{"id":391076,"date":"2025-11-20T00:53:21","date_gmt":"2025-11-20T00:53:21","guid":{"rendered":"https:\/\/www.europesays.com\/us\/391076\/"},"modified":"2025-11-20T00:53:21","modified_gmt":"2025-11-20T00:53:21","slug":"rare-microbial-relict-sheds-light-on-an-ancient-eukaryotic-supergroup","status":"publish","type":"post","link":"https:\/\/www.europesays.com\/us\/391076\/","title":{"rendered":"Rare microbial relict sheds light on an ancient eukaryotic supergroup"},"content":{"rendered":"
  • \n

    Lax, G. et al. Hemimastigophora is a novel supra-kingdom-level lineage of eukaryotes. Nature 564<\/b>, 410\u2013414 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Brown, M. W. et al. Phylogenomics places orphan protistan lineages in a novel eukaryotic super-group. Genome Biol. Evol. 10<\/b>, 427\u2013433 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Tikhonenkov, D. V. et al. Microbial predators form a new supergroup of eukaryotes. Nature 612<\/b>, 714\u2013719 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Janou\u0161kovec, J. et al. A new lineage of eukaryotes illuminates early mitochondrial genome reduction. Curr. Biol. 27<\/b>, 3717\u20133724 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Gawryluk, R. M. R. et al. Non-photosynthetic predators are sister to red algae. Nature 572<\/b>, 240\u2013243 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Sch\u00f6n, M. E. et al. Single cell genomics reveals plastid-lacking Picozoa are close relatives of red algae. Nat. Commun. 12<\/b>, 6651 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Gray, M. W. et al. The draft nuclear genome sequence and predicted mitochondrial proteome of Andalucia godoyi, a protist with the most gene-rich and bacteria-like mitochondrial genome. BMC Biol. 18<\/b>, 22 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Horv\u00e1thov\u00e1, L., et al. Analysis of diverse eukaryotes suggests the existence of an ancestral mitochondrial apparatus derived from the bacterial type II secretion system. Nat. Commun. 12<\/b>, 2947 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Burger, G., Gray, M. W., Forget, L. & Lang, B. F. Strikingly bacteria-like and gene-rich mitochondrial genomes throughout jakobid protists. Genome Biol. Evol. 5<\/b>, 418\u2013438 (2013).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Moreira, D., Blaz, J., Kim, E. & Eme, L. A gene-rich mitochondrion with a unique ancestral protein transport system. Curr. Biol. 34<\/b>, 3812\u20133819 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Burki, F., Roger, A. J., Brown, M. W. & Simpson, A. G. B. The new tree of eukaryotes. Trends Ecol. Evol. 35<\/b>, 43\u201355 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Luke\u0161, J., \u010cepi\u010dka, I. & Kol\u00edsko, M. Evolution: no end in sight for novel incredible (heterotrophic) protists. Curr. Biol. 34<\/b>, R55\u2013R58 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Sunagawa, S. et al. Tara Oceans: towards global ocean ecosystems biology. Nat. Rev. Microbiol. 18<\/b>, 428\u2013445 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    del Campo, J. et al. The protist cultural renaissance. Trends Microbiol. 32<\/b>, 128\u2013131 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Timmis, J. N., Ayliff, M. A., Huang, C. Y. & Martin, W. Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nat. Rev. Genet. 5<\/b>, 123\u2013135 (2004).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Gabald\u00f3n, T. & Huynen, M. A. Reconstruction of the proto-mitochondrial metabolism. Science 301<\/b>, 609 (2003).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Gawryluk, R. M. R. & Stairs, C. W. Diversity of electron transport chains in anaerobic protists. Biochim. Biophys. Acta Bioenerg. 1862<\/b>, 148334 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Namasivayam, S. et al. Massive invasion of organellar DNA drives nuclear genome evolution in Toxoplasma. Proc. Natl Acad. Sci. USA 120<\/b>, e2308569120 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    He, D., Fu, C.-J. & Baldauf, S. L. Multiple origins of eukaryotic cox15 suggest horizontal gene transfer from bacteria to jakobid mitochondrial DNA. Mol. Biol. Evol. 33<\/b>, 122\u2013133 (2016).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Milner, D. S., Wideman, J. G., Stairs, C. W., Dunn, C. D. & Richards, T. A. A functional bacteria-derived restriction modification system in the mitochondrion of a heterotrophic protist. PLoS Biol. 19<\/b>, e3001126 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Gray, M. W. Mosaic nature of the mitochondrial proteome: Implications for the origin and evolution of mitochondria. Proc. Natl Acad. Sci. USA 112<\/b>, 10133\u201310138 (2015).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Pyrih, J. et al. Vestiges of the bacterial signal recognition particle-based protein targeting in mitochondria. Mol. Biol. Evol. 38<\/b>, 3170\u20133187 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Eglit, Y. et al. Meteora sporadica, a protist with incredible cell architecture, is related to Hemimastigophora. Curr. Biol. 34<\/b>, 451\u2013459 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Shiryev, S. A. & Agarwala, R. Indexing and searching petabase-scale nucleotide resources. Nat. Methods 21<\/b>, 994\u20131002 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Lynch, M. D. J. & Neufeld, J. D. Ecology and exploration of the rare biosphere. Nat. Rev. Microbiol. 13<\/b>, 217\u2013229 (2015).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Forster, D. et al. Benthic protists: the under-charted majority. FEMS Microbiol. Ecol. 92<\/b>, fiw120 (2016).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Hausmann, K. Extrusive organelles in protists. Int. Rev. Cytol. 52<\/b>, 197\u2013276 (1978).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Tice, A. K., et al. PhyloFisher: a phylogenomic package for resolving eukaryotic relationships. PLoS Biol. 19<\/b>, e3001365 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Banos, H. et al. GTRpmix: a linked general time-reversible model for profile mixture models. Mol. Biol. Evol. 41<\/b>, msae174 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Si Quang, L., Gascuel, O. & Lartillot, N. Empirical profile mixture models for phylogenetic reconstruction. Bioinformatics 24<\/b>, 2317\u20132323 (2008).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Shimodaira, H. An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 51<\/b>, 492\u2013508 (2002).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Torruella, G., Galindo, L. J., Moreira, D. & L\u00f3pez-Garc\u00eda, P. Phylogenomics of neglected flagellated protists supports a revised eukaryotic tree of life. Curr. Biol. 35<\/b>, 198\u2013207 (2025).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Lartillot, N. & Philippe, H. Improvement of molecular phylogenetic inference and the phylogeny of Bilateria. Phil. Trans. R. Soc. B 363<\/b>, 1463\u20131472 (2008).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Cranford-Smith, T. & Huber, D. The way is the goal: how SecA transports proteins across the cytoplasmic membrane in bacteria. FEMS Microbiol. Lett. 365<\/b>, fny093 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Petr\u016f, M., Dohn\u00e1lek, V., F\u00fcssy, Z. & Dole\u017eal, P. Fates of Sec, Tat, and YidC translocases in mitochondria and other eukaryotic compartments. Mol. Biol. Evol. 38<\/b>, 5241\u20135254 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Smets, D., Loos, M. S., Karamanou, S. & Economou, A. Protein transport across the bacterial plasma membrane by the Sec pathway. Protein J. 38<\/b>, 262\u2013273 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Hsieh, Y. et al. SecA alone can promote protein translocation and ion channel activity. J. Biol. Chem. 286<\/b>, 44702\u201344709 (2011).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Hsieh, Y. et al. Dissecting structures and functions of SecA-only protein-conducting channels: ATPase, pore structure, ion channel activity, protein translocation, and interaction with SecYEG\/SecDF\u2022YajC. PLoS One 12<\/b>, e0178307 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    K\u00f6stlbacher, S., Panagiotou, K., Tamarit, D. & Ettema, T. J. G. WitChi: Efficient detection and pruning of compositional bias in phylogenomic alignments using empirical chi-squared testing. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2025.07.14.663642<\/a> (2025).<\/p>\n<\/li>\n

  • \n

    Tong, J. et al. Ancestral and derived protein import pathways in the mitochondrion of Reclinomonas americana. Mol. Biol. Evol. 28<\/b>, 1581\u20131591 (2011).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Dembech, E. et al. Identification of hidden associations among eukaryotic genes through statistical analysis of coevolutionary transitions. Proc. Natl Acad. Sci. USA 120<\/b>, e2218329120 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Alto, L. T. & Terman, J. R. in Semaphorin Signaling: Methods in Molecular Biology Vol. 1493 (ed. Terman, J. R.) 1\u201325 (Springer, 2017).<\/p>\n<\/li>\n

  • \n

    Hochstrasser, M. Origin and function of ubiquitin-like proteins. Nature 458<\/b>, 422\u2013429 (2009).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Pereira, R. V. et al. Ubiquitin-specific proteases are differentially expressed throughout the Schistosoma mansoni life cycle. Parasit. Vectors 8<\/b>, 349 (2015).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Burge, R. J., Damianou, A., Wilkinson, A. J., Rodenko, B. & Mottram, J. C. Leishmania differentiation requires ubiquitin conjugation mediated by a UBC2\u2013UEV1 E2 complex. PLoS Pathog. 16<\/b>, e1008784 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Rizos, I., Frada, M. J., Bittner, L. & Not, F. Life cycle strategies in free-living unicellular eukaryotes: diversity, evolution, and current molecular tools to unravel the private life of microorganisms. J. Eukaryot. Microbiol. 71<\/b>, e13052 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Hofstatter, P. G., Brown, M. W. & Lahr, D. J. G. Comparative genomics supports sex and meiosis in diverse Amoebozoa. Genome Biol. Evol. 10<\/b>, 3118\u20133128 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Sibbald, S. J. & Archibald, J. M. More protist genomes needed. Nat. Ecol. Evol. 1<\/b>, 0145 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Valt, M. & Hrub\u00e1, P. Chemical fixation of Solarion arienae for transmission electron microscopy. protocols.io https:\/\/doi.org\/10.17504\/protocols.io.kxygxyd5zl8j\/v2<\/a> (2024).<\/p>\n<\/li>\n

  • \n

    Valt, M. HPF-FS of Solarion arienae for transmission electron microscopy. protocols.io https:\/\/doi.org\/10.17504\/protocols.io.dm6gpzp15lzp\/v2<\/a> (2024).<\/p>\n<\/li>\n

  • \n

    Mastronarde, D. N. Automated electron microscope tomography using robust prediction of specimen movements. J. Struct. Biol. 152<\/b>, 36\u201351 (2005).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Mastronarde, D. N. & Held, S. R. Automated tilt series alignment and tomographic reconstruction in IMOD. J. Struct. Biol. 197<\/b>, 102\u2013113 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9<\/b>, 676\u2013682 (2012).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Bodian, D. A new method for staining nerve fibers and nerve endings in mounted paraffin sections. Anat. Rec. 65<\/b>, 89\u201397 (1936).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Nie, D. Morphology and taxonomy of the intestinal protozoa of the guinea-pig, Cavia porcella. J. Morphol. 86<\/b>, 381\u2013493 (1950).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Valt, M. & Kotyk, M. Permanent specimen preparation by protargol staining. protocols.io https:\/\/doi.org\/10.17504\/protocols.io.q26g71or9gwz\/v1<\/a> (2024).<\/p>\n<\/li>\n

  • \n

    Medlin, L., Elwood, H. J., Stickel, S. & Sogin, M. L. The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene 71<\/b>, 491\u2013499 (1988).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat. Biotechnol. 29<\/b>, 644\u2013652 (2011).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Bushmanova, E., Antipov, D., Lapidus, A. & Prjibelski, A. D. rnaSPAdes: a de novo transcriptome assembler and its application to RNA-seq data. GigaScience 8<\/b>, giz100 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30<\/b>, 772\u2013780 (2013).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Criscuolo, A. & Gribaldo, S. BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol. Biol. 10<\/b>, 210 (2010).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Minh, B. Q. et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37<\/b>, 1530\u20131534 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2 \u2013 approximately maximum-likelihood trees for large alignments. PLoS One 5<\/b>, e9490 (2010).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Guillou, L. et al. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy. Nucleic Acids Res. 41<\/b>, D597\u2013D604 (2012).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Capella-Guti\u00e9rrez, S., Silla-Mart\u00ednez, J. M. & Gabald\u00f3n, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25<\/b>, 1972\u20131973 (2009).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., Von Haeseler, A. & Jermiin, L. S. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat. Methods 14<\/b>, 587\u2013589 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Rio, D. C., Ares, M., Hannon, G. J. & Nilsen, T. W. Purification of RNA using TRIzol (TRI Reagent). Cold Spring Harb. Protoc. https:\/\/doi.org\/10.1101\/pdb.prot5439<\/a> (2010).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Fu, L., Niu, B., Zhu, Z., Wu, S. & Li, W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28<\/b>, 3150\u20133152 (2012).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Lafond-Lapalme, J., Duceppe, M.-O., Wang, S., Moffett, P. & Mimee, B. A new method for decontamination of de novo transcriptomes using a hierarchical clustering algorithm. Bioinformatics 33<\/b>, 1293\u20131300 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Cantalapiedra, C. P., Hern\u00e1ndez-Plaza, A., Letunic, I., Bork, P. & Huerta-Cepas, J. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol. Biol. Evol. 38<\/b>, 5825\u20135829 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Huerta-Cepas, J. et al. EggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 47<\/b>, D309\u2013D314 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    P\u00e1nek, T. et al. A new lineage of non-photosynthetic green algae with extreme organellar genomes. BMC Biol. 20<\/b>, 66 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30<\/b>, 2114\u20132120 (2014).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Kolmogorov, M. et al. metaFlye: scalable long-read metagenome assembly using repeat graphs. Nat. Methods 17<\/b>, 1103\u20131110 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Hu, J., Fan, J., Sun, Z. & Liu, S. NextPolish: a fast and efficient genome polishing tool for long-read assembly. Bioinformatics 36<\/b>, 2253\u20132255 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows\u2013Wheeler transform. Bioinformatics 25<\/b>, 1754\u20131760 (2009).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19<\/b>, 455\u2013477 (2012).<\/p>\n

    Article<\/a>\u00a0
    \n     MathSciNet<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Wu, Y.-W., Simmons, B. A. & Singer, S. W. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics 32<\/b>, 605\u2013607 (2016).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Kang, D. D. et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ 7<\/b>, e7359 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Gurevich, A., Saveliev, V., Vyahhi, N. & Tesler, G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29<\/b>, 1072\u20131075 (2013).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Manni, M., Berkeley, M. R., Seppey, M. & Zdobnov, E. M. BUSCO: assessing genomic data quality and beyond. Curr. Protoc. 1<\/b>, e323 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Challis, R., Richards, E., Rajan, J., Cochrane, G. & Blaxter, M. BlobToolKit \u2013 interactive quality assessment of genome assemblies. G3 10, 1361\u20131374 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Gabriel, L. et al. BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA. Genome Res. 34<\/b>, 769\u2013777 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Smit, A. F. A., Hubley, R. & Green, P. RepeatMasker Open-4.0 http:\/\/www.repeatmasker.org<\/a> (2013\u20132015).<\/p>\n<\/li>\n

  • \n

    Flynn, J. M. et al. RepeatModeler2 for automated genomic discovery of transposable element families. Proc. Natl Acad. Sci. USA 117<\/b>, 9451\u20139457 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Kim, D., Paggi, J. M., Park, C., Bennett, C. & Salzberg, S. L. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat. Biotechnol. 37<\/b>, 907\u2013915 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Danecek, P. et al. Twelve years of SAMtools and BCFtools. GigaScience 10<\/b>, giab008 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Tegenfeldt, F. et al. OrthoDB and BUSCO update: annotation of orthologs with wider sampling of genomes. Nucleic Acids Res. 53<\/b>, D516\u2013D522 (2025).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Sim\u00e3o, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31<\/b>, 3210\u20133212 (2015).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Huang, N. & Li, H. compleasm: a faster and more accurate reimplementation of BUSCO. Bioinformatics 39<\/b>, btad595 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Gabriel, L., Hoff, K. J., Br\u016fna, T., Borodovsky, M. & Stanke, M. TSEBRA: transcript selector for BRAKER. BMC Bioinformatics 22<\/b>, 566 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Br\u016fna, T., Gabriel, L. & Hoff, K. J. in Insect Genomics: Methods in Molecular Biology Vol. 2935 (eds Bonizzoni, M. & Ometto, L.) 67\u2013107 (Springer, 2025).<\/p>\n<\/li>\n

  • \n

    Jones, R. E. et al. Create, analyze, and visualize phylogenomic datasets using PhyloFisher. Curr. Protoc. 4<\/b>, e969 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Wang, H.-C., Minh, B. Q., Susko, E. & Roger, A. J. Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate phylogenomic estimation. Syst. Biol. 67<\/b>, 216\u2013235 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Anisimova, M., Gil, M., Dufayard, J.-F., Dessimoz, C. & Gascuel, O. Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes. Syst. Biol. 60<\/b>, 685\u2013699 (2011).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Guindon, S. et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59<\/b>, 307\u2013321 (2010).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Kishino, H., Miyata, T. & Hasegawa, M. Maximum likelihood inference of protein phylogeny and the origin of chloroplasts. J. Mol. Evol. 31<\/b>, 151\u2013160 (1990).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Susko, E., Field, C., Blouin, C. & Roger, A. J. Estimation of rates-across-sites distributions in phylogenetic substitution models. Syst. Biol. 52<\/b>, 594\u2013603 (2003).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Comte, A. et al. PhylteR: efficient identification of outlier sequences in phylogenomic datasets. Mol. Biol. Evol. 40, msad234 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Shen, X.-X., Hittinger, C. T. & Rokas, A. Contentious relationships in phylogenomic studies can be driven by a handful of genes. Nat. Ecol. Evol. 1<\/b>, 0126 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Huson, D. H. et al. Dendroscope: an interactive viewer for large phylogenetic trees. BMC Bioinformatics 8<\/b>, 460 (2007).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Lang, B. F. et al. Mitochondrial genome annotation with MFannot: a critical analysis of gene identification and gene model prediction. Front. Plant Sci. 14<\/b>, 1222186 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinformatics 10<\/b>, 421 (2009).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Zimmermann, L. et al. A completely reimplemented MPI bioinformatics toolkit with a new HHpred server at its core. J. Mol. Biol. 430<\/b>, 2237\u20132243 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Chan, P. P. & Lowe, T. M. in Gene Prediction: Methods in Molecular Biology Vol. 1962 (ed. Kollmar, M.) 1\u201314 (Springer, 2019).<\/p>\n<\/li>\n

  • \n

    Teufel, F. et al. SignalP 6.0 predicts all five types of signal peptides using protein language models. Nat. Biotechnol. 40<\/b>, 1023\u20131025 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Abramson, J. et al. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature 630<\/b>, 493\u2013500 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Pettersen, E. F. et al. UCSF Chimera\u2014a visualization system for exploratory research and analysis. J. Comput. Chem. 25<\/b>, 1605\u20131612 (2004).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Steinegger, M. & S\u00f6ding, J. Clustering huge protein sequence sets in linear time. Nat. Commun. 9<\/b>, 2542 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Richter, D. J. et al. EukProt: a database of genome-scale predicted proteins across the diversity of eukaryotes. Peer Community J. 2<\/b>, e56 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Soding, J., Biegert, A. & Lupas, A. N. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 33<\/b>, W244\u2013W248 (2005).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Krogh, A., Larsson, B., Von Heijne, G. & Sonnhammer, E. L. L. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305<\/b>, 567\u2013580 (2001).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Liu, Y., Schmidt, B. & Maskell, D. L. MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities. Bioinformatics 26<\/b>, 1958\u20131964 (2010).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Nguyen, L. T., Schmidt, H. A., Von Haeseler, A. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32<\/b>, 268\u2013274 (2015).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Hoang, D. T., Chernomor, O., Von Haeseler, A., Minh, B. Q. & Vinh, L. S. UFBoot2: improving the ultrafast bootstrap approximation. Mol. Biol. Evol. 35<\/b>, 518\u2013522 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Lartillot, N., Rodrigue, N., Stubbs, D. & Richer, J. PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment. Syst. Biol. 62<\/b>, 611\u2013615 (2013).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Sun, J. et al. OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes. Nucleic Acids Res. 51<\/b>, W397\u2013W403 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Emms, D. M. & Kelly, S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 20<\/b>, 238 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Tang, S., Lomsadze, A. & Borodovsky, M. Identification of protein coding regions in RNA transcripts. Nucleic Acids Res. 43<\/b>, e78 (2015).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Blum, M. et al. InterPro: the protein sequence classification resource in 2025. Nucleic Acids Res. 53<\/b>, D444\u2013D456 (2025).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Valt, M. et al. Molecular and supplementary data of Solarion arienae. Figshare https:\/\/doi.org\/10.6084\/m9.figshare.27182820<\/a> (2025).<\/p>\n<\/li>\n

  • \n

    Bertrand, D. et al. Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes. Nat. Biotechnol. 37<\/b>, 937\u2013944 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Zimin, A. V. et al. The MaSuRCA genome assembler. Bioinformatics 29<\/b>, 2669\u20132677 (2013).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Di Genova, A., Buena-Atienza, E., Ossowski, S. & Sagot, M. F. Efficient hybrid de novo assembly of human genomes with WENGAN. Nat. Biotechnol. 39<\/b>, 422\u2013430 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Field, H. I., Coulson, R. M. & Field, M. C. An automated graphics tool for comparative genomics: the Coulson plot generator. BMC Bioinformatics 14<\/b>, 141 (2013).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n","protected":false},"excerpt":{"rendered":"Lax, G. et al. Hemimastigophora is a novel supra-kingdom-level lineage of eukaryotes. Nature 564, 410\u2013414 (2018). Article\u00a0 CAS\u00a0…\n","protected":false},"author":3,"featured_media":391077,"comment_status":"","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[8],"tags":[186051,10046,24070,186052,10047,57092,159,76619,67,132,68],"class_list":{"0":"post-391076","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-science","8":"tag-classification-and-taxonomy","9":"tag-humanities-and-social-sciences","10":"tag-microbiology","11":"tag-mitochondrial-genome","12":"tag-multidisciplinary","13":"tag-phylogenetics","14":"tag-science","15":"tag-taxonomy","16":"tag-united-states","17":"tag-unitedstates","18":"tag-us"},"share_on_mastodon":{"url":"https:\/\/pubeurope.com\/@us\/115579300320426935","error":""},"_links":{"self":[{"href":"https:\/\/www.europesays.com\/us\/wp-json\/wp\/v2\/posts\/391076","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.europesays.com\/us\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.europesays.com\/us\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/us\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/us\/wp-json\/wp\/v2\/comments?post=391076"}],"version-history":[{"count":0,"href":"https:\/\/www.europesays.com\/us\/wp-json\/wp\/v2\/posts\/391076\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/us\/wp-json\/wp\/v2\/media\/391077"}],"wp:attachment":[{"href":"https:\/\/www.europesays.com\/us\/wp-json\/wp\/v2\/media?parent=391076"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.europesays.com\/us\/wp-json\/wp\/v2\/categories?post=391076"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.europesays.com\/us\/wp-json\/wp\/v2\/tags?post=391076"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}