Chromosome‐level genome assembly of the coastal horseshoe crab (Tachypleus gigas)

Abstract Horseshoe crabs, represented by only four extant species, have existed for around 500 million years. However, their existence is now under threat because of anthropogenic activities. The availability of genomic resources for these species will be valuable in planning appropriate conservation measures. Whole‐genome sequences are currently available for three species. In this study, we have generated a chromosome‐level genome assembly of the fourth species, the Asian coastal horseshoe crab ( Tachypleus gigas ; genome size 2.0 Gb). The genome assembly has a scaffold N50 value of 140 Mb with ~97% of the assembly mapped to 14 scaffolds representing 14 chromosomes of T. gigas . In addition, we have generated the complete mitochondrial genome sequence and deep‐coverage transcriptome assemblies for four tissues. A total of 26,159 protein‐coding genes were predicted in the genome. The T. gigas genome contains five Hox clusters similar to the mangrove horseshoe crab ( Carcinoscorpius rotundicauda ), suggesting that the common ancestor of horseshoe crabs already possessed five Hox clusters. Phylogenomic and divergence time analysis suggested that the American and Asian horseshoe crab lineages shared a common ancestor around the Silurian period (~436 Ma). Comparison of the T. gigas genome with those of other horseshoe crab species with chromosome‐level assemblies provided insights into the chromosomal rearrangement events that occurred during the emergence of these species. The genomic resources of T. gigas will be useful for understanding their genetic diversity and population structure and would help in designing strategies for managing and conserving their stocks across Asia.