Taxonomic groups annotated in the PR2 reference database

Groups with updated annotations

Groups with planned annotations

List of references used to annotate database

Eukaryotic taxonomy

• Adl SM., Bass D., Lane CE., Lukeš J., Schoch CL., Smirnov A., Agatha S., Berney C., Brown MW., Burki F., Cárdenas P., Čepička I., Chistyakova L., del Campo J., Dunthorn M., Edvardsen B., Eglit Y., Guillou L., Hampl V., Heiss AA., Hoppenrath M., James TY., Karpov S., Kim E., Kolisko M., Kudryavtsev A., Lahr DJG., Lara E., Le Gall L., Lynn DH., Mann DG., Massana i Molera R., Mitchell EAD., Morrow C., Park JS., Pawlowski JW., Powell MJ., Richter DJ., Rueckert S., Shadwick L., Shimano S., Spiegel FW., Torruella i Cortes G., Youssef N., Zlatogursky V., Zhang Q. 2019. Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes. Journal of Eukaryotic Microbiology 66:4–119. DOI: 10.1111/jeu.12691.
• Berney, Cédric, Nicolas Henry, Frédéric Mahé, Daniel J. Richter, et Colomban de Vargas. 2022. EukRibo: A Manually Curated Eukaryotic 18S RDNA Reference Database to Facilitate Identification of New Diversity. Preprint. BiorXiv. https://doi.org/10.1101/2022.11.03.515105.
• Brown, M.W., Heiss, A.A., Kamikawa, R., Inagaki, Y., Yabuki, A., Tice, A.K., Shiratori, T., Ishida, K.I., Hashimoto, T., Simpson, A.G. and Roger, A.J., 2018. Phylogenomics places orphan protistan lineages in a novel eukaryotic super-group. Genome biology and evolution, 10(2), pp.427-433.
• Burki, Fabien, Andrew J. Roger, Matthew W. Brown, et Alastair G.B. Simpson. 2020. The New Tree of Eukaryotes. Trends in Ecology and Evolution 35 (1): 43‑55. https://doi.org/10.1016/j.tree.2019.08.008.
• Gawryluk, R.M., Tikhonenkov, D.V., Hehenberger, E., Husnik, F., Mylnikov, A.P. and Keeling, P.J., 2019. Non-photosynthetic predators are sister to red algae. Nature, 572(7768), pp.240-243.
• Strassert, J.F., Jamy, M., Mylnikov, A.P., Tikhonenkov, D.V. and Burki, F., 2019. New phylogenomic analysis of the enigmatic phylum Telonemia further resolves the eukaryote tree of life. Molecular biology and evolution, 36(4), pp.757-765.

Chlorophyta

• Tragin, M., Lopes dos Santos, A., Christen, R., and Vaulot, D. (2016). Diversity and ecology of green microalgae in marine systems: an overview based on 18S rRNA gene sequences. Perspect. Phycol. 3, 141–154. doi:10.1127/pip/2016/0059.
• Lopes dos Santos A., Pollina T., Gourvil P., Corre E., Marie D., Garrido JL., Rodríguez F., Noël M-H., Vaulot D., Eikrem W. 2017. Chloropicophyceae, a new class of picophytoplanktonic prasinophytes. Scientific Reports 7:14019. DOI: 10.1038/s41598-017-12412-5.
• Daugbjerg N., Fassel NMD., Moestrup Ø. 2019. Microscopy and phylogeny of Pyramimonas tatianae sp. nov. (Pyramimonadales, Chlorophyta), a scaly quadriflagellate from Golden Horn Bay (eastern Russia) and formal description of Pyramimonadophyceae classis nova . European Journal of Phycology 0:1–15. DOI: 10.¹⁰⁸⁰⁄_09670262.2019.1638524

Ochrophyta/Stramenopiles

• Adl, S.M., Bass, D., Lane, C.E., Lukeš, J., Schoch, C.L., Smirnov, A., Agatha, S. et al. 2019. Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes. J. Eukaryot. Microbiol. 66:4–119.
• Andersen RA., Graf L., Malakhov Y., Yoon HS. 2017. Rediscovery of the Ochromonas type species Ochromonas triangulata (Chrysophyceae) from its type locality (Lake Veysove, Donetsk region, Ukraine). Phycologia 56:591–604. DOI: 10.²²¹⁶⁄₁₇-15.1.
• Arsenieff L., Le Gall F., Rigaut-Jalabert F., Mahé F., Sarno D., Gouhier L., Baudoux A-C., Simon N. 2020. Diversity and dynamics of relevant nanoplanktonic diatoms in the Western English Channel. The ISME Journal. DOI: 10.1038/s41396-020-0659-6.
• Barcytė, D., Eikrem, W., Engesmo, A., Seoane, S., Wohlmann, J., Horák, A., Yurchenko, T., & Eliáš, M. (2021). Olisthodiscus represents a new class of Ochrophyta. Journal of Phycology, 57(4), 1094‑1118. https://doi.org/10.1111/jpy.13155
• Charvet, Sophie, Warwick F. Vincent, et Connie Lovejoy. 2012. « Chrysophytes and Other Protists in High Arctic Lakes: Molecular Gene Surveys, Pigment Signatures and Microscopy ». Polar Biology 35 (5): 733‑48. https://doi.org/10.1007/s00300-011-1118-7.
• Derelle, R., López-García, P., Timpano, H. & Moreira, D. 2016. A Phylogenomic Framework to Study the Diversity and Evolution of Stramenopiles (= Heterokonts). Mol. Biol. Evol. 33:2890–8.
• Gaonkar, C.C., Piredda, R., Minucci, C., Mann, D.G., Montresor, M., Sarno, D. & Kooistra, W.H.C.F. 2018. Annotated 18S and 28S rDNA reference sequences of taxa in the planktonic diatom family Chaetocerotaceae. PLoS One. 13:e0208929.
• Han KY., Graf L., Reyes CP., Melkonian B., Andersen RA., Yoon HS., Melkonian M. 2018. A Re-investigation of Sarcinochrysis marina (Sarcinochrysidales, Pelagophyceae) from its Type Locality and the Descriptions of Arachnochrysis, Pelagospilus, Sargassococcus and Sungminbooa genera nov. Protist 169:79–106. DOI: 10.1016/j.protis.2017.12.004.
• Ichinomiya, M., dos Santos, A. L., Gourvil, P., Yoshikawa, S., Kamiya, M., Ohki, K., et al. (2016). Diversity and oceanic distribution of the Parmales (Bolidophyceae), a picoplanktonic group closely related to diatoms. ISME J. 10, 2419–2434. doi:10.1038/ismej.2016.38.
• Jirsová, D., Füssy, Z., Richtová, J., Gruber, A., & Oborník, M. (2019). Morphology, ultrastructure, and mitochondrial genome of the marine non-photosynthetic bicosoecid Cafileria marina gen. Et sp. Nov. Microorganisms, 7(8), 240. https://doi.org/10.3390/microorganisms7080240
• Massana, R., del Campo, J., Sieracki, M.E., Audic, S. & Logares, R. 2014. Exploring the uncultured microeukaryote majority in the oceans: reevaluation of ribogroups within stramenopiles. ISME J. 8:854–66.
• Pan, J., del Campo, J., & Keeling, P. J. (2017). Reference Tree and Environmental Sequence Diversity of Labyrinthulomycetes. Journal of Eukaryotic Microbiology, 64(1), 88–96. https://doi.org/10.1111/jeu.12342
• Schoenle, A., Hohlfeld, M., Rosse, M., Filz, P., Wylezich, C., Nitsche, F., & Arndt, H. (2020). Global comparison of bicosoecid Cafeteria-like flagellates from the deep ocean and surface waters, with reorganization of the family Cafeteriaceae. European Journal of Protistology, 73, 125665. https://doi.org/10.1016/j.ejop.2019.125665.
• Scoble, Josephine Margaret, et Thomas Cavalier-Smith. 2014. « Scale Evolution in Paraphysomonadida (Chrysophyceae): Sequence Phylogeny and Revised Taxonomy of Paraphysomonas, New Genus Clathromonas, and 25 New Species ». European Journal of Protistology 50 (5): 551‑92. https://doi.org/10.1016/j.ejop.2014.08.001.

Haptophyta

• Edvardsen, B., Egge, E. S., and Vaulot, D. (2016). Diversity and distribution of haptophytes revealed by environmental sequencing and metabarcoding – a review. Perspect. Phycol. 3, 77–91. doi:10.1127/pip/2016/0052.
• Kawachi, M., Nakayama, T., Kayama, M., Nomura, M., Miyashita, H., Bojo, O., Rhodes, L., Sym, S., Pienaar, R. N., Probert, I., Inouye, I., & Kamikawa, R. (2021). Rappemonads are haptophyte phytoplankton. Current Biology. https://doi.org/10.1016/j.cub.2021.03.012

Ciliates

• Agatha, S. and Strüder-Kypke, M.C. (2014) What Morphology and Molecules Tell Us about the Evolution of Oligotrichea (Alveolata, Ciliophora). Acta Protozool. 2014: 7790.
• Bachy, C., Gómez, F., López-García, P., Dolan, J.R., and Moreira, D. (2012) Molecular Phylogeny of Tintinnid Ciliates (Tintinnida, Ciliophora). Protist 163: 873–887.
• Boscaro V., Santoferrara L., Zhang Q., Gentekaki E., Syberg-Olsen M., del Campo J., Keeling P., 2018. EukRef–Ciliophora: A manually curated, phylogeny‐based database of small subunit rRNA gene sequences of ciliates. Environmental Microbiology, 20: 2218-2230.
• Ganser, Maximilian H., Luciana F. Santoferrara, et Sabine Agatha. 2022. « Molecular Signature Characters Complement Taxonomic Diagnoses: A Bioinformatic Approach Exemplified by Ciliated Protists (Ciliophora, Oligotrichea) ». Molecular Phylogenetics and Evolution 170 (mai): 107433. https://doi.org/10.1016/j.ympev.2022.107433.
• Santoferrara, L.F., Alder, V.V., and McManus, G.B. (2017) Phylogeny, classification and diversity of Choreotrichia and Oligotrichia (Ciliophora, Spirotrichea). Mol. Phylogenet. Evol. 112: 12–22.
• Zhang, Q., Agatha, S., Zhang, W., Dong, J., Yu, Y., Jiao, N., and Gong, J. (2017) Three rDNA Loci-Based Phylogenies of Tintinnid Ciliates (Ciliophora, Spirotrichea, Choreotrichida). J. Eukaryot. Microbiol. 64: 226–241.

Dinoflagellates

• Janouškovec, Jan, Gregory S. Gavelis, Fabien Burki, Donna Dinh, Tsvetan R. Bachvaroff, Sebastian G. Gornik, Kelley J. Bright, et al. 2017. Major Transitions in Dinoflagellate Evolution Unveiled by Phylotranscriptomics. Proceedings of the National Academy of Sciences 114 (2): E171–80. https://doi.org/10.1073/pnas.1614842114.
• LaJeunesse, Todd C., John Everett Parkinson, Paul W. Gabrielson, Hae Jin Jeong, James Davis Reimer, Christian R. Voolstra, and Scott R. Santos. 2018. Systematic Revision of Symbiodiniaceae Highlights the Antiquity and Diversity of Coral Endosymbionts. Current Biology 28 (16): 2570-2580.e6. https://doi.org/10.1016/j.cub.2018.07.008.
• Mordret, S., Piredda, R., Vaulot, D., Montresor, M., Kooistra, W.H.C.F. & Sarno, D. 2018. dinoref : A curated dinoflagellate (Dinophyceae) reference database for the 18S rRNA gene. Mol. Ecol. Resour. in press.

Apicomplexa

• del Campo J., Heger TJ., Rodríguez-Martínez R., Worden AZ., Richards TA., Massana R., Keeling PJ. 2019. Assessing the Diversity and Distribution of Apicomplexans in Host and Free-Living Environments Using High-Throughput Amplicon Data and a Phylogenetically Informed Reference Framework. Frontiers in Microbiology 10:1–15. DOI: 10.3389/fmicb.2019.02373.

Plastids

• Decelle, J., Romac, S., Stern, R.F., Bendif, E.M., Zingone, A., Audic, S., Guiry, M.D. et al. 2015. PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy. Mol. Ecol. Resour. 15:1435–144

Radiolaria

• Biard, T., Bigeard, E., Audic, S., Poulain, J., Stemmann, L., Not, F., 2017. Biogeography and diversity of Collodaria (Radiolaria) in the global ocean. Nat. Publ. Gr. 1–42. doi:10.1038/ismej.2017.12
  
• Capella-Gutiérrez, S., Silla-Martínez, J.M., Gabaldón, T., 2009. trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973. doi:10.1093/bioinformatics/btp348
  
• Cavalier-Smith, T., Chao, E.E., Lewis, R., 2018. Multigene phylogeny and cell evolution of chromist infrakingdom Rhizaria: contrasting cell organisation of sister phyla Cercozoa and Retaria. Protoplasma 255, 1517–1574. doi:10.1007/s00709-018-1241-1
  
• Decelle, J., Suzuki, N., Mahé, F., Vargas, C. De, Not, F., 2012b. Molecular Phylogeny and Morphological Evolution of the Acantharea (Radiolaria). Protist 163, 435–450. doi:10.1016/j.protis.2011.10.002
  
• Gouy, M., Guindon, S., Gascuel, O., 2010. SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building. Mol. Biol. Evol. 27, 221–224. doi:10.1093/molbev/msp259
  
• Katoh, K., Standley, D.M., 2013. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol. Biol. Evol. 30, 772–780. doi:10.1093/molbev/mst010
  
• Larsson, A. (2014). AliView: a fast and lightweight alignment viewer and editor for large data sets. Bioinformatics30(22): 3276-3278. http://dx.doi.org/10.1093/bioinformatics/btu531
  
• Nakamura, Y., Sandin, M.M., Suzuki N., Somiya R., Tuji A., Not, F, 2020. Phylogenetic revision of the order Entactinaria - Paleozoic relict Radiolaria (Rhizaria, SAR). Protist 171. doi:10.1016/j.protis.2019.125712
  
• Rambaut A (2016) FigTree version 1.4.3. http://tree.bio.ed.ac.uk/software/figtree/
  
• Sandin M.M., Biard T., Romac S., O’Dogherty L., Suzuki N., Not F., 2020. Morpho-molecular diversity and evolutionary analyses suggest hidden life styles in Spumellaria (Radiolaria) bioRxiv 2020.06.29.176917; doi: https://doi.org/10.¹¹⁰¹⁄₂₀₂₀.06.29.176917
  
• Sandin, M.M., Pillet, L., Biard, T., Poirier, C., Bigeard, E., Romac, S., Suzuki, N., Not, F., 2019. Time Calibrated Morpho-molecular Classification of Nassellaria (Radiolaria). Protist 170, 187–208. doi:10.1016/j.protis.2019.02.002
  
• Schloss, P.D., Westcott, S.L., Ryabin, T., Hall, J.R., Hartmann, M., Hollister, E.B., Lesniewski, R.A., Oakley, B.B., Parks, D.H., Robinson, C.J., Sahl, J.W., Stres, B., Thallinger, G.G., Van Horn, D.J., Weber, C.F., 2009. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537–7541.doi:10.1128/AEM.01541-09
• Stamatakis, A., 2014. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313. doi:10.1093/bioinformatics/btu033 Rognes, T., Flouri, T., Nichols, B., Quince, C., Mahé, F., 2016. VSEARCH: a versatile open source tool for metagenomics. PeerJ 4, e2584.doi:10.7717/peerj.2584
  

Excavata

• Hohlfeld, Manon, Claudia Meyer, Alexandra Schoenle, Frank Nitsche, et Hartmut Arndt. 2023. « Biogeography, Autecology, and Phylogeny of Percolomonads Based on Newly Described Species ». Journal of Eukaryotic Microbiology 70 (1): e12930. https://doi.org/10.1111/jeu.12930.

Provora

• Tikhonenkov, Denis V., Kirill V. Mikhailov, Ryan M. R. Gawryluk, Artem O. Belyaev, Varsha Mathur, Sergey A. Karpov, Dmitry G. Zagumyonnyi, et al. 2022. « Microbial Predators Form a New Supergroup of Eukaryotes ». Nature 612 (7941): 714‑19. https://doi.org/10.1038/s41586-022-05511-5.