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Chromosome-level assembly of the horseshoe crab genome provides insights into its genome evolution

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Listed:
  • Prashant Shingate

    (Comparative and Medical Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis)

  • Vydianathan Ravi

    (Comparative and Medical Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis)

  • Aravind Prasad

    (Comparative and Medical Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis)

  • Boon-Hui Tay

    (Comparative and Medical Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis)

  • Kritika M. Garg

    (Department of Biological Sciences, National University of Singapore)

  • Balaji Chattopadhyay

    (Department of Biological Sciences, National University of Singapore)

  • Laura-Marie Yap

    (School of Applied Sciences, Republic Polytechnic)

  • Frank E. Rheindt

    (Department of Biological Sciences, National University of Singapore)

  • Byrappa Venkatesh

    (Comparative and Medical Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis)

Abstract

The evolutionary history of horseshoe crabs, spanning approximately 500 million years, is characterized by remarkable morphological stasis and a low species diversity with only four extant species. Here we report a chromosome-level genome assembly for the mangrove horseshoe crab (Carcinoscorpius rotundicauda) using PacBio reads and Hi-C data. The assembly spans 1.67 Gb with contig N50 of 7.8 Mb and 98% of the genome assigned to 16 chromosomes. The genome contains five Hox clusters with 34 Hox genes, the highest number reported in any invertebrate. Detailed analysis of the genome provides evidence that suggests three rounds of whole-genome duplication (WGD), raising questions about the relationship between WGD and species radiation. Several gene families, particularly those involved in innate immunity, have undergone extensive tandem duplication. These expanded gene families may be important components of the innate immune system of horseshoe crabs, whose amebocyte lysate is a sensitive agent for detecting endotoxin contamination.

Suggested Citation

  • Prashant Shingate & Vydianathan Ravi & Aravind Prasad & Boon-Hui Tay & Kritika M. Garg & Balaji Chattopadhyay & Laura-Marie Yap & Frank E. Rheindt & Byrappa Venkatesh, 2020. "Chromosome-level assembly of the horseshoe crab genome provides insights into its genome evolution," Nature Communications, Nature, vol. 11(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-16180-1
    DOI: 10.1038/s41467-020-16180-1
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    Cited by:

    1. Bob Zimmermann & Juan D. Montenegro & Sofia M. C. Robb & Whitney J. Fropf & Lukas Weilguny & Shuonan He & Shiyuan Chen & Jessica Lovegrove-Walsh & Eric M. Hill & Cheng-Yi Chen & Katerina Ragkousi & Da, 2023. "Topological structures and syntenic conservation in sea anemone genomes," Nature Communications, Nature, vol. 14(1), pages 1-16, December.

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