Toward automatic reconstruction of a highly resolved tree of life

Francesca D Ciccarelli; Tobias Doerks; Christian von Mering; Christopher J Creevey; Berend Snel; Peer Bork

doi:10.1126/science.1123061

Toward automatic reconstruction of a highly resolved tree of life

Francesca D Ciccarelli, Tobias Doerks, Christian von Mering, Christopher J Creevey, Berend Snel, Peer Bork

Department of Life Sciences

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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.

Original language	English
Pages (from-to)	1283-1287
Number of pages	5
Journal	Science
Volume	311
Issue number	5765
DOIs	https://doi.org/10.1126/science.1123061
Publication status	Published - Mar 2006

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Toward automatic reconstruction of a highly resolved tree of lifeAccepted author manuscript, 1.59 MB

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title = "Toward automatic reconstruction of a highly resolved tree of life",

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.",

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note = "Ciccarelli, F. D., Doerks, T., von Mering, C., Creevey, C. J., Snel, B., Bork, P. (2006). Toward automatic reconstruction of a highly resolved tree of life. Science, 311 (5765), 1283-1287",

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AU - Ciccarelli, Francesca D

AU - Doerks, Tobias

AU - von Mering, Christian

AU - Creevey, Christopher J

AU - Snel, Berend

AU - Bork, Peer

N1 - Ciccarelli, F. D., Doerks, T., von Mering, C., Creevey, C. J., Snel, B., Bork, P. (2006). Toward automatic reconstruction of a highly resolved tree of life. Science, 311 (5765), 1283-1287

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N2 - 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.

AB - 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.

UR - http://hdl.handle.net/2160/26318

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JO - Science

JF - Science

IS - 5765

ER -

Toward automatic reconstruction of a highly resolved tree of life

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