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

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

Animals, Computational Biology/methods, Databases, Genetic/standards, Genome, Genomics/methods, Internet, Phylogeny
2045-2322
2015
Fang, Hai
58424580-2d92-4db2-934f-4c393989cea9
Oates, Matt E
c90996e2-2ae0-4784-9633-a1db986b1831
Pethica, Ralph B
61b397b6-421a-4a53-a103-16d4e44b38f9
Greenwood, Jenny M
00df7dba-f7a5-4088-b44c-b34a2e44df68
Sardar, Adam J
5792acdf-ef01-4d60-9482-ad4948b36683
Rackham, Owen J L
8122eb1f-6e9f-4da5-90e1-ce108ccbbcbf
Donoghue, Philip C J
5f3fdb63-0685-40b8-aa87-d71353474db2
Stamatakis, Alexandros
2634dded-0e0a-452d-8bf0-4c50177f75a8
de Lima Morais, David A
137185a3-88f7-4750-a5e8-dc30625ba808
Gough, Julian
019ed039-9fd4-45d6-aa7a-12a8fcf7245c
Fang, Hai
58424580-2d92-4db2-934f-4c393989cea9
Oates, Matt E
c90996e2-2ae0-4784-9633-a1db986b1831
Pethica, Ralph B
61b397b6-421a-4a53-a103-16d4e44b38f9
Greenwood, Jenny M
00df7dba-f7a5-4088-b44c-b34a2e44df68
Sardar, Adam J
5792acdf-ef01-4d60-9482-ad4948b36683
Rackham, Owen J L
8122eb1f-6e9f-4da5-90e1-ce108ccbbcbf
Donoghue, Philip C J
5f3fdb63-0685-40b8-aa87-d71353474db2
Stamatakis, Alexandros
2634dded-0e0a-452d-8bf0-4c50177f75a8
de Lima Morais, David A
137185a3-88f7-4750-a5e8-dc30625ba808
Gough, Julian
019ed039-9fd4-45d6-aa7a-12a8fcf7245c

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 and Gough, Julian (2013) A daily-updated tree of (sequenced) life as a reference for genome research. Scientific Reports, 3, 2015. (doi:10.1038/srep02015).

Record type: Article

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.

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More information

Published date: 2013
Keywords: Animals, Computational Biology/methods, Databases, Genetic/standards, Genome, Genomics/methods, Internet, Phylogeny

Identifiers

Local EPrints ID: 446540
URI: http://eprints.soton.ac.uk/id/eprint/446540
ISSN: 2045-2322
PURE UUID: 1d8a185e-a910-4e43-9cbc-7c1946da7597
ORCID for Owen J L Rackham: ORCID iD orcid.org/0000-0002-4390-0872

Catalogue record

Date deposited: 12 Feb 2021 17:32
Last modified: 17 Mar 2024 04:03

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Contributors

Author: Hai Fang
Author: Matt E Oates
Author: Ralph B Pethica
Author: Jenny M Greenwood
Author: Adam J Sardar
Author: Philip C J Donoghue
Author: Alexandros Stamatakis
Author: David A de Lima Morais
Author: Julian Gough

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