Chromosomal-level genome assembly of the long-spined sea urchin Diadema setosum (Leske, 1778)

Hong Kong Biodiversity Genomics Consortium Collaborators, Jerome H. L. Hui, Ting Fung Chan, Leo Lai Chan, Siu Gin Cheung, Chi Chiu Cheang, James Kar Hei Fang, Juan Diego Gaitan-Espitia, Stanley Chun Kwan Lau, Yik Hei Sung, Chris Kong Chu Wong, Kevin Yuk Lap Yip, Yingying Wei, Wai Lok So, Wenyan Nong, Apple Pui Yi Chui, Thomas Hei Wut Fong, Ho Yin Yip

Research output: Contribution to journalJournal articlepeer-review


The long-spined sea urchin Diadema setosum is an algal and coral feeder widely distributed in the Indo-Pacific that can cause severe bioerosion on the reef community. However, the lack of genomic information has hindered the study of its ecology and evolution. Here, we report the chromosomal-level genome (885.8 Mb) of the long-spined sea urchin D. setosum using a combination of PacBio long-read sequencing and Omni-C scaffolding technology. The assembled genome contains a scaffold N50 length of 38.3 Mb, 98.1% of complete BUSCO (Geno, metazoa_odb10) genes (the single copy score is 97.8% and the duplication score is 0.3%), and 98.6% of the sequences are anchored to 22 pseudo-molecules/chromosomes. A total of 27,478 gene models have were annotated, reaching a total of 28,414 transcripts, including 5,384 tRNA and 23,030 protein-coding genes. The high-quality genome of D. setosum presented here is a valuable resource for the ecological and evolutionary studies of this coral reef-associated sea urchin.

Original languageEnglish
Number of pages13
Publication statusPublished - 25 Apr 2024

Scopus Subject Areas

  • Biochemistry, Genetics and Molecular Biology (miscellaneous)
  • Biotechnology
  • Genetics
  • Molecular Medicine


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