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A daily-updated tree of (sequenced) life as a reference for genome research

Fang, Hai; Oates, Matt E.; Pethica, Ralph B.; Greenwood, Jenny M.; Sardar, Adam J.; Rackham, Owen J. L.; Donoghue, Philip C. J.; Stamatakis, Alexandros; Lima Morais, David A. de; Gough, Julian


We report a daily-updated sequenced/species Tree Of Life (sTOL) as a reference for the increasing number of cellular organisms with their genomes sequenced. The sTOL builds on a likelihood-based weight calibration algorithm to consolidate NCBI taxonomy information in concert with unbiased sampling of molecular characters from whole genomes of all sequenced organisms. Via quantifying the extent of agreement between taxonomic and molecular data, we observe there are many potential improvements that can be made to the status quo classification, particularly in the Fungi kingdom; we also see that the current state of many animal genomes is rather poor. To augment the use of sTOL in providing evolutionary contexts, we integrate an ontology infrastructure and demonstrate its utility for evolutionary understanding on: nuclear receptors, stem cells and eukaryotic genomes. The sTOL ( sTOL) provides a binary tree of (sequenced) life, and contributes to an analytical platform linking genome evolution, function and phenotype.

Verlagsausgabe §
DOI: 10.5445/IR/1000064375
Veröffentlicht am 09.05.2018
DOI: 10.1038/srep02015
Zitationen: 40
Web of Science
Zitationen: 33
Zitationen: 47
Cover der Publikation
Zugehörige Institution(en) am KIT Institut für Theoretische Informatik (ITI)
Publikationstyp Zeitschriftenaufsatz
Publikationsjahr 2013
Sprache Englisch
Identifikator ISSN: 2045-2322
KITopen-ID: 1000064375
Erschienen in Scientific reports
Verlag Nature Research
Band 3
Seiten Art. Nr.: 2015
Schlagwörter Phylogenetics, Databases, Classification and Taxonomy, Taxonomy
Nachgewiesen in Web of Science
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