Fig. 5: Complex IV genetic organisation and phylogeny.

a The physical genetic organisation of complex IV genes in Thermoplasmatota is conserved at the order level but highly variable at the phylum level. The complex IV loci in the genera Ferroplasma, Acidiplasma and Picrophilus (Thermoplasmatales 2), are different from those present in the rest of the Thermoplasmatales order (Thermoplasmatales 1). The black backslash (/) between genes indicate sections that are physically separated in the genome sequence, and white arrows represent hypothetical proteins. b The ML tree of the coxA subunit of haem-copper oxygen reductase shows that the Poseidoniales coxA gene clusters more closely with bacterial than other archaeal sequences, indicating an independent acquisition from a bacterial donor. Circles indicate collapsed clades. The Thaumarchaeaota, Lunaplasmatales and SW-10-69-26 branches are represented by the single genomes Cenarchaeum symbiosum A, Lunaplasmatales archaeon RBG-16-67-27 and Thermoplasmatota archaeon SW-10-69-26, respectively. Dots indicate branches with >75% UFBoot support. All analysed coxA genes are from A1 subfamily, apart from one bacterial clade belonging to A2 (labelled on the tree). The expanded coxA phylogenetic tree and trees of the genes coxB, ctaA and ctaB are presented in Supplementary Fig. 10–13.