A standardized archaeal taxonomy for the Genome Taxonomy Database (original) (raw)
Woese, C. R. & Fox, G. E. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl Acad. Sci. USA74, 5088–5090 (1977). ArticleCASPubMedPubMed Central Google Scholar
Gribaldo, S. & Brochier-Armanet, C. The origin and evolution of Archaea: a state of the art. Philos. Trans. R. Soc. Lond. B Biol. Sci.361, 1007–1022 (2006). ArticleCASPubMedPubMed Central Google Scholar
Zuo, G., Xu, Z. & Hao, B. Phylogeny and taxonomy of Archaea: a comparison of the whole-genome-based CVTree approach with 16S rRNA sequence analysis. Life5, 949–968 (2015). ArticleCASPubMedPubMed Central Google Scholar
Woese, C. R., Kandler, O. & Wheelis, M. L. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl Acad. Sci. USA87, 4576–4579 (1990). ArticleCASPubMedPubMed Central Google Scholar
Adam, P. S., Borrel, G., Brochier-Armanet, C. & Gribaldo, S. The growing tree of Archaea: new perspectives on their diversity, evolution and ecology. ISME J.https://doi.org/10.1038/ismej.2017.122 (2017).
Baker, B. J. et al. Diversity, ecology and evolution of Archaea. Nat. Microbiol.5, 887–900 (2020). ArticlePubMed Google Scholar
Spang, A., Caceres, E. F. & Ettema, T. J. G. Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life. Science357, eaaf3883 (2017). ArticlePubMed Google Scholar
Barns, S. M., Delwiche, C. F., Palmer, J. D. & Pace, N. R. Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc. Natl Acad. Sci. USA93, 9188–9193 (1996). ArticleCASPubMedPubMed Central Google Scholar
Huber, H. et al. A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature417, 63–67 (2002). ArticleCASPubMed Google Scholar
Hallam, S. J. et al. Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. Proc. Natl Acad. Sci. USA103, 18296–18301 (2006). ArticleCASPubMedPubMed Central Google Scholar
Brochier-Armanet, C., Boussau, B., Gribaldo, S. & Forterre, P. Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nat. Rev. Microbiol.6, 245–252 (2008). ArticleCASPubMed Google Scholar
Nunoura, T. et al. Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group. Nucleic Acids Res.39, 3204–3223 (2011). ArticleCASPubMed Google Scholar
Kozubal, M. A. et al. Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park. ISME J.7, 622–634 (2013). ArticleCASPubMed Google Scholar
Meng, J. et al. Genetic and functional properties of uncultivated MCG Archaea assessed by metagenome and gene expression analyses. ISME J.8, 650–659 (2014). ArticleCASPubMed Google Scholar
Guy, L., Spang, A., Saw, J. H. & Ettema, T. J. G. ‘Geoarchaeote NAG1’ is a deeply rooting lineage of the archaeal order Thermoproteales rather than a new phylum. ISME J.8, 1353–1357 (2014). ArticleCASPubMedPubMed Central Google Scholar
Guy, L. & Ettema, T. J. G. The archaeal ‘TACK’ superphylum and the origin of eukaryotes. Trends Microbiol.19, 580–587 (2011). ArticleCASPubMed Google Scholar
Vanwonterghem, I. et al. Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota. Nat. Microbiol.1, 16170 (2016). ArticleCASPubMed Google Scholar
Rinke, C. et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature499, 431–437 (2013).
Zaremba-Niedzwiedzka, K. et al. Asgard Archaea illuminate the origin of eukaryotic cellular complexity. Nature541, 353–358 (2017). ArticleCASPubMed Google Scholar
Castelle, C. J. et al. Genomic expansion of domain Archaea highlights roles for organisms from new phyla in anaerobic carbon cycling. Curr. Biol.16, 690–701 (2015). Article Google Scholar
Probst, A. J. et al. Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface. Nat. Microbiol.3, 328–336 (2018). ArticleCASPubMedPubMed Central Google Scholar
Probst, A. J. et al. Biology of a widespread uncultivated archaeon that contributes to carbon fixation in the subsurface. Nat. Commun.5, 5497 (2014). ArticleCASPubMed Google Scholar
Seitz, K. W., Lazar, C. S., Hinrichs, K.-U., Teske, A. P. & Baker, B. J. Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction. ISME J.10, 1696–1705 (2016). ArticleCASPubMedPubMed Central Google Scholar
Petitjean, C., Deschamps, P., López-García, P. & Moreira, D. Rooting the domain Archaea by phylogenomic analysis supports the foundation of the new kingdom Proteoarchaeota. Genome Biol. Evol.7, 191–204 (2014). ArticlePubMedPubMed Central Google Scholar
Petitjean, C., Deschamps, P., López-García, 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, 1242–1254 (2015). ArticleCASPubMed Google Scholar
Parker, C. T., Tindall, B. J. & Garrity, G. M. International Code of Nomenclature of Prokaryotes. Int. J. Syst. Evol. Microbiol.69, S1–S111 (2019). Article Google Scholar
Oren, A. et al. Proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes. Int. J. Syst. Evol. Microbiol.65, 4284–4287 (2015). ArticleCASPubMed Google Scholar
Whitman, W. B. Modest proposals to expand the type material for naming of prokaryotes. Int. J. Syst. Evol. Microbiol.66, 2108–2112 (2016). ArticleCASPubMed Google Scholar
Chuvochina, M. et al. The importance of designating type material for uncultured taxa. Syst. Appl. Microbiol.42, 15–21 (2019). ArticlePubMed Google Scholar
Murray, R. G. E. & Stackebrandt, E. Taxonomic note: implementation of the provisional status Candidatus for incompletely described procaryotes. Int. J. Syst. Evol. Microbiol.45, 186–187 (1995). CAS Google Scholar
Oren, A. A plea for linguistic accuracy—also for Candidatus taxa. Int. J. Syst. Evolut. Microbiol.67, 1085–1094 (2017). Article Google Scholar
Parks, D. H. et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat. Biotechnol.36, 996–1004 (2018). ArticleCASPubMed Google Scholar
Parks, D. H. et al. A complete domain-to-species taxonomy for Bacteria and Archaea. Nat. Biotechnol.38, 1079–1086 (2020). ArticleCASPubMed Google Scholar
Haft, D. H. et al. RefSeq: an update on prokaryotic genome annotation and curation. Nucleic Acids Res.46, D851–D860 (2018). ArticleCASPubMed Google Scholar
Parks, D. H. et al. A complete domain-to-species taxonomy for Bacteria and Archaea. Nat. Biotechnol.38, 1079–1086 (2020).
Parks, D. H. et al. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat. Microbiol.2, 1533–1542 (2017). ArticleCASPubMed Google Scholar
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, 216–235 (2018). ArticleCASPubMed Google Scholar
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, 268–274 (2015). ArticleCASPubMed Google Scholar
Marin, J., Battistuzzi, F. U., Brown, A. C. & Hedges, S. B. The timetree of prokaryotes: new insights into their evolution and speciation. Mol. Biol. Evol.34, 437–446 (2017). CASPubMed Google Scholar
Sieber, C. M. K. et al. Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nat. Microbiol.3, 836–843 (2018). ArticleCASPubMedPubMed Central Google Scholar
Dombrowski, N. et al. Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution. Nat. Commun.11, 3939 (2020). ArticleCASPubMedPubMed Central Google Scholar
Galtier, N. & Lobry, J. R. Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes. J. Mol. Evol.44, 632–636 (1997). ArticleCASPubMed Google Scholar
Segata, N., Börnigen, D., Morgan, X. C. & Huttenhower, C. PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nat. Commun.4, 2304 (2013). ArticlePubMed Google Scholar
Ali, R. H., Bogusz, M. & Whelan, S. Identifying clusters of high confidence homologies in multiple sequence alignments. Mol. Biol. Evol.36, 2340–2351 (2019). ArticleCASPubMedPubMed Central Google Scholar
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, 210 (2010). ArticlePubMedPubMed Central Google Scholar
Raymann, K., Brochier-Armanet, C. & Gribaldo, S. The two-domain tree of life is linked to a new root for the Archaea. Proc. Natl Acad. Sci. USA112, 6670–6675 (2015). ArticleCASPubMedPubMed Central Google Scholar
Williams, T. A. et al. Integrative modeling of gene and genome evolution roots the archaeal tree of life. Proc. Natl Acad. Sci. USA114, E4602–E4611 (2017). ArticleCASPubMedPubMed Central Google Scholar
Whitman, W. B. et al. Proposal of the suffix –ota to denote phyla. Addendum to ‘Proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes’. Int. J. Syst. Evol. Microbiol.68, 967–969 (2018). ArticlePubMed Google Scholar
Jungbluth, S. P., Amend, J. P. & Rappé, M. S. Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids. Sci. Data4, sdata201737 (2017).
Reysenbach, A.-L. Class I. Thermoprotei class. nov. in Bergey’s Manual of Systematic Bacteriology Volume 1: The Archaea and the Deeply Branching and Phototrophic Bacteria (eds Garrity, G. et al.) 169–210 (Springer Verlag, 2001).
Stieglmeier, M. et al. Nitrososphaera viennensis gen. nov., sp. nov., an aerobic and mesophilic, ammonia-oxidizing archaeon from soil and a member of the archaeal phylum Thaumarchaeota. Int. J. Syst. Evol. Microbiol.64, 2738–2752 (2014). ArticleCASPubMedPubMed Central Google Scholar
Elkins, J. G. et al. A korarchaeal genome reveals insights into the evolution of the Archaea. Proc. Natl Acad. Sci. USA105, 8102–8107 (2008). ArticleCASPubMedPubMed Central Google Scholar
Oren, A., Garrity, G. M., Parker, C. T., Chuvochina, M. & Trujillo, M. E. Lists of names of prokaryotic Candidatus taxa. Int. J. Syst. Evol. Microbiol.https://doi.org/10.1099/ijsem.0.003789 (2020).
Fuchs, T., Huber, H., Burggraf, S. & Stetter, K. O. 16S rDNA-based phylogeny of the archaeal order Sulfolobales and reclassification of Desulfurolobus ambivalens as Acidianus ambivalens comb. nov. Syst. Appl. Microbiol.19, 56–60 (1996). ArticleCAS Google Scholar
Quehenberger, J., Shen, L., Albers, S.-V., Siebers, B. & Spadiut, O. _Sulfolobus_—a potential key organism in future biotechnology. Front. Microbiol8, 2474 (2017). ArticlePubMedPubMed Central Google Scholar
Minegishi, H. et al. Further refinement of the phylogeny of the Halobacteriaceae based on the full-length RNA polymerase subunit B′ (rpoB′) gene. Int. J. Syst. Evol. Microbiol.60, 2398–2408 (2010). ArticlePubMed Google Scholar
Sorokin, D. Y. et al. Natronolimnobius sulfurireducens sp. nov. and Halalkaliarchaeum desulfuricum gen. nov., sp. nov., the first sulfur-respiring alkaliphilic Haloarchaea from hypersaline alkaline lakes. Int. J. Syst. Evol. Microbiol.69, 2662–2673 (2019). ArticleCASPubMed Google Scholar
Sorokin, D. Y. et al. Sulfur respiration in a group of facultatively anaerobic natronoarchaea ubiquitous in hypersaline soda lakes. Front. Microbiol.9, 2359 (2018). ArticlePubMedPubMed Central Google Scholar
Mendler, K. et al. AnnoTree: visualization and exploration of a functionally annotated microbial tree of life. Nucleic Acids Res.https://doi.org/10.1093/nar/gkz246 (2019).
Chaumeil, P.-A., Mussig, A. J., Hugenholtz, P. & Parks, D. H. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformaticshttps://doi.org/10.1093/bioinformatics/btz848 (2019).
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, 1043–1055 (2015). ArticleCASPubMedPubMed Central Google Scholar
McDonald, D. et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of Bacteria and Archaea. ISME J.6, 610–618 (2012). ArticleCASPubMed Google Scholar
Kalvari, I. et al. Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families. Nucleic Acids Res.46, D335–D342 (2018). ArticleCASPubMed Google Scholar
Nawrocki, E. Structural RNA Homology Search and Alignment Using Covariance Models PhD thesis, Washington Univ. St Louis (2009).
Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2—approximately maximum-likelihood trees for large alignments. PLoS ONE5, e9490 (2010). ArticlePubMedPubMed Central Google Scholar
Kozlov, A. M., Aberer, A. J. & Stamatakis, A. ExaML version 3: a tool for phylogenomic analyses on supercomputers. Bioinformatics31, 2577–2579 (2015). ArticleCASPubMedPubMed Central Google Scholar
Lartillot, N. & Philippe, H. A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol. Biol. Evol.21, 1095–1109 (2004). ArticleCASPubMed Google Scholar
Zhou, X., Shen, X.-X., Hittinger, C. T. & Rokas, A. Evaluating fast maximum likelihood-based phylogenetic programs using empirical phylogenomic data sets. Mol. Biol. Evol.35, 486–503 (2018). ArticleCASPubMed Google Scholar
Quang, L. S., Gascuel, O. & Lartillot, N. Empirical profile mixture models for phylogenetic reconstruction. Bioinformatics24, 2317–2323 (2008). ArticleCAS Google Scholar
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol.30, 772–780 (2013). ArticleCASPubMedPubMed Central Google Scholar
Robinson, D. F. & Foulds, L. R. Comparison of phylogenetic trees. Math. Biosci.53, 131–147 (1981). Article Google Scholar
Kupczok, A., Schmidt, H. A. & von Haeseler, A. Accuracy of phylogeny reconstruction methods combining overlapping gene data sets. Algorithms Mol. Biol.5, 37 (2010). ArticlePubMedPubMed Central Google Scholar
Letunic, I. & Bork, P. Interactive tree of life (iTOL) v4: recent updates and new developments. Nucleic Acids Res.47, W256–W259 (2019). ArticleCASPubMedPubMed Central Google Scholar