Main changes A single SSU database From version 4.14.0, a single SSU database is provided which contains sequences for: 18S rRNA from nuclear and nucleomorph 16S rRNA from plastid, apicoplast, chromatophore, mitochondrion 16S rRNA from a small selection of bacteria The rationale is that the database can now be used to detect bacterial sequences that are amplified with either 18S rRNA or "universal" primers. These sequences can be further assigned with Silva or GTDB. In order to allow correct assignation with software such as DECIPHER (IDTax) for organelle, the taxonomy is appended with 4 letters corresponding to the organelle Organelle Taxonomy suffix nucleus nucleomorph :nucl plastid :plas apicoplast :apic chromatophore :chrom mitochondrion :mito Major groups for which taxonomy has been updated Apicomplexa Labyrinthulids Radiolaria Foraminifera Radiolaria Quarantined sequences (makes sense in these COVID times...) We are introducing sequences that have been quarantined. These sequences have been reassigned with DECIPHER IDTax but the bootstrap values were low or they have been flagged as problematic by DECIPHER during the LeaningTax phase. These sequences are not provided with the current version but will be added in the future avec verification of their taxonomic assignement. List of sequences added or updated Added: 9,710 Updated: 25,298 Quarantined: 614 Removed: 462 Contributors Daniel Vaulot - General curation, Bacteria and Archaea Alex Schoenle - Cafeteria Miguel Sandin - Radiolaria Raphael Morard - Forams Frédéric Mahé - Detecting sequences reverse-complemented or complemented Anna Maria Fiore-Donno - Detecting chimeras, ITS and badly assigned sequences Javier del Campo and EukRef team - Excavata, 16S plastid, Apicmplexa, Labyrinthulids Taxonomic groups updated Alveolata - Javier del Campo Apicomplexa 9955 sequences updated or added. 303 sequences quarantined needing phylogeny assignment. 583 taxonomy entries revised Chlorophyta Ostrobium : 2 sequences added Stramenopiles Labyrinthulids - Javier del Campo Sequences updated or added: 1280 Sequences quarantined: 133 Taxonomy fully revised: 69 species Cafeteria - Alex Schoenle following Schoenle et al. (2020) sequences updated: 30 sequences added: 31 script Cafileria marina: 8 sequences added Haptophyta Rappephyceae - Kawachi et al. (2021) Rappemonads moved into Rappephyceae 4 sequences added Radiolaria - Miguel Sandin Total number of valid sequences: 4471 Taxa updated or added: 232 entries Sequences added: 66 Sequences updated (including new sequences): 4619 Sequences annotated as chimera: 343 Process and scripts to build phylogeny from Miguel script to upload to PR2 Foraminifera - Raphaël Morard Total number of validated sequences: 3839 Taxonomy updated or added: 315 entries Sequences added: 1149 Sequences updated (including new sequences): 2164 script to upload to PR2 Excavata - Javier del Campo and EUkref team EUkref team: Martin Kolisko, Olga Flegontova, Anna Karnkowska, Gordon Lax, Julia M. Maritz, Tomáš Pánek, Petr Táborský, Jane M. Carlton, Ivan Cepička6, Aleš Horák, Julius Lukeš, Alastair G.B. Simpson, and Vera Tai Total number of validated sequences: 6265 Taxa updated or added: 735 Sequences added from GenBank: 75 Sequences updated (existing + new): 1347 + 2875 Sequences quarantined: 104 Metadata updated with eukref fields: 6091 16S plastid sequences (Ostreobium and Apicomplexa)- Javier del Campo 87 sequences reassigned 482 sequences added Bacteria, Archaea - Daniel Vaulot Sequences added: 7945 Taxa added: 1571 These sequences originate from Silva seed alignment v. 132 as found on the mothur site They are used as "control" sequences when assigning metabarcodes, especially for primers that are either "universal", i.e. amplify both 18S and 16S or that are "imperfect", in the sense that they also amplify a small fraction of the 16S sequences. Sequences uploaded but not yet annotated 8763 18S rRNA sequences added from GenBank - 2020-05-27 to 2021-03-23 - Script Sequences removed Potential chimera in Radiolaria: 343 (M. Sandin) Bad sequences: 6 (F. Mahé) chimeras: 95 (A M Fiore-Donno) ITS: 20 (A M Fiore-Donno) Badly assigned: 6 (A M Fiore-Donno) Sequences modified (F. Mahé) complemented: 26 reverse complemented: 114 + 189 Script Metadata added A large number of metadata have been downloaded from GenBank such as GebNak taxonomy and references associated with sequences. References Stramenopiles 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. 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 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 Haptophyta 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 Radiolaria Adl, S. M., Bass, D., Lane, C. E., Lukeš, J., Schoch, C. L., Smirnov, A., et al. 2019. Revisions to the classification, nomenclature, and diversity of eukaryotes. J. Eukaryot. Microbiol. 66, 4–119. doi:10.1111/jeu.12691 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 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 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 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/ 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 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 Database structure pr2_main quarantined_version: sequences flagged as quarantined will need to be re-assigned latter. pr2_metadata gb_references: removed (empty) gb_locus: removed (empty) gb_division: addede - Three letter code for Genbank division (eg PLN, ENV...) Metadata added The following fields were populated from GenBank when the data were missing (413,230 records updated) gb_taxonomy gb_project gb_authors, gb_publication, gb_journal gb_sequence gb_division gb_date Scripts Scripts are just provided to show some of the procedures used to update the PR2 database. Do not try to run them, they will not work as they require access to the MySQL PR2 database.