Liu Y et al. (2024), A chromosome-level genome assembly of tropical ...

ECB-ART-53496

Sci Data 2024 Dec 18;111:1382. doi: 10.1038/s41597-024-04255-3.

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A chromosome-level genome assembly of tropical purple sea urchin Heliocidaris crassispina.

Liu Y , Chen T , Ma B , Yin J , Ren C , Jiang X , Wang Y , Pan W , Huang J , Yu S , Luo P .

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Heliocidaris crassispina is a tropical sea urchin that holds both ecological and economic value and serves as an ideal experimental animal. This study first employed a combination of PacBio HiFi and Hi-C sequencing data to present a high-quality, chromosome-level assembly of H. crassispina genome. This assembled genome spanned 709.77 Mb, with a contig N50 length of 4.98 Mb and a scaffold N50 length of 33.23 Mb. The assembly was anchored on 21 pseudo-chromosomes, covering 98.32% of the genome. A total of 18,665 protein-coding genes were identified, and BUSCO analysis revealed a completeness score of 97.1%. Additionally, non-coding RNAs (ncRNAs) were annotated, including miRNAs, rRNAs, tRNAs and snRNAs, providing a more complete functional understanding of the genome. The high-quality reference genome will enrich the current echinoderm genomic resources and provide a solid foundation for future studies on H. crassispina, including resource surveys, genomic breeding, and marine ranch management.

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	Fig. 1. Photos of H. crassispina and workflow of genome sequencing. (A) H. crassispina photographed underwater. (B) H&E staining of female H. crassispina gonad. (C) The work flow used for genome sequencing.
	Fig. 2. Genome assembly of H. crassispina. (A) Genome-wide heatmap of Hi-C interactions among 21 chromosomes in H. crassispina. Colors from light to dark represent the logarithm of contact density strength. (B) Synteny between the genomes of H. crassispina and two other species: H. erythrogramma and H. tuberculata. The green blocks represent chromosomes of H. crassispina, the blue blocks represent the chromosomes of H. erythrogramma and the purple blocks represent chromosomes of H. tuberculata.
	Fig. 3. The genome landscape of H. crassispina. From outer to inner circles: (A) marker distribution across 21 chromosomes on megabase scales (B) GC content, (C) repeat sequences, (D) ncRNAs, (E) gene density, (A–E) are drawn in non-overlapping 1 Mb sliding windows.
	Fig. 4. Structural and functional annotation of the H. crassispina genome. (A) Comparisons of the genetic structure of H. crassispina with other echinoderms, including CDS length, exon length, exon number, gene length, and intron length. (B) Functional annotation of protein-coding genes in various databases, including InterPro, KEGG, Nr, and Swiss-Prot.