Phylogenetic position and mitochondrial genome evolution of ‘orphan’ eukaryotic lineages

The overall shape of the tree of eukaryotes has been brought into focus by large-scale phylogenomic analyses, highlighting a small number of highly diverse clades, or ‘supergroups’ ^1-4 . A handful of so-called ‘orphan’ lineages, however, branch in uncertain positions outside known supergroups, leaving some areas of the tree unresolved. Subsets of four such orphan groups, the provorans ⁵ , meteorids ⁶ , hemimastigophorans ⁷ , and telonemids ^8,9 , occasionally branch together in phylogenomic analyses ^6,10,11 , and the available mitochondrial genomes from two of them are similarly gene-rich ^5,6,12 , altogether raising the possibility that these lineages form a single clade with ancestrally gene-rich mitochondria. Unfortunately, they are currently underrepresented and seldom – if ever – included together in the same analysis. Despite the fact that telonemids have been studied for far longer than the others, their position remains unstable ^10,13,14 , and no mitochondrial genome from a telonemid culture is available. Here, we characterize a transcriptome and the mitochondrial genome of a newly described telonemid, Microkorses curacao gen. et sp. nov. We find telonemid mitochondria are also gene-rich, but with different genes retained than in provorans and meteorids. Our phylogenomic analyses show that provorans, hemimastigophorans, and meteorids form a well-supported but previously unrecognized supergroup, here dubbed the ‘prometheids’, while telonemids branch within an existing supergroup, the haptists. Overall, our analyses show that several orphan groups of eukaryotes that individually fail to be placed with confidence in the tree actually fit neatly into the emerging framework of eukaryotic relationships once more representatives are sampled.