Horseshoe crab genomes reveal the evolution of genes and microRNAs after three rounds of whole genome duplication

Wenyan Nong, Zhe Qu, Yiqian Li, Tom Barton-Owen, Annette Y.P. Wong, Ho Yin Yip, Hoi Ting Lee, Satya Narayana, Tobias Baril, Thomas Swale, Jianquan Cao, Ting Fung Chan, Hoi Shan Kwan, Sai Ming Ngai, Gianni Panagiotou, Pei Yuan Qian, Jian Wen Qiu, Kevin Y. Yip, Noraznawati Ismail, Siddhartha PatiAkbar John, Stephen S. Tobe, William G. Bendena, Siu Gin Cheung, Alexander Hayward, Jerome H.L. Hui*

*Corresponding author for this work

Research output: Contribution to journalJournal articlepeer-review

22 Citations (Scopus)


Whole genome duplication (WGD) has occurred in relatively few sexually reproducing invertebrates. Consequently, the WGD that occurred in the common ancestor of horseshoe crabs ~135 million years ago provides a rare opportunity to decipher the evolutionary consequences of a duplicated invertebrate genome. Here, we present a high-quality genome assembly for the mangrove horseshoe crab Carcinoscorpius rotundicauda (1.7 Gb, N50 = 90.2 Mb, with 89.8% sequences anchored to 16 pseudomolecules, 2n = 32), and a resequenced genome of the tri-spine horseshoe crab Tachypleus tridentatus (1.7 Gb, N50 = 109.7 Mb). Analyses of gene families, microRNAs, and synteny show that horseshoe crabs have undergone three rounds (3R) of WGD. Comparison of C. rotundicauda and T. tridentatus genomes from populations from several geographic locations further elucidates the diverse fates of both coding and noncoding genes. Together, the present study represents a cornerstone for improving our understanding of invertebrate WGD events on the evolutionary fates of genes and microRNAs, at both the individual and population level. We also provide improved genomic resources for horseshoe crabs, of applied value for breeding programs and conservation of this fascinating and unusual invertebrate lineage.

Original languageEnglish
Article number83
Number of pages11
JournalCommunications Biology
Issue number1
Publication statusPublished - 19 Jan 2021

Scopus Subject Areas

  • Medicine (miscellaneous)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)


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