Abstract
The evolutionary history of horseshoe crabs, spanning approximately 500 million years, is characterized by remarkable morphological stasis and a low species diversity with only four extant species. Here we report a chromosome-level genome assembly for the mangrove horseshoe crab (Carcinoscorpius rotundicauda) using PacBio reads and Hi-C data. The assembly spans 1.67 Gb with contig N50 of 7.8 Mb and 98% of the genome assigned to 16 chromosomes. The genome contains five Hox clusters with 34 Hox genes, the highest number reported in any invertebrate. Detailed analysis of the genome provides evidence that suggests three rounds of whole-genome duplication (WGD), raising questions about the relationship between WGD and species radiation. Several gene families, particularly those involved in innate immunity, have undergone extensive tandem duplication. These expanded gene families may be important components of the innate immune system of horseshoe crabs, whose amebocyte lysate is a sensitive agent for detecting endotoxin contamination.
Highlights
The evolutionary history of horseshoe crabs, spanning approximately 500 million years, is characterized by remarkable morphological stasis and a low species diversity with only four extant species
Analysis of Horseshoe crabs (HSCs) genomes has indicated the presence of a large number of duplicate genes with some families containing more than two paralogues which has led to the suggestion that the HSC lineage experienced two whole-genome duplication (WGD) events[5,6]
HSCs are ancient marine chelicerates that have changed very little over 500 million years of evolution. Despite their long evolutionary history, HSCs are currently represented by only four extant species
Summary
The evolutionary history of horseshoe crabs, spanning approximately 500 million years, is characterized by remarkable morphological stasis and a low species diversity with only four extant species. Analysis of HSC genomes has indicated the presence of a large number of duplicate genes with some families containing more than two paralogues which has led to the suggestion that the HSC lineage experienced two whole-genome duplication (WGD) events[5,6] These genome assemblies were highly fragmented (contig N50 length 0.4–1.4 kb and scaffold N50 length 2.9 kb) and lacked synteny information that is essential for reliably inferring WGD events. Recently a chromosome-level assembly (contig N50 length 1.7 Mb) of the tri-spine HSC was generated using long Nanopore reads[8] This highly-contiguous assembly was found to contain two Hox gene clusters, raising the possibility that the HSC lineage has experienced only one WGD event akin to arachnopulmonates. These developments have resulted in the tri-spine HSC and the Atlantic HSC being, respectively listed as “Endangered” and “Vulnerable” in the IUCN
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