Horseshoe crab genomes reveal the evolution of genes and microRNAs after three rounds of whole genome duplication

Whole genome duplication
(WGD) has occurred in relatively few sexually reproducing invertebrates.
Consequently, the WGD that occurred in the common ancestor of horseshoe crabs
~135 million years ago provides a rare opportunity to decipher the evolutionary
consequences of a duplicated invertebrate genome. Here, we present a
high-quality genome assembly for the mangrove horseshoe crab Carcinoscorpius
rotundicauda (1.7Gb, N50 = 90.2Mb, with 89.8% sequences anchored to 16
pseudomolecules, 2n = 32), and a resequenced genome of the tri-spine horseshoe
crab Tachypleus tridentatus (1.7Gb, N50 = 109.7Mb). Analyses of gene families, microRNAs, and synteny show that
horseshoe crabs have undergone three rounds (3R) of WGD. Comparison of C.
rotundicauda and T. tridentatus genomes from populations from several geographic locations
further elucidates the diverse fates of both coding and noncoding genes. Together,
the present study represents a cornerstone for improving our understanding of
invertebrate WGD events on the evolutionary fates of genes and microRNAs, at both
the individual and population level. We also provide improved genomic
resources for horseshoe crabs, of applied value for breeding programs and
conservation of this fascinating and unusual invertebrate lineage.