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Verlagsausgabe
DOI: 10.5445/IR/1000064375
Veröffentlicht am 09.05.2018
Originalveröffentlichung
DOI: 10.1038/srep02015
Scopus
Zitationen: 31
Web of Science
Zitationen: 22

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; de Lima Morais, David A.; Gough, Julian

Abstract:
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 (http://supfam.org/SUPERFAMILY/ sTOL) provides a binary tree of (sequenced) life, and contributes to an analytical platform linking genome evolution, function and phenotype.


Zugehörige Institution(en) am KIT Institut für Theoretische Informatik (ITI)
Publikationstyp Zeitschriftenaufsatz
Jahr 2013
Sprache Englisch
Identifikator ISSN: 2045-2322
URN: urn:nbn:de:swb:90-643751
KITopen ID: 1000064375
Erschienen in Scientific reports
Band 3
Seiten Art. Nr.: 2015
Schlagworte Phylogenetics, Databases, Classification and Taxonomy, Taxonomy
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