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Mantamonads were long considered to represent an “orphan” lineage in the tree of eukaryotes, likely branching near the most frequently assumed position for the root of eukaryotes. Recent phylogenomic analyses have placed them as part of the “CRuMs” supergroup, along with collodictyonids and rigifilids. This supergroup appears to branch at the base of Amorphea, making it of special importance for understanding the deep evolutionary history of eukaryotes. However, the lack of representative species and complete genomic data associated with them has hampered the investigation of their biology and evolution. Here, we isolated and described two new species of mantamonads, Mantamonas vickermani sp. nov. and Mantamonas sphyraenae sp. nov., for each of which we generated transcriptomic sequence data, as well as a high-quality genome for the latter. The estimated size of the M. sphyraenae genome is 25 Mb; our de novo assembly appears to be highly contiguous and complete with 9,416 predicted protein-coding genes. This near-chromosome-scale genome assembly is the first described for the CRuMs supergroup., The authors thank Drs. J.Z. Xiang, D. Xu, and H. Shang at the Weill Cornell’s Genome Resources Core Facility for their assistance with Illumina sequencing. We also thank Dr. S. Goodwin in the NGS sequencing core at Cold Spring Harbor Laboratory for her help with PacBio sequencing, Drs. J.A. Burns and A.A. Pittis for their initial data analysis efforts and K. Lukacs for her help with maintaining the M. sphyraenae cultures. This work was funded by the Simons Foundation Grant awards to EK (SF-382790 & SF-876199). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (ERC Starting Grant No 803151 to L.E., and ERC Advanced Grants No 322669 and 787904 to P.L.-G. and D.M., respectively). L.J.G. was funded by the Horizon 2020 research and innovation programme under the European Marie Skłodowska-Curie Individual Fellowship H2020-MSCA-IF-2020 (grant agreement no. 101022101 - FungEye). GT was supported by the 2019 BP 00208 Beatriu de Pinos-3 Postdoctoral Program (BP3; 801370). Work in the Dacks lab is supported by Discovery Grants from the Natural Sciences and Engineering Research Council of Canada (RES0043758, RES0046091)., Peer Reviewed, "Article signat per 17 autors/es: Jazmin Blaz, Luis Javier Galindo, Aaron A. Heiss, Harpreet Kaur, Guifré Torruella, Ashley Yang, L. Alexa Thompson, Alexander Filbert, Sally Warring, Apurva Narechania, Takashi Shiratori, Ken-ichiro Ishida, Joel B. Dacks, Purificación López-García, David Moreira, Eunsoo Kim & Laura Eme", Postprint (published version)

Ancyromonads are small biflagellated protists with a bean-shaped morphology. They are cosmopolitan in marine, freshwater, and soil environments, where they attach to surfaces while feeding on bacteria. These poorly known grazers stand out by their uncertain phylogenetic position in the tree of eukaryotes, forming a deep-branching “orphan” lineage that is considered key to a better understanding of the early evolution of eukaryotes. Despite their ecological and evolutionary interest, only limited knowledge exists about their true diversity. Here, we aimed to characterize ancyromonads better by integrating environmental surveys with behavioral observation and description of cell morphology, for which sample isolation and culturing are indispensable. We studied 18 ancyromonad strains, including 14 new isolates and seven new species. We described three new and genetically divergent genera: Caraotamonas, Nyramonas, and Olneymonas, together encompassing four species. The remaining three new species belong to the already-known genera Fabomonas and Ancyromonas. We also raised Striomonas, formerly a subgenus of Nutomonas, to full genus status, on morphological and phylogenetic grounds. We studied the morphology of diverse ancyromonads under light and electron microscopy and carried out molecular phylogenetic analyses, also including 18S rRNA gene sequences from several environmental surveys. Based on these analyses, we have updated the taxonomy of Ancyromonadida., This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (ERC Starting Grant No 803151 to L.E. and ERC Advanced Grants No 322669 and 787904 to P.L.-G. and D.M., respectively). GT was supported by the 2019 BP 00208 Beatriu de Pinos-3 Postdoctoral Program (BP3; 801370). LG was funded by the Horizon 2020 research and innovation programme under the European Marie Skłodowska-Curie Individual Fellowship H2020-MSCA-IF-2020 (grant agreement no. 101022101 —FungEye). We are thankful for access to the Imagerie-Gif core facility at the Institute for Integrative Biology of the Cell (Gif-sur-Yvette, France) and the Electron Microscopy Facility (EMF) of the Institut de Biologie Paris-Seine (Paris, France). We thank members of the UNICELL single-cell genomics platform (https://www.deemteam.fr/en/unicell) for help in cell isolation and rRNA gene sequencing. We also thank Kaleigh Lukacs for assistance with culture maintenance., Peer Reviewed, "Article signat per 12 autors/es: Naoji Yubuki, Guifré Torruella, Luis Javier Galindo, Aaron A. Heiss, Maria Cristina Ciobanu, Takashi Shiratori, Ken-ichiro Ishida, Jazmin Blaz, Eunsoo Kim, David Moreira, Purificación López-García, Laura Eme", Postprint (published version)

Apusomonads are cosmopolitan bacterivorous biflagellate protists usually gliding on freshwater and marine sediment or wet soils. These nanoflagellates form a sister lineage to opisthokonts and may have retained ancestral features helpful to understanding the early evolution of this large supergroup. Although molecular environmental analyses indicate that apusomonads are genetically diverse, few species have been described. Here, we morphologically characterize 11 new apusomonad strains. Based on molecular phylogenetic analyses of the rRNA gene operon, we describe four new strains of the known species Multimonas media, Podomonas capensis, Apusomonas proboscidea, and Apusomonas australiensis, and rename Thecamonas oxoniensis as Mylnikovia oxoniensis n. gen., n. comb. Additionally, we describe four new genera and six new species: Catacumbia lutetiensis n. gen. n. sp., Cavaliersmithia chaoae n. gen. n. sp., Singekia montserratensis n. gen. n. sp., Singekia franciliensis n. gen. n. sp., Karpovia croatica n. gen. n. sp., and Chelonemonas dolani n. sp. Our comparative analysis suggests that apusomonad ancestor was a fusiform biflagellate with a dorsal pellicle, a plastic ventral surface, and a sleeve covering the anterior flagellum, that thrived in marine, possibly oxygen-poor, environments. It likely had a complex cell cycle with dormant and multiple fission stages, and sex. Our results extend known apusomonad diversity, allow updating their taxonomy, and provide elements to understand early eukaryotic evolution., The authors acknowledge the importance of previous studies on these protists by several researchers and thank T. Cavalier-Smith, E. Chao, D. Patterson, A. Mylnikov, and S. A. Karpov for their legacy and, in specific cases, useful discussion and collaboration. We thank J. Dolan for access to samples from Villefranche-sur-Mer from which C. dolani was cultured, A. Guillén, author of ‘Proyecto agua’, for sending samples from the Sanabria glacial lake, and J. Favate for collecting the material from which SPRINTER was isolated. We also thank Kaleigh Lukacs for assisting with culture maintenance. This work was supported by the European Research Council (ERC) Advanced Grants ‘Protistworld’ and ‘Plast‐Evol’ (322669 and 787904, respectively) the Horizon 2020 research and innovation program under the Marie Skłodowska-Curie ITN project SINGEK H2020-MSCA-ITN-2015-675752 (http://www.singek.eu/). GT was supported by the 2019 BP 00208 Beatriu de Pinos-3 Postdoctoral Program (BP3; 801370), Peer Reviewed, Postprint (author's final draft)

This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling in the intervening years has massively increased the genetic information at hand. Consequently, we have discovered novel clades, exciting new genera and uncovered a massive species level diversity beyond the morphological species descriptions. Several clades known from environmental samples only have now found their home. Sampling soils, deeper marine waters and the deep sea will continue to fill us with surprises. The main changes in this revision are the confirmation that eukaryotes form at least two domains, the loss of monophyly in the Excavata, robust support for the Haptista and Cryptista. We provide suggested primer sets for DNA sequences from environmental samples that are effective for each clade. We have provided a guide to trophic functional guilds in an appendix, to facilitate the interpretation of environmental samples, and a standardized taxonomic guide for East Asian users.

This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling in the intervening years has massively increased the genetic information at hand. Consequently, we have discovered novel clades, exciting new genera and uncovered a massive species level diversity beyond the morphological species descriptions. Several clades known from environmental samples only have now found their home. Sampling soils, deeper marine waters and the deep sea will continue to fill us with surprises. The main changes in this revision are the confirmation that eukaryotes form at least two domains, the loss of monophyly in the Excavata, robust support for the Haptista and Cryptista. We provide suggested primer sets for DNA sequences from environmental samples that are effective for each clade. We have provided a guide to trophic functional guilds in an appendix, to facilitate the interpretation of environmental samples, and a standardized taxonomic guide for East Asian users

This revision of the classification of eukaryotes, which updates that of Adl et al. [J. Eukaryot. Microbiol. 52 (2005) 399], retains an emphasis on the protists and incorporates changes since 2005 that have resolved nodes and branches in phylogenetic trees. Whereas the previous revision was successful in re-introducing name stability to the classification, this revision provides a classification for lineages that were then still unresolved. The supergroups have withstood phylogenetic hypothesis testing with some modifications, but despite some progress, problematic nodes at the base of the eukaryotic tree still remain to be statistically resolved. Looking forward, subsequent transformations to our understanding of the diversity of life will be from the discovery of novel lineages in previously under-sampled areas and from environmental genomic information.