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

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

*Corresponding author for this work

Research output: Contribution to journalArticle (Academic Journal)peer-review

36 Citations (Scopus)

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.

Original languageEnglish
Article number2015
Pages (from-to)2015
Number of pages10
JournalScientific Reports
Volume3
DOIs
Publication statusPublished - 18 Jun 2013

Keywords

  • HIDDEN MARKOV-MODELS
  • PROTEOMES
  • SUPERFAMILY
  • ASSIGNMENT
  • DATABASE
  • PATTERNS
  • RECONSTRUCTION
  • PHYLOGENY
  • PROTEIN DOMAINS
  • EVOLUTION

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