkably, core genes are conserved even in integrated plasmids that have lost replication genes and/or replication origins suggesting that they may be beneficial for their hosts. We hypothesize that the core proteins encode for a novel type of DNA/protein transfer mechanism, explaining the widespread oceanic distribution of the pT26‐2 plasmid family.

Exploring short k-mer profiles in cells and mobile elements from Archaea highlights the major influence of both the ecological niche and evolutionary history

“…Whether it could be achieved is, however, uncertain. The fact that we could detect recent HGTs but that several ancient evolutionary connections [ 54 , 57 ] were not detected in our analysis suggests that the genome composition in short k-mers must evolve rapidly. The acquisition or loss of adaptation to extreme conditions played a strong role in the evolution of archaea (e.g.…”

Archaeal tyrosine recombinases

“… 2017 ; Badel et al . 2019 , 2020 ). Partial sequences <150 residues were eliminated from the initial dataset and redundancy was reduced using the UCLUST program (Edgar 2010 ) to eliminate sequences sharing >90% identity (Fig.…”

“… 2018 ; Badel et al . 2019 ). The TopoIb and TopoIb_2 families both contained the Topoisom_I central domain (PF01028).…”

“… 2015 ) or they can be longer than 100 bp for some Thermococcales elements (102 bp for PkuNCB100_IP1 and 243 bp for TIRI33c_IE1) (Badel et al . 2019 , 2020 ). Interestingly, the large att site of these two Thermococcales MGEs encompassed the shorter att site of the closely related integrases from the PHV1 and TGV1 viruses, respectively (Badel et al .…”

“… 2017 ; Badel et al . 2019 , 2020 ). Additional nucleotides are required in order to encompass the anticodon loop and the proximal stem extremity (Fig.…”