Annotated genes and nonannotated genomes: cross-species use of Gene Ontology in ecology and evolution research

Primmer, C. R., Papakostas, S., Leder, E. H., Davis, M. J. and Ragan, M. A. (2013) Annotated genes and nonannotated genomes: cross-species use of Gene Ontology in ecology and evolution research. Molecular Ecology, 22 12: 3216-3241. doi:10.1111/mec.12309


Author Primmer, C. R.
Papakostas, S.
Leder, E. H.
Davis, M. J.
Ragan, M. A.
Title Annotated genes and nonannotated genomes: cross-species use of Gene Ontology in ecology and evolution research
Journal name Molecular Ecology   Check publisher's open access policy
ISSN 0962-1083
1365-294X
Publication date 2013-06-01
Year available 2013
Sub-type Article (original research)
DOI 10.1111/mec.12309
Open Access Status Not yet assessed
Volume 22
Issue 12
Start page 3216
End page 3241
Total pages 26
Place of publication Oxford, United Kingdom
Publisher Wiley-Blackwell
Language eng
Abstract Recent advances in molecular technologies have opened up unprecedented opportunities for molecular ecologists to better understand the molecular basis of traits of ecological and evolutionary importance in almost any organism. Nevertheless, reliable and systematic inference of functionally relevant information from these masses of data remains challenging. The aim of this review is to highlight how the Gene Ontology (GO) database can be of use in resolving this challenge. The GO provides a largely species-neutral source of information on the molecular function, biological role and cellular location of tens of thousands of gene products. As it is designed to be species-neutral, the GO is well suited for cross-species use, meaning that, functional annotation derived from model organisms can be transferred to inferred orthologues in newly sequenced species. In other words, the GO can provide gene annotation information for species with nonannotated genomes. In this review, we describe the GO database, how functional information is linked with genes/gene products in model organisms, and how molecular ecologists can utilize this information to annotate their own data. Then, we outline various applications of GO for enhancing the understanding of molecular basis of traits in ecologically relevant species. We also highlight potential pitfalls, provide step-by-step recommendations for conducting a sound study in nonmodel organisms, suggest avenues for future research and outline a strategy for maximizing the benefits of a more ecological and evolutionary genomics-oriented ontology by ensuring its compatibility with the GO.
Keyword Gene annotation
Genomics
Ontology
Proteomics
Transcriptomics
Q-Index Code C1
Q-Index Status Confirmed Code
Grant ID 137710
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2014 Collection
Institute for Molecular Bioscience - Publications
 
Versions
Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 36 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 36 times in Scopus Article | Citations
Google Scholar Search Google Scholar
Created: Sun, 21 Jul 2013, 10:05:52 EST by System User on behalf of Institute for Molecular Bioscience