Figure 1

A. Schematic representation of the domain organisation of Topo IB sequences from three eucarya, two thaumarchaeota, two bacteria and three viruses (the multiple alignment of these sequences is provided as Additional Files 1). Coloured boxes delineate the putative functional domains according to the PFAM database http://pfam.sanger.ac.uk/: Topoisom_I_N (PF02919, Eukaryotic DNA topoisomerase I, DNA binding fragment) in red, Topoisom_I (PF01028, Eukaryotic DNA topoisomerase I, catalytic core) in blue and virDNA-Topo-I_N (PF09266, Viral DNA topoisomerase I, N-terminal) in light-green. The N-ter regions of viral Topo IB is similar in size and share conserved residues with bacterial and mimiviral homologues, suggesting the presence of a virDNA-Topo-I_N-like domain in these sequences (in dark-green). B. Alternative evolutionary scenarios explaining the presence of Topo IB in Thaumarchaeota. Filled blue diamonds indicate the presence of a Topo IB coding gene. Empty blue diamonds indicate a Topo IB coding gene that were present in the ancestor of the corresponding lineage and lost during its evolution. Blue crosses indicate the loss events of Topo IB coding genes. (a) A Topo IB coding gene was acquired by the ancestor of Thaumarchaeota via horizontal gene transfer (blue arrow) from a eukaryotic lineage. (b), (c) and (d) A Topo IB coding gene was present in the ancestor of Archaea and Eucarya and was subsequently lost in the ancestor of Crenarchaeota and Euryarchaeota, in agreement with a thaumarchaeal rooting of the archaeal tree (B). The Topo IB coding gene was independently lost in the ancestors of Euryarchaeota and Crenarchaeota according to an euryarchaeal or crenarchaeal rooting of the archaeal tree (C and D).