Homeobox gene and microRNA duplication in Chelicerata

Animals have evolved a vast array of morphological phenotypes that has probably been generated by the evolution of core development toolkit genes. The expansion of these toolkits via gene duplications is correlated with the evolution of multi-cellilarly and morphological complexity in metazoans. Small tandem duplications are a common source of additional genetic material in animals, while larger-scale events are relatively rarer and until recently whole genome duplications (WGDs) had only been described in vertebrates and rotifers. Interestingly though, recent research in chelicerates, a sister-group to the other arthropods, has provided compelling evidence of WGDs in the lineages of Xiphosura (horseshoe crabs) and Arachnopulmonata (spiders, scorpions). To gain further support and insights to these possible WGD events, homeobox genes and microRNAs (miRNAs) were systematically identified and characterised in chelicerates with evidence for WGDs as well as lineages with no data supporting WGD. The identified pervasive duplication of homeobox genes and miRNAs in arachnopulmonates, which may have been caused by a WGD event that is independent of those in xiphosurans. Analysis of the spider Parasteatoda tepidariorum genome identified duplicate Hox, NK, SINE, TALE and LIM clusters and several miRNA clusters, providing extensive synteny support for a WGD in this lineage. Furthermore, the expression patterns of homeobox paralogs have diverged during embryogenesis and may represent cases of sub- and neo-functionalisation. Additionally, the mir-3791 family in P. tepidariorum has expanded due to the proposed WGD and further tandem duplications. This family has orthology to the insect and nematode miRNAs that are involved in the maternal to zygotic transition (MZT). A subset of Pt-mir-3791 paralogs were also predicted to be involved in the MZT in the spider, possible indicating a more ancestral role of this miRNA family than previously thought. These results offer additional support for WGDs in chelicerates as well as regulatory divergences between paralogs that may correspond to morphological evolution. These findings provide an excellent platform to further compare vertebrate and invertebrate lineages that have independently experienced WGDs and to understand the role of these events in the evolution of animal diversity