Data from: Ancestral whole genome duplication in the marine chelicerate horseshoe crabs

Whole-genome duplication (WGD) results in new genomic resources that can
be exploited by evolution for rewiring genetic regulatory networks in
organisms. In metazoans, WGD occurred before the last common ancestor of
vertebrates, and has been postulated as a major evolutionary force that
contributed to their speciation and diversification of morphological
structures. Here, we have sequenced genomes from three of the four extant
species of horseshoe crabs—Carcinoscorpius rotundicauda, Limulus
polyphemus and Tachypleus tridentatus. Phylogenetic and sequence analyses
of their Hox and other homeobox genes, which encode crucial transcription
factors and have been used as indicators of WGD in animals, strongly
suggests that WGD happened before the last common ancestor of these marine
chelicerates >135 million years ago. Signatures of
subfunctionalisation of paralogues of Hox genes are revealed in the
appendages of two species of horseshoe crabs. Further, residual homeobox
pseudogenes are observed in the three lineages. The existence of WGD in
the horseshoe crabs, noted for relative morphological stasis over
geological time, suggests that genomic diversity need not always be
reflected phenotypically, in contrast to the suggested situation in
vertebrates. This study provides evidence of ancient WGD in the ecdysozoan
lineage, and reveals new opportunities for studying genomic and regulatory
evolution after WGD in the Metazoa.