All Animals Are Not Equal: Some Genomes Are More Equal Than Others

Among vertebrate species, the human and mouse genome assemblies are the most complete and extensively annotated.  The HUGO Gene Nomenclature Committee (HGNC) and the Mouse Genomic Nomenclature Committee (MGNC), in collaboration with the research community, have established a parallel nomenclature for protein-coding genes across these two genomes.  This standardised nomenclature has also been adopted by the only other existing gene nomenclature committees for vertebrate species: rat, chicken, Anolis, Xenopus and zebrafish.  There a number of other vertebrate species, such as dog, pig and cow, which have established research communities and good quality genome assemblies, but are currently without a dedicated nomenclature committee. As a result orthologous genes in these species may be named inconsistently, and there is a risk of information about these genes being difficult to retrieve.  To solve this problem, the HGNC hosted the “Gene Nomenclature Across Species” meeting in 2009, which included invited representatives from vertebrate and comparative genomics projects.  All delegates agreed that consensus gene naming, based on HGNC nomenclature, should be extended to other vertebrate genomes and that the HGNC should coordinate this work.

The HGNC already maintains the HCOP tool that aggregates orthology predictions between human and model organisms from a range of external data sources.  We will expand this tool to create 1:1 ortholog pair datasets between human and other vertebrates, using chimp, dog and pig as prototypes, in order to map HGNC symbols to these genes.  Complex gene families where orthology is difficult to determine will require specialised community consultation.  We will initially collaborate with experts from the olfactory receptor and cytochrome P450 communities to produce cross-species nomenclature schemas for these gene families.  We plan to create a vertebrate gene nomenclature portal, GeneFam, to present these data.

Our intention is that the benefit of standardised gene nomenclature is not restricted to human and other select genomes but instead should eventually be extended to encompass all vertebrates.

If you have questions or comments, please contact us at hgnc@genenames.org or visit www.genenames.org.