23Running head: Phylogeny and putative MRO functions in a new metamonad clade.
25Abstract 28 We here report the phylogenetic position of barthelonids, small anaerobic flagellates 29 previously examined using light microscopy alone. Barthelona spp. were isolated from 30 geographically distinct regions and we established five laboratory strains. Transcriptomic data 31 generated from one Barthelona strain (PAP020) was used for large-scale, multi-gene 32 phylogenetic (phylogenomic) analyses. Our analyses robustly placed strain PAP020 at the 33 base of the Fornicata clade, indicating that barthelonids represent a deep-branching 34 Metamonad clade. Considering the anaerobic/microaerophilic nature of barthelonids and 35 preliminary electron microscopy observations on strain PAP020, we suspected that 36 barthelonids possess functionally and structurally reduced mitochondria (i.e. mitochondrion-37 related organelles or MROs). The metabolic pathways localized in the MRO of strain PAP020 38 were predicted based on its transcriptomic data and compared with those in the MROs of 39 fornicates. Strain PAP020 is most likely incapable of generating ATP in the MRO, as no 40 mitochondrial/MRO enzymes involved in substrate-level phosphorylation were detected. 41 Instead, we detected the putative cytosolic ATP-generating enzyme (acetyl-CoA synthetase), 42 suggesting that strain PAP020 depends on ATP generated in the cytosol. We propose two 43 separate losses of substrate-level phosphorylation from the MRO in the clade containing 44 barthelonids and (other) fornicates.45 46