Abstract
BackgroundInterspecies sequence comparison is a powerful tool to extract functional or evolutionary information from the genomes of organisms. A number of studies have compared protein sequences or promoter sequences between mammals, which provided many insights into genomics. However, the correlation between protein conservation and promoter conservation remains controversial.ResultsWe examined promoter conservation as well as protein conservation for 6,901 human and mouse orthologous genes, and observed a very weak correlation between them. We further investigated their relationship by decomposing it based on functional categories, and identified categories with significant tendencies. Remarkably, the 'ribosome' category showed significantly low promoter conservation, despite its high protein conservation, and the 'extracellular matrix' category showed significantly high promoter conservation, in spite of its low protein conservation.ConclusionOur results show the relation of gene function to protein conservation and promoter conservation, and revealed that there seem to be nonparallel components between protein and promoter sequence evolution.
Highlights
Interspecies sequence comparison is a powerful tool to extract functional or evolutionary information from the genomes of organisms
Promoter sequence comparison between human and mouse We began the analysis with 8,429 promoter pairs of oneto-one orthologous genes between human and mouse
Relationship between gene function and promoter conservation Based on the promoter sequence comparison between human and mouse for the 6,901 genes, we investigated the relationship between gene function and promoter conservation
Summary
Interspecies sequence comparison is a powerful tool to extract functional or evolutionary information from the genomes of organisms. A number of studies have compared protein sequences or promoter sequences between mammals, which provided many insights into genomics. Comparative analysis is a powerful approach to extract functional or evolutionary information from biological sequences (reviewed in [1,2,3]). There were many pioneering works on the molecular evolution of mammalian protein sequences [4], which were followed by large scale comparative analyses between species. Makalowski et al [7] performed a comparative analysis for 1,196 cDNA pairs between human and rodents. These studies revealed that the evolutionary rates of protein sequences depend on the protein functions. Ribosomal proteins and Ras-like GTPases are highly conserved [7], while proteins for antimicrobial host defenses are highly divergent [6]
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