Abstract
BackgroundIt is expected that genes that are expressed early in development and have a complex expression pattern are under strong purifying selection and thus evolve slowly. Hox genes fulfill these criteria and thus, should have a low evolutionary rate. However, some observations point to a completely different scenario. Hox genes are usually highly conserved inside the homeobox, but very variable outside it.ResultsWe have measured the rates of nucleotide divergence and indel fixation of three Hox genes, labial (lab), proboscipedia (pb) and abdominal-A (abd-A), and compared them with those of three genes derived by duplication from Hox3, bicoid (bcd), zerknüllt (zen) and zerknüllt-related (zen2), and 15 non-Hox genes in sets of orthologous sequences of three species of the genus Drosophila. These rates were compared to test the hypothesis that Hox genes evolve slowly. Our results show that the evolutionary rate of Hox genes is higher than that of non-Hox genes when both amino acid differences and indels are taken into account: 43.39% of the amino acid sequence is altered in Hox genes, versus 30.97% in non-Hox genes and 64.73% in Hox-derived genes. Microsatellites scattered along the coding sequence of Hox genes explain partially, but not fully, their fast sequence evolution.ConclusionThese results show that Hox genes have a higher evolutionary dynamics than other developmental genes, and emphasize the need to take into account indels in addition to nucleotide substitutions in order to accurately estimate evolutionary rates.
Highlights
It is expected that genes that are expressed early in development and have a complex expression pattern are under strong purifying selection and evolve slowly
Our results showed that Hox-derived genes are evolving much faster and with less functional constraint than Hox and non-Hox genes
Many studies so far have largely focused on Hox gene homeobox sequences, and have demonstrated that they are highly conserved across species
Summary
It is expected that genes that are expressed early in development and have a complex expression pattern are under strong purifying selection and evolve slowly. Hox genes are homeobox containing genes involved in the specification of regional identities along the anteroposterior body axis and, play a fundamental role in animal development [1]. They encode transcription factors that regulate the expression of other genes downstream in the regulatory cascade of development and have been found in all metazoans, including flies, worms, tunicates, lampreys, fish and tetrapods. In winged insects, including Drosophila, Hox and ftz lost their homeotic function, that is, their ability to transform the characteristics of one body part into those of another body part [17,18], and their expression domains are no longer arranged along the anteroposterior axis of the embryo. Despite its high sequence divergence across species, it has been maintained for more than 60 Myr [19]
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