{"id":16,"date":"2024-04-04T08:51:37","date_gmt":"2024-04-04T05:51:37","guid":{"rendered":"https:\/\/sisu.ut.ee\/eukaryome\/references\/"},"modified":"2024-04-04T08:52:32","modified_gmt":"2024-04-04T05:52:32","slug":"references","status":"publish","type":"page","link":"https:\/\/sisu.ut.ee\/eukaryome\/references\/","title":{"rendered":"References"},"content":{"rendered":"<p style=\"text-align: justify\">\n\t<span><span lang=\"ET\"><span style=\"sans-serif\">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.<\/span><\/span><\/span>\n<\/p>\n<p style=\"text-align: justify\">\n\t<span><span lang=\"ET\"><span style=\"sans-serif\">T<\/span><\/span><span><span style=\"sans-serif\">o 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<\/span><\/span><span lang=\"ET\"><span style=\"sans-serif\">:<\/span><\/span><\/span>\n<\/p>\n<ul style=\"list-style-type:circle\">\n<li style=\"text-align: justify\">\n\t\tGalindo, L.J.;\u00a0Torruella, G.;\u00a0Moreira, D.;\u00a0Eglit, Y.;\u00a0Simpson, A.G.;\u00a0V\u00f6lcker, E.;\u00a0Clau\u00df, S.;\u00a0L\u00f3pez-Garc\u00eda, 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\u00a0 \u00a0DOI:\u00a0<a href=\"https:\/\/doi.org\/10.1098\/rstb.2019.0094\">10.1098\/rstb.2019.0094<\/a>\n\t<\/li>\n<li style=\"text-align: justify\">\n\t\tKarst, S.M.;\u00a0Dueholm, M.S.;\u00a0McIlroy, S.J.;\u00a0Kirkegaard, R.H.;\u00a0Nielsen, P.H.;\u00a0Albertsen, M. 2018. Retrieval of a million high\u2010quality, full-length microbial 16S and 18S rRNA gene sequences without primer bias. Nature Biotechnology 36: 190\u2013195 DOI:\u00a0<a href=\"https:\/\/doi.org\/10.1038\/nbt.4045\">10.1038\/nbt.4045<\/a>\n\t<\/li>\n<li style=\"text-align: justify\">\n\t\tLabarre, A.;\u00a0L\u00f3pez-Escard\u00f3, D.;\u00a0Latorre, F.;\u00a0Leonard, G.;\u00a0Bucchini, F.;\u00a0Obiol, A.;\u00a0Cruaud, C.;\u00a0Sieracki, M.E.;\u00a0Jaillon, O.;\u00a0Wincker, P.;\u00a0Vandepoele, K. Comparative genomics reveals new functional insights in uncultured MAST species. The ISME Journal. 2021 Jun;15(6):1767-81\u00a0 \u00a0 DOI:\u00a0<a href=\"https:\/\/doi.org\/10.1038\/s41396-020-00885-8\">10.1038\/s41396-020-00885-8<\/a>\n\t<\/li>\n<li style=\"text-align: justify\">\n\t\tStrassert, J.F.;\u00a0Jamy, M.;\u00a0Mylnikov, A.P.;\u00a0Tikhonenkov, D.V.;\u00a0Burki, F. 2019. New phylogenomic analysis of the enigmatic phylum Telonemia further resolves the eukaryote tree of life. Molecular Biology and Evolution 36: 757-765. \u00a0 \u00a0 \u00a0DOI:\u00a0<a href=\"https:\/\/doi.org\/10.1098\/rstb.2019.0094\">10.1098\/rstb.2019.0094<\/a>\n\t<\/li>\n<li style=\"text-align: justify\">\n\t\t<span><span style=\"sans-serif\">Tikhonenkov, D.V.;\u00a0Mikhailov, K.V.;\u00a0Gawryluk, R.M.;\u00a0Belyaev, A.O.;\u00a0Mathur, V.;\u00a0Karpov, S.A.;\u00a0Zagumyonnyi, D.G.;\u00a0Borodina, A.S.; Prokina, K.I.;\u00a0Mylnikov, A.P.; Aleoshin, V.V. 2022. Microbial predators form a new supergroup of eukaryotes. Nature 612: 714\u2013719 \u00a0 \u00a0 DOI:\u00a0<\/span><\/span><a href=\"https:\/\/doi.org\/10.1038\/s41586-022-05511-5\">10.1038\/s41586-022-05511-5<\/a>\n\t<\/li>\n<li style=\"text-align: justify\">\n\t\tTorruella, G.;\u00a0de Mendoza, A.;\u00a0Grau-Bove, X.;\u00a0Anto, M.;\u00a0Chaplin, M.A.;\u00a0del Campo, J.;\u00a0Eme, L.;\u00a0P\u00e9rez-Cord\u00f3n, G.;\u00a0Whipps, C.M.;\u00a0Nichols, K.M.;\u00a0Paley, R. 2015. Phylogenomics reveals convergent evolution of lifestyles in close relatives of animals and fungi. Current Biology 25: 2404-2410\u00a0\u00a0\u00a0\u00a0DOI:\u00a0<a href=\"https:\/\/doi.org\/10.1016\/j.cub.2015.07.053\">10.1016\/j.cub.2015.07.053<\/a>\n\t<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>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 &#8230;<\/p>\n","protected":false},"author":163,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"inline_featured_image":false,"footnotes":""},"class_list":["post-16","page","type-page","status-publish","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/sisu.ut.ee\/eukaryome\/wp-json\/wp\/v2\/pages\/16","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sisu.ut.ee\/eukaryome\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sisu.ut.ee\/eukaryome\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sisu.ut.ee\/eukaryome\/wp-json\/wp\/v2\/users\/163"}],"replies":[{"embeddable":true,"href":"https:\/\/sisu.ut.ee\/eukaryome\/wp-json\/wp\/v2\/comments?post=16"}],"version-history":[{"count":1,"href":"https:\/\/sisu.ut.ee\/eukaryome\/wp-json\/wp\/v2\/pages\/16\/revisions"}],"predecessor-version":[{"id":143,"href":"https:\/\/sisu.ut.ee\/eukaryome\/wp-json\/wp\/v2\/pages\/16\/revisions\/143"}],"wp:attachment":[{"href":"https:\/\/sisu.ut.ee\/eukaryome\/wp-json\/wp\/v2\/media?parent=16"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}