Abstract
Chinese horseshoe crabs (Tachypleus tridentatus), ancient marine arthropods dating back to the mid-Palaeozoic Era, have provided valuable resources for the detection of bacterial or fungal contamination. However, excessive exploitation for the amoebocyte lysate of Tachypleus has dramatically decreased the population of the Chinese horseshoe crabs. Thus, we present sequencing, assembly and annotation of T. tridentatus, with the hope of understanding the genomic feature of the living fossil and assisting scientists with the protection of this endangered species. The final genome contained a total size of 1.943 Gb, covering 90.23% of the estimated genome size. The transcriptome of three larval stages was constructed to investigate the candidate gene involved in the larval development and validate annotation. The completeness of the genome and gene models was estimated by BUSCO, reaching 96.2% and 95.4%, respectively. The synonymous substitution distribution of paralogues revealed that T. tridentatus had undergone two rounds of whole-genome duplication. All genomic and transcriptome data have been deposited in public databases, ready to be used by researchers working on horseshoe crabs.
Highlights
Background & SummaryHorseshoe crabs in the world are represented by two extant populations following a particular geographical distribution[1]
T. tridentatus, the tri-spine horseshoe crab, the largest of the living horseshoe crab species, was once widespread along the coast of Fujian, Hainan and Beibu Gulf Bay[2], but the population has drastically decreased for various reasons, such as environmental pollution, decreasing coastline and excessive exploitation for blood extracts
The release of the T. tridentatus genome and transcriptome in this study provides a crucial resource for future efforts to adopt better strategies to conserve the endangered Asian horseshoe crab and to take it as the model species to foster study on marine chelicerates
Summary
Horseshoe crabs in the world are represented by two extant populations following a particular geographical distribution[1]. After filtering out the low quality, adaptor-contaminated or PCR duplication reads of genome sequencing, we applied the KMERFREQ_AR v2.0.415 and JELLYFISH v1.116 to evaluate the genome size, heterozygosis and repetition by calculating the frequency of 17-mers and used the Platanus v1.2.417 to assemble the genome using all clean reads from PE and MP libraries. Another round of gap-filling steps was performed based on the assembly results, utilizing GapCloser v1.12-r615. The release of the T. tridentatus genome and transcriptome in this study provides a crucial resource for future efforts to adopt better strategies to conserve the endangered Asian horseshoe crab and to take it as the model species to foster study on marine chelicerates
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