Draft genomic and transcriptome resources for marine chelicerate Tachypleus tridentatus

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.

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

“…The draft genome of T. tridentatus can provide the Chelicerata clade another high-quality publicly available sequence, and would provide an important source for eliminating the uncertainty associated with the evolution of Chelicerata. To date, two papers describing the T. tridentatus genome have been published, revealing 2.16 Gb and 1.94 Gb T. tridentatus genomes, providing valuable genomic and transcriptomic resources for future studies to exploit horseshoe crabs [52,53]. Using a parallel experiment, the assembly size in this study was between the two previous T. tridentatus assemblies.…”

Horseshoe crab genomes reveal the evolutionary fates of genes and microRNAs after three rounds (3R) of whole genome duplication

“…To date, the only repeat data available for horseshoe crabs are two independent analyses of the tri-spine horseshoe crab T. tridentatus , which identified a repeat content of 34.61% (Gong et al 2019), and 39.96% (Liao et al 2019). In the present study, we provide the first analysis of repeat content in the genomes of different horseshoe crab species, by analysing repeats in our genome assembly for T. tridentatus , as well as our assembly for the mangrove horseshoe crab, C. rotunicauda .…”

“…Initial efforts to analyse WGD in extant horseshoe crabs were from low-depth and genotyping-by-sequencing which hindered the understanding of WGD in these taxa (Nossa et al 2014; Kenny et al 2016). Recently, there have been two resequencing efforts for the horseshoe crab T. tridentatus (Gong et al 2019; Liao et al 2019), but our T. tridentatus genome assembly has the largest contig N50 (Figure 1C). Furthermore, our assembly for C. rotundicauda represents the first close to chromosomal-level genome assembly for this species.…”

“…All extant horseshoe crabs are estimated to have diverged from a common ancestor that existed ~135 Mya (Obst et al 2012), and they share an ancestral WGD (Kenny et al 2016). A high-quality genome assembly was recently announced as a genomic resource for T. tridentatus (Gong et al 2019; Liao et al 2019), leaving an exciting research opportunity to analyse the genomes of other horseshoe crab species to understand how WGD reshapes the genome and rewires genetic regulatory network in invertebrates.…”

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

“…tridentatus and L. polyphemus have all the coagulation-related genes while other related species lack a part of the coagulation pathway ( (43,44). Using a parallel experiment, the assembly size in this study was between the two previous T. tridentatus assemblies.…”