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

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 o...

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Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6504836/
https://www.ncbi.nlm.nih.gov/pubmed/23778980
http://dx.doi.org/10.1038/srep02015
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author 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
author_facet 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
author_sort Fang, Hai
collection PubMed
description 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.
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spelling pubmed-65048362019-05-21 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 Sci Rep Article 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. Nature Publishing Group 2013-06-18 /pmc/articles/PMC6504836/ /pubmed/23778980 http://dx.doi.org/10.1038/srep02015 Text en Copyright © 2013, Macmillan Publishers Limited. All rights reserved http://creativecommons.org/licenses/by-nc-nd/3.0/ This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-nd/3.0/
spellingShingle Article
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
A daily-updated tree of (sequenced) life as a reference for genome research
title A daily-updated tree of (sequenced) life as a reference for genome research
title_full A daily-updated tree of (sequenced) life as a reference for genome research
title_fullStr A daily-updated tree of (sequenced) life as a reference for genome research
title_full_unstemmed A daily-updated tree of (sequenced) life as a reference for genome research
title_short A daily-updated tree of (sequenced) life as a reference for genome research
title_sort daily-updated tree of (sequenced) life as a reference for genome research
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6504836/
https://www.ncbi.nlm.nih.gov/pubmed/23778980
http://dx.doi.org/10.1038/srep02015
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