The early evolution of eukaryotes and their adaptations to low-oxygen environments are fascinating open questions in biology. Genome-scale data from novel eukaryotes, and particularly from free-living lineages, are the key to answering these questions. The Parabasalia are a major group of anaerobic eukaryotes that form the most speciose lineage of Metamonada. The most well-studied are parasitic parabasalids, including Trichomonas vaginalis and Tritrichomonas foetus, but very little genome-scale data are available for free-living members of the group. Here, we sequenced the transcriptome of Pseudotrichomonas keilini, a free-living parabasalian. Comparative genomic analysis indicated that P. keilini possesses a metabolism and gene complement that are in many respects similar to its parasitic relative T. vaginalis and that in the time since their most recent common ancestor, it is the T. vaginalis lineage that has experienced more genomic change, likely due to the transition to a parasitic lifestyle. Features shared between P. keilini and T. vaginalis include a hydrogenosome (anaerobic mitochondrial homolog) that we predict to function much as in T. vaginalis and a complete glycolytic pathway that is likely to represent one of the primary means by which P. keilini obtains ATP. Phylogenomic analysis indicates that P. keilini branches within a clade of endobiotic parabasalids, consistent with the hypothesis that different parabasalid lineages evolved toward parasitic or free-living lifestyles from an endobiotic, anaerobic, or microaerophilic common ancestor.

Centre for Environment Fisheries and Aquaculture Science Lowestoft UK

Department of Zoology Faculty of Science Charles University 128 00 Prague Czech Republic

Institute of Ecology and Evolution University of Edinburgh Edinburgh EH9 3FL UK

Institute of Vertebrate Biology Czech Academy of Sciences 603 00 Brno Czech Republic

School of Biological Sciences University of Bristol Bristol BS8 1TH UK

School of Life Sciences Arizona State University Tempe AZ 85287 USA

Zobrazit více v PubMed

Adl  SM, Leander  BS, Simpson  AG, Archibald  JM, Anderson  OR, Bass  D, Bowser  SS, Brugerolle  G, Farmer  MA, Karpov  S, et al.  Diversity, nomenclature, and taxonomy of protists. Syst Biol.  2007:56(4):684–689. 10.1080/10635150701494127. PubMed DOI

Bishop  A. Observations upon a “Trichomonas” from pond water. Parasitology. 1935:27(2):246–256. 10.1017/S0031182000015110. DOI

Bishop  A. A note upon the systematic position of “Trichomonas” keilini (Bishop, 1935). Parasitology. 1939:31(4):469–472. 10.1017/S0031182000012993. DOI

Brugerolle  G, Lee  J. Phylum Parabasalia. In: Lee  JJ, Leedale  GF, Bradbury  PC, editors. An illustrated guide to the protozoa: organisms traditionally referred to as protozoa, or newly discovered groups. Lawrence, Kansas, USA: Society of Protozoologists; 2000. p. 1196–1250.

Burki  F, Roger  AJ, Brown  MW, Simpson  AGB. The new tree of eukaryotes. Trends Ecol Evol.  2020:35(1):43–55. 10.1016/j.tree.2019.08.008. PubMed DOI

Čepička  I, Dolan  MF, Gile  GH. Parabasalia. In: Archibald  JM, Simpson  AGB, Slamovits  CH, Margulis  L, Melkonian  M, Chapman  DJ, Corliss  JO, editors. Handbook of the protists. Cham: Springer International Publishing; 2017. p. 1–44.

Cepicka  I, Hampl  V, Kulda  J. Critical taxonomic revision of parabasalids with description of one new genus and three new species. Protist. 2010:161(3):400–433. 10.1016/j.protis.2009.11.005. PubMed DOI

Cerón-Romero  MA, Fonseca  MM, de Oliveira Martins  L, Posada  D, Katz  LA. Phylogenomic analyses of 2,786 genes in 158 lineages support a root of the eukaryotic tree of life between opisthokonts and all other lineages. Genome Biol Evol.  2022:14(8):evac119. 10.1093/gbe/evac119. PubMed DOI PMC

Céza  V, Kotyk  M, Kubánková  A, Yubuki  N, Šťáhlavský  F, Silberman  JD, Čepička  I. Free-living trichomonads are unexpectedly diverse. Protist. 2022:173(4):125883. 10.1016/j.protis.2022.125883. PubMed DOI

Csűös  M. Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood. Bioinformatics. 2010:26(15):1910–1912. 10.1093/bioinformatics/btq315. PubMed DOI

Derelle  R, Philippe  H, Colbourne  JK. Broccoli: combining phylogenetic and network analyses for orthology assignment. Mol Biol Evol.  2020:37(11):3389–3396. 10.1093/molbev/msaa159. PubMed DOI

Donné  A. Animalcules observés dans les matières purulentes et le produit des sécrétions des organes génitaux de l'homme et da la femme. CR Acad Sci. 1836:3:385–386.

Fiori  PL, Rappelli  P, Addis  MF, Mannu  F, Cappuccinelli  P. Contact-dependent disruption of the host cell membrane skeleton induced by Trichomonas vaginalis. Infect Immun.  1997:65(12):5142–5148. 10.1128/iai.65.12.5142-5148.1997. PubMed DOI PMC

Haas  BJ, Papanicolaou  A, Yassour  M, Grabherr  M, Blood  PD, Bowden  J, Couger  MB, Eccles  D, Li  B, Lieber  M, et al.  De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity. Nat Protoc.  2013:8(8):1494–1512. 10.1038/nprot.2013.084. PubMed DOI PMC

Handrich  MR, Garg  SG, Sommerville  EW, Hirt  RP, Gould  SB. Characterization of the BspA and Pmp protein family of trichomonads. Parasit Vectors.  2019:12(1):406. 10.1186/s13071-019-3660-z. PubMed DOI PMC

Hrdy  I, Hirt  RP, Dolezal  P, Bardonová  L, Foster  PG, Tachezy  J, Martin Embley  T. Trichomonas hydrogenosomes contain the NADH dehydrogenase module of mitochondrial complex I. Nature. 2004:432(7017):618–622. 10.1038/nature03149. PubMed DOI

Leger  MM, Kolisko  M, Kamikawa  R, Stairs  CW, Kume  K, Čepička  I, Silberman  JD, Andersson  JO, Xu  F, Yabuki  A, et al.  Organelles that illuminate the origins of Trichomonas hydrogenosomes and Giardia mitosomes. Nat Ecol Evol.  2017:1(4):0092. 10.1038/s41559-017-0092. PubMed DOI PMC

Lewis  WH, Lind  AE, Sendra  KM, Onsbring  H, Williams  TA, Esteban  GF, Hirt  RP, Ettema  TJG, Embley  TM. Convergent evolution of hydrogenosomes from mitochondria by gene transfer and loss. Mol Biol Evol.  2019:37(2):524–539. 10.1093/molbev/msz239. PubMed DOI PMC

Maciejowski  WJ, Gile  GH, Jerlström-Hultqvist  J, Dacks  JB. Ancient and pervasive expansion of adaptin-related vesicle coat machinery across Parabasalia. Int J Parasitol.  2023:53(4):233–245. 10.1016/j.ijpara.2023.01.002. PubMed DOI

Menezes  CB, Frasson  AP, Tasca  T. Trichomoniasis-are we giving the deserved attention to the most common non-viral sexually transmitted disease worldwide?  Microb Cell. 2016:3:404. 10.15698/mic2016.09.526. PubMed DOI PMC

Morel  B, Schade  P, Lutteropp  S, Williams  TA, Szöllősi  GJ, Stamatakis  A. SpeciesRax: a tool for maximum likelihood species tree inference from gene family trees under duplication, transfer, and loss. Mol Biol Evol. 2022:39(2):msab365. 10.1093/molbev/msab365. PubMed DOI PMC

Morel  B, Williams  TA, Stamatakis  A, Szöllősi  GJ. AleRax: a tool for gene and species tree co-estimation and reconciliation under a probabilistic model of gene duplication, transfer, and loss. Bioinformatics. 2024:40(4):btae162. 10.1093/bioinformatics/btae162. PubMed DOI PMC

Oyhenart  J, Breccia  JD. Evidence for repeated gene duplications in Tritrichomonas foetus supported by EST analysis and comparison with the Trichomonas vaginalis genome. Vet Parasitol.  2014:206(3-4):267–276. 10.1016/j.vetpar.2014.09.024. PubMed DOI

Peña-Diaz  P, Lukeš  J. Fe–S cluster assembly in the supergroup Excavata. J Biol Inorg Chem.  2018:23(4):521–541. 10.1007/s00775-018-1556-6. PubMed DOI PMC

Pereira-Neves  A, Benchimol  M. Phagocytosis by Trichomonas vaginalis: new insights. Biol Cell.  2007:99(2):87–101. 10.1042/BC20060084. PubMed DOI

Petrin  D, Delgaty  K, Bhatt  R, Garber  G. Clinical and microbiological aspects of Trichomonas vaginalis. Clin Microbiol Rev.  1998:11(2):300–317. 10.1128/CMR.11.2.300. PubMed DOI PMC

Schneider  RE, Brown  MT, Shiflett  AM, Dyall  SD, Hayes  RD, Xie  Y, Loo  JA, Johnson  PJ. The Trichomonas vaginalis hydrogenosome proteome is highly reduced relative to mitochondria, yet complex compared with mitosomes. Int J Parasitol.  2011:41(13-14):1421–1434. 10.1016/j.ijpara.2011.10.001. PubMed DOI PMC

Sibbald  SJ, Archibald  JM. More protist genomes needed. Nat Ecol Evol.  2017:1(5):145. 10.1038/s41559-017-0145. PubMed DOI

Simão  FA, Waterhouse  RM, Ioannidis  P, Kriventseva  EV, Zdobnov  EM. BUSCO: assessing genome assembly and annotation completeness with single–copy orthologs. Bioinform. 2015:31(19):3210–3212. PubMed

Stairs  CW, Leger  MM, Roger  AJ. Diversity and origins of anaerobic metabolism in mitochondria and related organelles. Philos Trans R Soc B Biol Sci. 2015:370(1678):20140326. 10.1098/rstb.2014.0326. PubMed DOI PMC

Stairs  CW, Táborský  P, Salomaki  ED, Kolisko  M, Pánek  T, Eme  L, Hradilová  M, Vlček  Č, Jerlström-Hultqvist  J, Roger  AJ, et al.  Anaeramoebae are a divergent lineage of eukaryotes that shed light on the transition from anaerobic mitochondria to hydrogenosomes. Curr Biol.  2021:31(24):5605–5612.e5. 10.1016/j.cub.2021.10.010. PubMed DOI

Williamson  K, Eme  L, Baños  H, McCarthy  C, Susko  E, Kamikawa  R, Orr  RJS, Muñoz-Gómez  SA, Simpson  AGB, Roger  AJ. A robustly rooted tree of eukaryotes reveals their excavate ancestry. bioRxiv 611237. 10.1101/2024.09.04.611237, 16 September 2024, preprint: not peer reviewed. DOI

Yamin  MA, Ma  Y. Flagellates of the orders Trichomonadida Kirby, Oxymonadida Grassé, and Hypermastigida Grassi & Foà reported from lower termites (Isoptera families Mastotermitidae, Kalotermitidae, Hodotermitidae, Termopsidae, Rhinotermitidae, and Serritermitidae) and from the wood-feeding roach Cryptocercus (Dictyoptera: Cryptocercidae). Sociobiol. 1979:4(1):5–119.

Yubuki  N, Céza  V, Cepicka  I, Yabuki  A, Inagaki  Y, Nakayama  T, Inouye  I, Leander  BS. Cryptic diversity of free-living parabasalids, Pseudotrichomonas keilini and Lacusteria cypriaca n. g., n. sp., as inferred from small subunit rDNA sequences. J Eukaryot Microbiol.  2010:57(6):554–561. 10.1111/j.1550-7408.2010.00509.x. PubMed DOI