References

EUKARYOME includes curated rRNA genes from recent (meta)genomics and (meta)transcriptomics and long-read (meta)barcoding studies. The original taxonomic annotations are updated based on information in recently published databases and datasets as well as changes in phylogeny-based hierarchical taxonomy.

To cover several very recently described phylum- and kingdom-level taxa and the genetic variation therein, we downloaded raw (meta)genome and (meta)transcriptome data from several studies:

  • Galindo, L.J.; Torruella, G.; Moreira, D.; Eglit, Y.; Simpson, A.G.; Völcker, E.; Clauß, S.; López-García, P. 2019. Combined cultivation and single-cell approaches to the phylogenomics of nucleariid amoebae, close relatives of fungi. Philosophical Transactions of the Royal Society B. 374:20190094   DOI: 10.1098/rstb.2019.0094
  • Karst, S.M.; Dueholm, M.S.; McIlroy, S.J.; Kirkegaard, R.H.; Nielsen, P.H.; Albertsen, M. 2018. Retrieval of a million high‐quality, full-length microbial 16S and 18S rRNA gene sequences without primer bias. Nature Biotechnology 36: 190–195 DOI: 10.1038/nbt.4045
  • Labarre, A.; López-Escardó, D.; Latorre, F.; Leonard, G.; Bucchini, F.; Obiol, A.; Cruaud, C.; Sieracki, M.E.; Jaillon, O.; Wincker, P.; Vandepoele, K. Comparative genomics reveals new functional insights in uncultured MAST species. The ISME Journal. 2021 Jun;15(6):1767-81    DOI: 10.1038/s41396-020-00885-8
  • Strassert, J.F.; Jamy, M.; Mylnikov, A.P.; Tikhonenkov, D.V.; Burki, F. 2019. New phylogenomic analysis of the enigmatic phylum Telonemia further resolves the eukaryote tree of life. Molecular Biology and Evolution 36: 757-765.      DOI: 10.1098/rstb.2019.0094
  • Tikhonenkov, D.V.; Mikhailov, K.V.; Gawryluk, R.M.; Belyaev, A.O.; Mathur, V.; Karpov, S.A.; Zagumyonnyi, D.G.; Borodina, A.S.; Prokina, K.I.; Mylnikov, A.P.; Aleoshin, V.V. 2022. Microbial predators form a new supergroup of eukaryotes. Nature 612: 714–719     DOI: 10.1038/s41586-022-05511-5
  • Torruella, G.; de Mendoza, A.; Grau-Bove, X.; Anto, M.; Chaplin, M.A.; del Campo, J.; Eme, L.; Pérez-Cordón, G.; Whipps, C.M.; Nichols, K.M.; Paley, R. 2015. Phylogenomics reveals convergent evolution of lifestyles in close relatives of animals and fungi. Current Biology 25: 2404-2410    DOI: 10.1016/j.cub.2015.07.053
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