The draft genome of horseshoe crab Tachypleus tridentatus reveals its evolutionary scenario and well-developed innate immunity

Abstract

Background: Horseshoe crabs are ancient marine arthropods with a long evolutionary history extending back approximately 450 million years, which may benefit from their innate immune systems. However, the genetic mechanisms underlying their abilities of distinguishing and defending against invading microbes are still unclear.Results: Here, we describe the 2.06 Gbp genome assembly of Tachypleus tridentatus with 24,222 predicted proteincoding genes. Comparative genomics shows that T. tridentatus and the Atlantic horseshoe crab Limulus polyphemus have the most orthologues shared among two species, including genes involved in the immune-related JAK-STAT signalling pathway. Divergence time dating results show that the last common ancestor of Asian horseshoe crabs (including T. tridentatus and C. rotundicauda) and L. polyphemus appeared approximately 130 Mya (121-141), and the split of the two Asian horseshoe crabs was dated to approximately 63 Mya (57-69). Hox gene analysis suggests two clusters in both horseshoe crab assemblies. Surprisingly, selective analysis of immune-related gene families revealed the high expansion of conserved pattern recognition receptors. Genes involved in the IMD and JAK-STAT signal transduction pathways also exhibited a certain degree of expansion in both genomes. Intact coagulation cascade-related genes were present in the T. tridentatus genome with a higher number of coagulation factor genes. Moreover, most reported antibacterial peptides have been identified in T. tridentatus with their potentially effective antimicrobial sites. Conclusions:The draft genome of T. tridentatus would provide important evidence for further clarifying the taxonomy and evolutionary relationship of Chelicerata. The expansion of conserved immune signalling pathway genes, coagulation factors and intact antimicrobial peptides in T. tridentatus constitutes its robust and effective innate immunity for self-defence in marine environments with an enormous number of invading pathogens and may affect the quality of the adaptive properties with regard to complicated marine environments.

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

“…Spiders and scorpions, on the other hand, possess two Hox clusters due to one round of whole-genome duplication that occurred in their common ancestor (Schwager et al, 2017). Sequencing of the whole-genome of T. tridentatus, a species closely related to T. gigas, showed that it contained two Hox clusters, suggesting one round of whole-genome duplication in this lineage (Gong et al, 2019;Zhou et al, 2020). However, a recent study involving sequencing and analysis of the genome of C. rotundicauda revealed the presence of five Hox clusters (Shingate et al, 2020), which suggested at least two rounds of whole-genome duplication.…”

Immune Responses to Gram-Negative Bacteria in Hemolymph of the Chinese Horseshoe Crab, Tachypleus tridentatus

“…As a group of living fossil, horseshoe crabs in morphology have barely changed in the past 200 million years. Previous studies have shown that its hemolymph contains a rich repertoire of innate immune molecules, so horseshoe crab is a useful invertebrate model for exploring the innate immune mechanism (7)(8)(9)(10)(11). The resistance of horseshoe crabs to pathogenic invasion depends entirely on the hard carapace and the innate immune system including humoral and cellular responses (2).…”

The Easter Egg Weevil (Pachyrhynchus) genome reveals synteny in Coleoptera across 200 million years of evolution

“…The combination of long-read DNA and Hi-C sequencing was successful in resolving a large and highly repetitive insect genome. To date, this is the largest insect genome and one of the largest arthropod genomes assembled to chromosome scale, the horseshoe crab's (Tachypleus tridentatus) being only slightly larger (2.06 Gb vs 2.05 Gb) (Zhou et al 2020). This is remarkable because the assembly of relatively large and highly repetitive insect genomes into highly contiguous ones such as this was previously unattainable (Li et al 2020).…”