The chicken gene nomenclature committee report

Chicken is the foremost non-mammalian vertebrate biomedical model organism and it is a principal biomedical model for understanding basic biology, behaviour and disease. As the de facto model bird genome, chicken also occupies a unique and important evolutionary niche and chicken is often used in comparative and evolutionary genomics. Comparative research using chicken has made seminal contributions to understanding infectious disease, cancer, cell biology, embryology, gene regulation, immunology, and nutrition. However, lack of standardized gene nomenclature prevents researchers from exploiting the full potential of the chicken for comparative and functional genomic studies. Currently, chicken genes are published under more than one name and one name sometimes refers to unrelated genes. Moreover, a large number of chicken genes were predicted during the final stages of the chicken genomic sequence assembly based on sequence similarity to known (mammalian) genes, chicken ESTs and de novo prediction [1]. Updates of gene models and gene prediction pipelines from different sources have compounded this problem. Standardized nomenclature will facilitate communication between scientists and enable comparative biology studies.

The HUGO Gene Nomenclature Committee (HGNC) approves a unique short-form abbreviation (gene symbol) and a longer descriptive name for human genes [2]. Gene symbols are unique Latin letters and Arabic numerals (<7 characters) that facilitate computation. The longer descriptive gene name aims to convey the character or function of the gene and yet be concise. Assigning names and the unique short abbreviations necessitates corresponding with authors, reading the literature and performing data analyses. When possible the symbol used in publications is retained but if the symbol has already been used for another gene or if the gene is a member of a gene family an alternative symbol is approved. Interspecies nomenclature confusion is avoided by assigning the same gene symbol to orthologous genes.

Since chicken is the model avian genome, determining core orthologs that exist between avian and mammalian species is particularly informative [1, 3–6]. The utility of standardized orthologous gene names is one of the strongest arguments for approved nomenclature and cooperation between the nomenclature committees of different species. Analyzing comparative maps without standardized gene nomenclature is difficult. Despite a proposal for a standardized chicken gene nomenclature in 1995 [7], it wasn't until the 2007 Chicken Development Meeting (April, Barcelona, Spain) that a Chicken Gene Nomenclature and Annotation Workshop was convened to create a pipeline for standardizing chicken nomenclature. A Chicken Gene Nomenclature Committee (CGNC) had been formed several years earlier and NCBI recognizes the CGNC as the official chicken gene naming entity. At the 2008 Avian Genome Meeting, Ensembl representatives also adopted HGNC approved nomenclature for genes with direct human orthologs and for which Ensembl and NCBI concur regarding their identity.

The chicken research community formally embraced standardized gene nomenclature more than a decade ago [7]. In keeping with HGNC guidelines, chicken genes will be assigned a unique gene symbol and gene name in consultation with researchers and in concordance with assigned human gene nomenclature, where such nomenclature exists for human:chicken ortholog pairs. The CGNC will work closely with existing vertebrate gene nomenclature committees and both HGNC and Mouse Gene Nomenclature Committee (MGNC) representatives serve as advisors on the CGNC. Current HGNC guidelines http://www.genenames.org/guidelines.html state that gene names should be brief and specific and should convey the character or function of the gene, the first letter of the symbol should be the same as that of the name in order to facilitate alphabetical listing and grouping, gene names should follow American spelling and tissue specificity and molecular weight designations should be avoided. Gene symbols must be unique, be representative of the descriptive gene name, should contain only Latin letters and Arabic numerals, should not contain punctuation, should not contain "G" for gene, and should not contain any reference to species (eg. "c" or "ch" for chicken).

The CGNC database aims to capture aliases or synonyms for chicken genes. In many cases where a standardized gene name is applied to a chicken gene there will be other names used to report this gene – often based on separate reports of the gene in published literature. By making this data available, researchers will be able to better find and evaluate available literature for the gene(s) they are studying.

Traditionally, where human genes names are based on orthology to other species, the name of the originating species is included in the gene name. However, due to the increasing number of sequenced species and use of orthologs to assign nomenclature, CGNC will not denote species in assigning gene names. For example the human gene name for HGNC:30387 is vitelline membrane outer layer 1 homolog (chicken) and in chicken this will become vitelline membrane outer layer 1.

The chicken genome has become the "foundation reference genome" for assembly and annotation of genome sequences for all archosaurs. Both turkey and zebra finch are undergoing genome sequencing (turkey because of its importance as an agricultural species and as a biomedical model for aging, while zebra finch is a biomedical model for behaviour and vocalization). Genome sequencing of these avian species utilizes chicken genome information to facilitate assembly and annotation. EST projects are already underway for additional bird species (eg. quail and condor) and in the three to five year timeframe, it is likely that sequencing of additional bird genomes will be undertaken. Moreover, comparative genetics studies in other archosaur species, including crocodile and alligator, are leveraging chicken gene information. Chicken's importance as a reference genome for these non-mammalian species underlines the fundamental importance of chicken in increasing numbers comparative genomics studies. Standardized gene nomenclature for chicken serves as a stepping off point for many other non-mammalian species.

Although work to provide standardized nomenclature for chicken genes is ongoing, the CGNC relies on the support of the research community. Only with community input and support will gene nomenclature be relevant for community needs, facilitate comparative biology and promote data exchange among both researchers and public resources. Researchers may submit comments, erratum and suggestions or requests for gene names to genenames@roslin.ed.ac.uk. The CGNC will publish regular reports of progress and calls for working groups to study gene families at avian conferences and using avian newsgroups.