Homeobox Gene Duplication and Divergence in Arachnids

Homeobox genes are key toolkit genes that regulate the development of metazoans and changes in their regulation and copy number are thought to have contributed to the evolution of phenotypic diversity. We recently identified a whole genome duplication (WGD) event that occurred in an ancestor of spiders and scorpions (Arachnopulmonata) and that many homeobox genes, including two Hox clusters, appear to have been retained in arachnopulmonates. To better understand the consequences of this ancient WGD and the evolution of arachnid homeobox genes, we have characterised and compared the homeobox repertoires in a range of arachnids. We found that many families and clusters of these genes are duplicated in all studied arachnopulmonates (Parasteatoda tepidariorum, Pholcus phalangioides, Centruroides sculpturatus and Mesobuthus martensii) compared with non-arachnopumonate arachnids (Phalangium opilio, Neobisium carcinoides, Hesperochernes sp. and Ixodes scapularis). To assess divergence in the roles of homeobox ohnologs, we analysed the expression of P. tepidariorum homeobox genes during embryogenesis and found pervasive changes in the level and timing of their expression. Furthermore, we compared the spatial expression of a subset of P. tepidariorum ohnologs with their single copy orthologs in P. opilio embryos. We found evidence for both subfunctionlisation and likely neofunctionalisation of these genes in the spider. Overall our results show a high level of retention of homeobox genes in spiders and scorpions post WGD, which is likely to have made a major contribution to their developmental evolution and diversification through pervasive subfunctionlisation and neofunctionalisation, and paralleling the outcome of WGD in vertebrates.