A Daily-updated Tree of (sequenced) Life As a Reference for Genome Research

Overview

Journal Sci Rep

Specialty Science

Date 2013 Jun 20

PMID 23778980

Citations 25

Authors

Hai Fang

Matt E 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

Affiliations

Soon will be listed here.

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.

Citing Articles

Protein structures unravel the signatures and patterns of deep time evolution.

Harish A QRB Discov. 2024; 5:e3.

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Iterative Variable Gene Discovery from Whole Genome Sequencing with a Bootstrapped Multiresolution Algorithm.

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The SUPERFAMILY 2.0 database: a significant proteome update and a new webserver.

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What is an archaeon and are the Archaea really unique?.

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