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Mol Ecol Resour. 2019 May;19(3):744-756. doi: 10.1111/1755-0998.12988.

Chromosomal level reference genome of Tachypleus tridentatus provides insights into evolution and adaptation of horseshoe crabs.

Gong L1,2, Fan G3,4, Ren Y5, Chen Y1,2, Qiu Q5, Liu L1,2, Qin Y5, Liu B1,2, Jiang L1,2, Li H6, Zeng Y7,8, Gao Q7, Zhang C5, Wang Z5, Jiang H1,2, Tian J3, Zhang H3, Liu X3, Xu X3, Wang W1,5,7, Lü Z1,2, Li Y5.

Author information

National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China.
National Engineering Research Center for Facilitated Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China.
BGI-Qingdao, BGI-Shenzhen, Qingdao, China.
State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China.
Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China.
College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.


Horseshoe crabs including Tachypleus tridentatus are a group of marine arthropods and living fossil species which have existed on the earth for ~500 million years. However, the genetic mechanisms underlying their unique adaptive ability are still unclear. Here, we assembled the first chromosome-level T. tridentatus genome, and proved that this genome is of high quality with contig N50 1.69 Mb. By comparison with other arthropods, some gene families of T. tridentatus experienced significant expansion, which are related to several signaling pathways, endonuclease activities, and metabolic processes. Based on the results of comparative analysis of genomics and 27 transcriptomes from nine tissues, we found that the expanded Dscam genes are located at key hub positions of immune network. Furthermore, the Dscam genes showed higher levels of expression in the yellow connective tissue (the birthplace of blood cells with strong differentiation capability) than the other eight tissues. Besides, the Dscam genes are positively correlated with the expression of the core immunity gene, clotting factor B, which is involved in the coagulation cascade reaction. The effective and unusual immune ability endowed by the expansion and expression of Dscam genes in the horseshoe crab may be a factor that makes the species have a strong environmental adaptability within ~500 million years. The high quality chromosome level genome of a horseshoe crab and unique genomic features reported in this study provide important data resources for future studies on the evolution of marine ecological systems.


Dscam gene; coagulation cascade reaction; genome; horseshoe crab; immune system

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