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Sea cucumber is a morphologically diverse and ecologically important clade of echinoderms. The sea cucumber Apostichopus japonicus is the most economically valuable species of sea cucumber. The initial assembly of the A. japonicus genome was released in 2017. However, this genome assembly is fragmented and lacks relative position information of genes on chromosomes. In this study, we produced a high-quality chromosome-level genome of A. japonicus using Pacbio HiFi long-reads and Hi-C sequencing data. The assembled A. japonicus genome spanned 671.60 Mb with a contig N50 size of 17.20 Mb and scaffold N50 size of 29.65 Mb. A total of 99.9% of the assembly was anchored to 23 chromosomes. In total, 19,828 genes were annotated, and 97.2% of BUSCO genes were fully represented. This high-quality genome of A. japonicus will not only aid in the development of sustainable aquaculture practices, but also lay a foundation for a deeper understanding of their genetic makeup, evolutionary history, and ecological adaptation.
Fig. 1. A circos plot of 23 chromosomes of A. japonicus genome. The tracks from inside to outside are: bar plot for gene density profile, the distributions of transposable element and 23 chromosomes.
Fig. 2. Genome-wide Hi-C heatmap of Apostichopus japonicus.
Fig. 3. Distribution of divergence rates for TEs in the A. japonicus genome.
Fig. 4. Comparisons of the genomic elements of closely related species.
Fig. 5. Gene prediction and functional annotation of the A. japonicus genome. (a) Venn diagram of the gene set prediction. (b) Venn diagram of functional annotation based on different databases.
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