{"id":433337,"date":"2026-02-19T02:27:08","date_gmt":"2026-02-19T02:27:08","guid":{"rendered":"https:\/\/www.newsbeep.com\/uk\/433337\/"},"modified":"2026-02-19T02:27:08","modified_gmt":"2026-02-19T02:27:08","slug":"oxygen-metabolism-in-descendants-of-the-archaeal-eukaryotic-ancestor","status":"publish","type":"post","link":"https:\/\/www.newsbeep.com\/uk\/433337\/","title":{"rendered":"Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor"},"content":{"rendered":"

Vosseberg, J. et al. The emerging view on the origin and early evolution of eukaryotic cells. Nature 633, 295\u2013305 (2024).<\/p>\n

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

Eme, L. et al. Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes. Nature 618, 992\u2013999 (2023).<\/p>\n

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

Spang, A. et al. Proposal of the reverse flow model for the origin of the eukaryotic cell based on comparative analyses of Asgard archaeal metabolism. Nat. Microbiol. 4, 1138\u20131148 (2019).<\/p>\n

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

Tamarit, D. et al. Description of Asgardarchaeum abyssi gen. nov. spec. nov., a novel species within the class Asgardarchaeia and phylum Asgardarchaeota in accordance with the SeqCode. Syst. Appl. Microbiol. 47, 126525 (2024).<\/p>\n

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

Spang, A. et al. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 521, 173\u2013179 (2015).<\/p>\n

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

Zaremba-Niedzwiedzka, K. et al. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 541, 353\u2013358 (2017).<\/p>\n

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

Martin, W. & M\u00fcller, M. The hydrogen hypothesis for the first eukaryote. Nature 392, 37\u201341 (1998).<\/p>\n

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

L\u00f3pez-Garc\u00eda, P. & Moreira, D. The Syntrophy hypothesis for the origin of eukaryotes revisited. Nat. Microbiol. 5, 655\u2013667 (2020).<\/p>\n

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

Moreira, D. & Lopez-Garcia, P. Symbiosis between methanogenic archaea and delta-proteobacteria as the origin of eukaryotes: the syntrophic hypothesis. J. Mol. Evol. 47, 517\u2013530 (1998).<\/p>\n

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

Imachi, H. et al. Isolation of an archaeon at the prokaryote-eukaryote interface. Nature 577, 519\u2013525 (2020).<\/p>\n

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

Rodrigues-Oliveira, T. et al. Actin cytoskeleton and complex cell architecture in an Asgard archaeon. Nature 613, 332\u2013339 (2023).<\/p>\n

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

Imachi, H. et al. Eukaryotes\u2019 closest relatives are internally simple syntrophic archaea. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2025.02.26.640444<\/a> (2025).<\/p>\n

Zhang, J. et al. Deep origin of eukaryotes outside Heimdallarchaeia within Asgardarchaeota. Nature 642, 990\u2013998 (2025).<\/p>\n

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

Mahendrarajah, T. A. et al. ATP synthase evolution on a cross-braced dated tree of life. Nat. Commun. 14, 7456 (2023).<\/p>\n

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

Martijn, J., Vosseberg, J., Guy, L., Offre, P. & Ettema, T. J. G. Deep mitochondrial origin outside the sampled alphaproteobacteria. Nature 557, 101\u2013105 (2018).<\/p>\n

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

Mu\u00f1oz-G\u00f3mez, S. A. et al. Site-and-branch-heterogeneous analyses of an expanded dataset favour mitochondria as sister to known Alphaproteobacteria. Nat. Ecol. Evol. 6, 253\u2013262 (2022).<\/p>\n

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

Lyons, T. W., Reinhard, C. T. & Planavsky, N. J. The rise of oxygen in Earth\u2019s early ocean and atmosphere. Nature 506, 307\u2013315 (2014).<\/p>\n

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

Lyons, T. W., Diamond, C. W., Planavsky, N. J., Reinhard, C. T. & Li, C. Oxygenation, life, and the planetary system during earth\u2019s middle history: an overview. Astrobiology 21, 906\u2013923 (2021).<\/p>\n

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

Bulzu, P.-A. et al. Casting light on Asgardarchaeota metabolism in a sunlit microoxic niche. Nat. Microbiol. 4, 1129\u20131137 (2019).<\/p>\n

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

Liu, Y. et al. Expanded diversity of Asgard archaea and their relationships with eukaryotes. Nature 593, 553\u2013557 (2021).<\/p>\n

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

Mu\u00f1oz-G\u00f3mez, S. A. Energetics and evolution of anaerobic microbial eukaryotes. Nat. Microbiol. 8, 197\u2013203 (2023).<\/p>\n

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

Sousa, F. L., Neukirchen, S., Allen, J. F., Lane, N. & Martin, W. F. Lokiarchaeon is hydrogen dependent. Nat. Microbiol. 1, 16034 (2016).<\/p>\n

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

Dombrowski, N., Teske, A. P. & Baker, B. J. Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments. Nat. Commun. 9, 4999 (2018).<\/p>\n

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

Li, M. et al. Active bacterial and archaeal communities in coastal sediments: Biogeography pattern, assembly process and co-occurrence relationship. Sci. Total Environ. 750, 142252 (2021).<\/p>\n

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

Guo, X., Li, Y., Song, G., Zhao, L. & Wang, J. Adaptation of Archaeal communities to summer hypoxia in the sediment of Bohai Sea. Ecol. Evol. 15, e70768 (2025).<\/p>\n

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

Gong, X. et al. New globally distributed bacterial phyla within the FCB superphylum. Nat. Commun. 13, 7516 (2022).<\/p>\n

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

Langwig, M. V. et al. Large-scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups. ISME J. 16, 307\u2013320 (2021).<\/p>\n

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

Gong, X. et al. Contrasting archaeal and bacterial community assembly processes and the importance of rare taxa along a depth gradient in shallow coastal sediments. Sci. Total Environ. 852, 158411 (2022).<\/p>\n

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

K\u00f6stlbacher, S. et al. Prediction of eukaryotic cellular complexity in Asgard archaea using structural modelling. Nat. Microbiol. https:\/\/doi.org\/10.1038\/s41564-026-02273-y<\/a> (2026).<\/p>\n

Williams, T. A., Cox, C. J., Foster, P. G., Sz\u00f6ll\u0151si, G. J. & Embley, T. M. Phylogenomics provides robust support for a two-domains tree of life. Nat. Ecol. Evol. 4, 138\u2013147 (2020).<\/p>\n

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

Tully, B. J., Graham, E. D. & Heidelberg, J. F. The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans. Sci. Data 5, 170203 (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

Rodriguez-R, L. M., Tsementzi, D., Luo, C. & Konstantinidis, K. T. Iterative subtractive binning of freshwater chronoseries metagenomes identifies over 400 novel species and their ecologic preferences. Environ. Microbiol. 22, 3394\u20133412 (2020).<\/p>\n

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

Glasl, B. et al. Comparative genome-centric analysis reveals seasonal variation in the function of coral reef microbiomes. ISME J. 14, 1435\u20131450 (2020).<\/p>\n

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

Rezaei Somee, M. et al. Distinct microbial community along the chronic oil pollution continuum of the Persian Gulf converge with oil spill accidents. Sci. Rep. 11, 11316 (2021).<\/p>\n

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

Barnum, T. P. et al. Predicting microbial growth conditions from amino acid composition. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2024.03.22.586313<\/a> (2024).<\/p>\n

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

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

Stairs, C. W. et al. Chlamydial contribution to anaerobic metabolism during eukaryotic evolution. Sci. Adv. 6, eabb7258 (2020).<\/p>\n

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

Geiger, O., Sanchez-Flores, A., Padilla-Gomez, J. & Degli Esposti, M. Multiple approaches of cellular metabolism define the bacterial ancestry of mitochondria. Sci. Adv. 9, eadh0066 (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

Mills, D. B. et al. Eukaryogenesis and oxygen in Earth history. Nat. Ecol. Evol. 6, 520\u2013532 (2022).<\/p>\n

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

Woodcroft, B. J. et al. Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper. Nat. Biotechnol. https:\/\/doi.org\/10.1038\/s41587-025-02738-1<\/a> (2025).<\/p>\n

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

Yu, H., Schut, G. J., Haja, D. K., Adams, M. W. W. & Li, H. Evolution of complex I-like respiratory complexes. J. Biol. Chem. 296, 100740 (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

Greening, C. et al. Minimal and hybrid hydrogenases are active from archaea. Cell 187, 3357\u20133372.e19 (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

Valentin-Alvarado, L. E. et al. Asgard archaea modulate potential methanogenesis substrates in wetland soil. Nat. Commun. 15, 6384 (2024).<\/p>\n

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

Yu, H. et al. Structure of an ancient respiratory system. Cell 173, 1636\u20131649.e16 (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

Zhu, J., Vinothkumar, K. R. & Hirst, J. Structure of mammalian respiratory complex I. Nature 536, 354\u2013358 (2016).<\/p>\n

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

Baradaran, R., Berrisford, J. M., Minhas, G. S. & Sazanov, L. A. Crystal structure of the entire respiratory complex I. Nature 494, 443\u2013448 (2013).<\/p>\n

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

Schuller, J. M. et al. Structural adaptations of photosynthetic complex I enable ferredoxin-dependent electron transfer. Science 363, 257\u2013260 (2019).<\/p>\n

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

Kravchuk, V. et al. A universal coupling mechanism of respiratory complex I. Nature 609, 808\u2013814 (2022).<\/p>\n

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

Chadwick, G. L., Hemp, J., Fischer, W. W. & Orphan, V. J. Convergent evolution of unusual complex I homologs with increased proton pumping capacity: energetic and ecological implications. ISME J. 12, 2668\u20132680 (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

Rinke, C. et al. A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.). ISME J. 13, 663\u2013675 (2019).<\/p>\n

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

Banci, L., Bertini, I., Cavallaro, G. & Rosato, A. The functions of Sco proteins from genome-based analysis. J. Proteome Res. 6, 1568\u20131579 (2007).<\/p>\n

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

Gribaldo, S., Talla, E. & Brochier-Armanet, C. Evolution of the haem copper oxidases superfamily: a rooting tale. Trends Biochem. Sci. 34, 375\u2013381 (2009).<\/p>\n

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

Alcott, L. J., Mills, B. J. W., Bekker, A. & Poulton, S. W. Earth\u2019s Great Oxidation Event facilitated by the rise of sedimentary phosphorus recycling. Nat. Geosci. 15, 210\u2013215 (2022).<\/p>\n

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

Canfield, D. E. Carbon cycle evolution before and after the Great Oxidation of the atmosphere. Am. J. Sci. 321, 297\u2013331 (2021).<\/p>\n

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

Riedman, L. A., Porter, S. M., Lechte, M. A., dos Santos, A. & Halverson, G. P. Early eukaryotic microfossils of the late Palaeoproterozoic Limbunya Group, Birrindudu Basin, northern Australia. Pap. Palaeontol. 9, e1538 (2023).<\/p>\n

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

Seitz, K. W. et al. Asgard archaea capable of anaerobic hydrocarbon cycling. Nat. Commun. 10, 1822 (2019).<\/p>\n

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

Martin, W. F. et al. Late Mitochondrial Origin Is an Artifact. Genome Biol. Evol. 9, 373\u2013379 (2017).<\/p>\n

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

Pittis, A. A. & Gabald\u00f3n, T. Late acquisition of mitochondria by a host with chimaeric prokaryotic ancestry. Nature 531, 101\u2013104 (2016).<\/p>\n

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

Ettema, T. J. G. Evolution: mitochondria in the second act. Nature 531, 39\u201340 (2016).<\/p>\n

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

Agi\u0107, H. in Prebiotic Chemistry and the Origin of Life (eds Neubeck, A. & McMahon, S.) 255\u2013289 (Springer, 2021).<\/p>\n

Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884\u2013i890 (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, D., Liu, C.-M., Luo, R., Sadakane, K. & Lam, T.-W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31, 1674\u20131676 (2015).<\/p>\n

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

Alneberg, J. et al. Binning metagenomic contigs by coverage and composition. Nat. Methods 11, 1144\u20131146 (2014).<\/p>\n

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

Kang, D. D. et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ 7, 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

Uritskiy, G. V., DiRuggiero, J. & Taylor, J. MetaWRAP\u2014a flexible pipeline for genome-resolved metagenomic data analysis. Microbiome 6, 158 (2018).<\/p>\n

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

Sieber, C. M. K. et al. Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nat. Microbiol. 3, 836\u2013843 (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

Karst, S. M., Kirkegaard, R. H. & Albertsen, M. mmgenome: a toolbox for reproducible genome extraction from metagenomes. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/059121<\/a> (2016).<\/p>\n

Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043\u20131055 (2015).<\/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

Hugoson, E., Lam, W. T. & Guy, L. miComplete: weighted quality evaluation of assembled microbial genomes. Bioinformatics 36, 936\u2013937 (2020).<\/p>\n

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

De Anda, V. et al. MEBS, a software platform to evaluate large (meta)genomic collections according to their metabolic machinery: unraveling the sulfur cycle. Gigascience 6, gix096 (2017).<\/p>\n

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

Shen, W., Le, S., Li, Y. & Hu, F. SeqKit: a cross-platform and ultrafast toolkit for FASTA\/Q file manipulation. PLoS ONE 11, e0163962 (2016).<\/p>\n

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

Aroney, S. T. N. et al. CoverM: read alignment statics for metagenomics. Bioinformatics 41, btaf147 (2025).<\/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

Chaumeil, P.-A., Mussig, A. J., Hugenholtz, P. & Parks, D. H. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 36, 1925\u20131927 (2020).<\/p>\n

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

Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010).<\/p>\n

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

Rawlings, N. D., Barrett, A. J. & Bateman, A. MEROPS: the peptidase database. Nucleic Acids Res. 38, D227\u2013D233 (2010).<\/p>\n

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

Hern\u00e1ndez-Plaza, A. et al. eggNOG 6.0: enabling comparative genomics across 12 535 organisms. Nucleic Acids Res. 51, D389\u2013D394 (2023).<\/p>\n

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

S\u00f8ndergaard, D., Pedersen, C. N. S. & Greening, C. HydDB: a web tool for hydrogenase classification and analysis. Sci. Rep. 6, 34212 (2016).<\/p>\n

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

Hunter, S. et al. InterPro: the integrative protein signature database. Nucleic Acids Res. 37, D211\u2013D215 (2009).<\/p>\n

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

Sayers, E. W. et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 39, D38\u2013D51 (2011).<\/p>\n

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

Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068\u20132069 (2014).<\/p>\n

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

Parks, D. H. et al. GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Res. 50, D785\u2013D794 (2022).<\/p>\n

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

Parks, D. H. et al. Author Correction: recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat. Microbiol. 3, 253 (2018).<\/p>\n

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

Sch\u00e4ffer, A. A. et al. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res. 29, 2994\u20133005 (2001).<\/p>\n

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

Petitjean, C., Deschamps, P., L\u00f3pez-Garc\u00eda, P., Moreira, D. & Brochier-Armanet, C. Extending the conserved phylogenetic core of archaea disentangles the evolution of the third domain of life. Mol. Biol. Evol. 32, 1242\u20131254 (2015).<\/p>\n

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

Deorowicz, S., Debudaj-Grabysz, A. & Gudy\u015b, A. FAMSA: fast and accurate multiple sequence alignment of huge protein families. Sci. Rep. 6, 33964 (2016).<\/p>\n

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

Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 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

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, 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

Minh, B. Q. et al. Corrigendum to: IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 2461 (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

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, 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

Hoang, D. T., Chernomor, O., von Haeseler, A., Minh, B. Q. & Vinh, L. S. UFBoot2: improving the ultrafast bootstrap approximation. Mol. Biol. Evol. 35, 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

Guindon, S. et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 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

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, 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

Susko, E. & Roger, A. J. On reduced amino acid alphabets for phylogenetic inference. Mol. Biol. Evol. 24, 2139\u20132150 (2007).<\/p>\n

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

Steenwyk, J. L. et al. BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data. Genetics 221, iyac079 (2022).<\/p>\n

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

Olm, M. R., Brown, C. T., Brooks, B. & Banfield, J. F. dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 11, 2864\u20132868 (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

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

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

Contreras-Moreira, B. & Vinuesa, P. GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. Appl. Environ. Microbiol. 79, 7696\u20137701 (2013).<\/p>\n

Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583\u2013589 (2021).<\/p>\n

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

Evans, R. et al. Protein complex prediction with AlphaFold-Multimer. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2021.10.04.463034<\/a> (2022).<\/p>\n

Mirdita, M. et al. ColabFold: making protein folding accessible to all. Nat. Methods 19, 679\u2013682 (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

Mirdita, M., Steinegger, M. & S\u00f6ding, J. MMseqs2 desktop and local web server app for fast, interactive sequence searches. Bioinformatics 35, 2856\u20132858 (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

Berman, H. M. et al. The Protein Data Bank. Nucleic Acids Res. 28, 235\u2013242 (2000).<\/p>\n

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

van Kempen, M. et al. Fast and accurate protein structure search with Foldseek. Nat. Biotechnol. 42, 243\u2013246 (2024).<\/p>\n

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

Dong, R., Peng, Z., Zhang, Y. & Yang, J. mTM-align: an algorithm for fast and accurate multiple protein structure alignment. Bioinformatics 34, 1719\u20131725 (2018).<\/p>\n

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

Pettersen, E. F. et al. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30, 70\u201382 (2021).<\/p>\n

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

Appler, K. E. et al. Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor. Figshare https:\/\/figshare.com\/s\/f139faeb05653d1adf6b<\/a> (2026).<\/p>\n","protected":false},"excerpt":{"rendered":"Vosseberg, J. et al. The emerging view on the origin and early evolution of eukaryotic cells. Nature 633,…\n","protected":false},"author":2,"featured_media":433338,"comment_status":"","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[7],"tags":[7952,4390,59,4230,4231,90,56,54,55],"class_list":["post-433337","post","type-post","status-publish","format-standard","has-post-thumbnail","category-science","tag-biodiversity","tag-evolution","tag-gb","tag-humanities-and-social-sciences","tag-multidisciplinary","tag-science","tag-uk","tag-united-kingdom","tag-unitedkingdom"],"_links":{"self":[{"href":"https:\/\/www.newsbeep.com\/uk\/wp-json\/wp\/v2\/posts\/433337","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.newsbeep.com\/uk\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.newsbeep.com\/uk\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/uk\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/uk\/wp-json\/wp\/v2\/comments?post=433337"}],"version-history":[{"count":0,"href":"https:\/\/www.newsbeep.com\/uk\/wp-json\/wp\/v2\/posts\/433337\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/uk\/wp-json\/wp\/v2\/media\/433338"}],"wp:attachment":[{"href":"https:\/\/www.newsbeep.com\/uk\/wp-json\/wp\/v2\/media?parent=433337"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.newsbeep.com\/uk\/wp-json\/wp\/v2\/categories?post=433337"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.newsbeep.com\/uk\/wp-json\/wp\/v2\/tags?post=433337"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}