Abstract
BackgroundWith the rapid growth in the availability of genome sequence data, the automated identification of orthologous genes between species (orthologs) is of fundamental importance to facilitate functional annotation and studies on comparative and evolutionary genomics. Genes with no apparent orthologs between the bovine and human genome may be responsible for major differences between the species, however, such genes are often neglected in functional genomics studies.ResultsA BLAST-based method was exploited to explore the current annotation and orthology predictions in Ensembl. Genes with no orthologs between the two genomes were classified into groups based on alignments, ontology, manual curation and publicly available information. Starting from a high quality and specific set of orthology predictions, as provided by Ensembl, hidden relationship between genes and genomes of different mammalian species were unveiled using a highly sensitive approach, based on sequence similarity and genomic comparison.ConclusionsThe analysis identified 3,801 bovine genes with no orthologs in human and 1010 human genes with no orthologs in cow, among which 411 and 43 genes, respectively, had no match at all in the other species. Most of the apparently non-orthologous genes may potentially have orthologs which were missed in the annotation process, despite having a high percentage of identity, because of differences in gene length and structure. The comparative analysis reported here identified gene variants, new genes and species-specific features and gave an overview of the other side of orthology which may help to improve the annotation of the bovine genome and the knowledge of structural differences between species.
Highlights
With the rapid growth in the availability of genome sequence data, the automated identification of orthologous genes between species is of fundamental importance to facilitate functional annotation and studies on comparative and evolutionary genomics
In this work we developed a BLAST-based method to explore the current annotation of the bovine genome and to describe those genes that were classified as being nonorthologous between bovine and other mammalian species, according to Ensembl classification
The data used here consisted of genes found to be non-orthologous between cow and human which were further filtered to constitute a core of mammalian orthologs by adding to the comparison the gene sets of mouse and dog, currently the most complete mammalian genomes in terms of sequence information [35,36]
Summary
With the rapid growth in the availability of genome sequence data, the automated identification of orthologous genes between species (orthologs) is of fundamental importance to facilitate functional annotation and studies on comparative and evolutionary genomics. With the rapid increase in the amount of genome sequence data available, the automated identification of orthologous genes between species becomes of fundamental importance to facilitate functional annotation and for comparative or evolutionary genomics. Orthologs typically retain similar domain architecture and function and such conservation is an important component in comparative analysis as well as in the annotation of proteins of unknown function, in the characterization of gene function, for evolutionary genomics and the identification of conserved regulatory elements. Errors in ortholog predictions can significantly affect downstream analyses; as a result there has been increasing interest in high quality ortholog prediction techniques
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