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
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.
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
A large number of metadata have been downloaded from GenBank such as GebNak taxonomy and references associated with sequences.
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
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
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