Abstract
BackgroundWhen orthologous sequences from species distributed throughout an optimal range of divergence times are available, comparative genomics is a powerful tool to address problems such as the identification of the forces that shape gene structure during evolution, although the functional constraints involved may vary in different genes and lineages.ResultsWe identified and annotated in the MitoComp2 dataset the orthologs of 68 nuclear genes controlling oxidative phosphorylation in 11 Drosophilidae species and in five non-Drosophilidae insects, and compared them with each other and with their counterparts in three vertebrates (Fugu rubripes, Danio rerio and Homo sapiens) and in the cnidarian Nematostella vectensis, taking into account conservation of gene structure and regulatory motifs, and preservation of gene paralogs in the genome. Comparative analysis indicates that the ancestral insect OXPHOS genes were intron rich and that extensive intron loss and lineage-specific intron gain occurred during evolution. Comparison with vertebrates and cnidarians also shows that many OXPHOS gene introns predate the cnidarian/Bilateria evolutionary split. The nuclear respiratory gene element (NRG) has played a key role in the evolution of the insect OXPHOS genes; it is constantly conserved in the OXPHOS orthologs of all the insect species examined, while their duplicates either completely lack the element or possess only relics of the motif.ConclusionOur observations reinforce the notion that the common ancestor of most animal phyla had intron-rich gene, and suggest that changes in the pattern of expression of the gene facilitate the fixation of duplications in the genome and the development of novel genetic functions.
Highlights
When orthologous sequences from species distributed throughout an optimal range of divergence times are available, comparative genomics is a powerful tool to address problems such as the identification of the forces that shape gene structure during evolution, the functional constraints involved may vary in different genes and lineages
We recently identified and annotated the Oxidative phosphorylation (OXPHOS) genes orthologs in nine more Drosophilidae genomes, in another Culicidae species, and in three non Dipteran insect species, i.e. Bombyx mori, Apis mellifera and Tribolium castaneum, and we have compiled the MitoComp2 dataset [13], that provides an integrated view of the data obtained
We focused our attention primarily on the genomic regions that in D. melanogaster contain the nuclear respiratory gene element (NRG), a palindromic 10-bp motif (RTTAYRTAAY) shared by all nuclear OXPHOS genes listed in Table 1 and by many other nuclear genes involved in the biogenesis and function of the mitochondrion [31]
Summary
When orthologous sequences from species distributed throughout an optimal range of divergence times are available, comparative genomics is a powerful tool to address problems such as the identification of the forces that shape gene structure during evolution, the functional constraints involved may vary in different genes and lineages. BMC Evolutionary Biology 2007, 7:215 http://www.biomedcentral.com/1471-2148/7/215 approach led to significant progress in clarifying the molecular mechanisms that control gene evolution and the origin of the differences in gene structure between eukaryotic species [2], showing that changes in exonintron structure are largely independent of protein sequence evolution [3]. Studies involving as large as possible a number of different species and gene subsets are needed, because selective pressures may differ significantly between different evolutionary lineages and between particular types of genes [8]. Oxidative phosphorylation (OXPHOS), the primary energy-producing biological process in all aerobic organisms [9], generates ATP using the products of both nuclear and mitochondrial genes (OXPHOS genes); because they encode products organized in the respiratory complexes spanning the inner mitochondrial membrane, OXPHOS genes are subject to specific evolutionary constraints, e.g. because coordinate evolution is required to maintain the stochiometric balance between components of multisubunit complexes [10]
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