Ancestral whole-genome duplication in the marine chelicerate horseshoe crabs

Abstract

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 4135 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.

Global map of oxytocin/vasopressin-like neuropeptide signalling in insects

“…We also analysed four different Daphnia magna transcripts of inotocin receptors, which are probably the result of alternative splicing since these sequences are almost identical except for minor deletions/insertions in intracellular loop 3 as well transmembrane domains 3 and 5. The presence of multiple copies in some of the species could be explained by whole genome or large scale duplication events, which have been reported for Limulus polyphemus 2627, Ixodes scapularis 28, Calanus finmarchicus 29 and Strigamia maritima 30. Local and whole genome duplication and deletion events during vertebrate evolution led to different number of gene copies (two or more) of oxytocin/vasopressin receptors and precursors within distinct vertebrate species3132.…”

Chromosomal level reference genome of Tachypleus tridentatus provides insights into evolution and adaptation of horseshoe crabs

“…Both the busco and mapping rate tests showed that this assembled genome of T. tridentatus is a high quality reference genome of horseshoe crab. In addition, the quality of our assembled chromosome‐level genome is obviously higher than the released horseshoe crab versions (Supporting Information Table S6; Kenny et al, ; Nossa et al, ).…”

New genes from old: asymmetric divergence of gene duplicates and the evolution of development

“…WGD occurred twice at the base of vertebrates [13,14], once in the stem lineage of teleost fish [15][16][17], one or more times in cyprinid fish [18], once in salmonid fish [19], two or more times in chelicerates [20,21] and once in rotifers [22]; undoubtedly more cases will be discovered. However, a clear finding is that gene loss is extensive after WGD, possibly reaching as high as 85% of duplicates in some cases [23].…”