Dataset Information

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.

SUBMITTER: Liao YY

PROVIDER: S-EPMC6390705 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature

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Draft genomic and transcriptome resources for marine chelicerate Tachypleus tridentatus.

Liao Yong Yan YY Xu Peng Wei PW Kwan Kit Yue KY Ma Zhi Yun ZY Fang Huai Yi HY Xu Jun Yang JY Wang Peng Liang PL Yang Shao Yu SY Xie Shang Bo SB Xu Shu Qing SQ Qian Dan D Li Wei Feng WF Bai Li Rong LR Zhou Da Jie DJ Zhang Yan Qiu YQ Lei Juan J Liu Ke K Li Fan F Li Jian J Zhu Peng P Wang Yu Jun YJ Wu Hai Ping HP Xu You Hou YH Huang Hu H Zhang Chi C Liu Jin Xia JX Han Jun Feng JF

Scientific data 20190226

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 as ...[more]

PMID: 30806641

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Project description: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 protein-coding 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.

Dataset Information

Draft genomic and transcriptome resources for marine chelicerate Tachypleus tridentatus.

Publications

Draft genomic and transcriptome resources for marine chelicerate Tachypleus tridentatus.

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