Toward automatic reconstruction of a highly resolved tree of life - PubMed (original) (raw)
. 2006 Mar 3;311(5765):1283-7.
doi: 10.1126/science.1123061.
Affiliations
- PMID: 16513982
- DOI: 10.1126/science.1123061
Free article
Toward automatic reconstruction of a highly resolved tree of life
Francesca D Ciccarelli et al. Science. 2006.
Free article
Erratum in
- Science. 2006 May 5;312(5774):697
Abstract
We have developed an automatable procedure for reconstructing the tree of life with branch lengths comparable across all three domains. The tree has its basis in a concatenation of 31 orthologs occurring in 191 species with sequenced genomes. It revealed interdomain discrepancies in taxonomic classification. Systematic detection and subsequent exclusion of products of horizontal gene transfer increased phylogenetic resolution, allowing us to confirm accepted relationships and resolve disputed and preliminary classifications. For example, we place the phylum Acidobacteria as a sister group of delta-Proteobacteria, support a Gram-positive origin of Bacteria, and suggest a thermophilic last universal common ancestor.
Similar articles
- Phylogenetic signal in the eukaryotic tree of life.
Sanderson MJ. Sanderson MJ. Science. 2008 Jul 4;321(5885):121-3. doi: 10.1126/science.1154449. Science. 2008. PMID: 18599787 - Estimation of phylogenetic inconsistencies in the three domains of life.
Soria-Carrasco V, Castresana J. Soria-Carrasco V, et al. Mol Biol Evol. 2008 Nov;25(11):2319-29. doi: 10.1093/molbev/msn176. Epub 2008 Aug 12. Mol Biol Evol. 2008. PMID: 18701430 - Phylogenetics and the cohesion of bacterial genomes.
Daubin V, Moran NA, Ochman H. Daubin V, et al. Science. 2003 Aug 8;301(5634):829-32. doi: 10.1126/science.1086568. Science. 2003. PMID: 12907801 - Ancient gene transfer as a tool in phylogenetic reconstruction.
Huang J, Gogarten JP. Huang J, et al. Methods Mol Biol. 2009;532:127-39. doi: 10.1007/978-1-60327-853-9_7. Methods Mol Biol. 2009. PMID: 19271182 Review. - Birth of the domains Bacteria, Archaea and Eucarya and of major taxa within them: a hypothesis.
Zorzopulos J. Zorzopulos J. Rev Argent Microbiol. 2003 Oct-Dec;35(4):175-82. Rev Argent Microbiol. 2003. PMID: 14976868 Review.
Cited by
- CoCoPyE: feature engineering for learning and prediction of genome quality indices.
Birth N, Leppich N, Schirmacher J, Andreae N, Steinkamp R, Blanke M, Meinicke P. Birth N, et al. Gigascience. 2024 Jan 2;13:giae079. doi: 10.1093/gigascience/giae079. Gigascience. 2024. PMID: 39452613 Free PMC article. - Expanded diversity of Asgard archaea and their relationships with eukaryotes.
Liu Y, Makarova KS, Huang WC, Wolf YI, Nikolskaya AN, Zhang X, Cai M, Zhang CJ, Xu W, Luo Z, Cheng L, Koonin EV, Li M. Liu Y, et al. Nature. 2021 May;593(7860):553-557. doi: 10.1038/s41586-021-03494-3. Epub 2021 Apr 28. Nature. 2021. PMID: 33911286 Free PMC article. - Small secreted peptides encoded on the wheat (triticum aestivum L.) genome and their potential roles in stress responses.
Tian D, Xie Q, Deng Z, Xue J, Li W, Zhang Z, Dai Y, Zheng B, Lu T, De Smet I, Guo Y. Tian D, et al. Front Plant Sci. 2022 Sep 21;13:1000297. doi: 10.3389/fpls.2022.1000297. eCollection 2022. Front Plant Sci. 2022. PMID: 36212358 Free PMC article. - NCBI prokaryotic genome annotation pipeline.
Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. Tatusova T, et al. Nucleic Acids Res. 2016 Aug 19;44(14):6614-24. doi: 10.1093/nar/gkw569. Epub 2016 Jun 24. Nucleic Acids Res. 2016. PMID: 27342282 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources