Experimental-confirmation and functional-annotation of predicted proteins in the chicken genome

Abstract

Background: The chicken genome was sequenced because of its phylogenetic position as a non-mammalian vertebrate, its use as a biomedical model especially to study embryology and development, its role as a source of human disease organisms and its importance as the major source of animal derived food protein. However, genomic sequence data is, in itself, of limited value; generally it is not equivalent to understanding biological function. The benefit of having a genome sequence is that it provides a basis for functional genomics. However, the sequence data currently available is poorly structurally and functionally annotated and many genes do not have standard nomenclature assigned.

Results: We analysed eight chicken tissues and improved the chicken genome structural annotation by providing experimental support for the in vivo expression of 7,809 computationally predicted proteins, including 30 chicken proteins that were only electronically predicted or hypothetical translations in human. To improve functional annotation (based on Gene Ontology), we mapped these identified proteins to their human and mouse orthologs and used this orthology to transfer Gene Ontology (GO) functional annotations to the chicken proteins. The 8,213 orthology-based GO annotations that we produced represent an 8% increase in currently available chicken GO annotations. Orthologous chicken products were also assigned standardized nomenclature based on current chicken nomenclature guidelines.

Conclusion: We demonstrate the utility of high-throughput expression proteomics for rapid experimental structural annotation of a newly sequenced eukaryote genome. These experimentally-supported predicted proteins were further annotated by assigning the proteins with standardized nomenclature and functional annotation. This method is widely applicable to a diverse range of species. Moreover, information from one genome can be used to improve the annotation of other genomes and inform gene prediction algorithms.

Figure 1

Chicken predicted proteins identified from different tissues. Proteomic based analysis was used to demonstrate the in vivo expression of electronically predicted chicken proteins. (A) The number of predicted chicken proteins identified from each tissue, with the proportion of proteins that were identified in more than one tissue indicated. (B) The majority of proteins were identified in more than one tissue.

Figure 2

Chicken – human/mouse orthologs. (A) The number of identified predicted proteins that had either human or mouse 1:1 orthologs. (B) Distribution of orthologs identified by different orthology prediction methods. The 4 most commonly used ortholog prediction tools are Homologene, Ensembl, InParanoid and Treefam. Human/mouse orthologs were identified for 77% of the identified chicken proteins (see additional file 3).

Figure 3

Overview of cellular component transferred to orthologous chicken predicted proteins. The GO annotations are summarized to broad terms of cellular component. These GO annotations are publicly available via the AgBase database [4].

Figure 4

Overview of molecular function transferred to orthologous chicken predicted proteins. The GO annotations are summarized to broad terms of molecular function. These GO annotations are publicly available via the AgBase database [4].

Figure 5

Overview of biological processes transferred to orthologous chicken predicted proteins. The GO annotations are summarized to broad terms of biological processes. These GO annotations are publicly available via the AgBase database [4].