Genomes with a low contig N50 are generally highly fragmented, resulting in the poor annotation of protein-coding genes and non-coding sequences 24. However, the existing genome versions are far behind the growing demand of in-depth study on A. japonicus genome using Hi-C technology based on the 2017 genome assembly version 23. japonicus genome with 29,451 protein-coding genes 1 (Table 1). published 952 Mb (contig N50 of 45 Kb and scaffold N50 of 196 Kb) of the A. A total of 30,350 protein-coding genes were annotated in that genome version 22 (Table 1). japonicus genome with the assembly of 805 Mb (contig N50 of 190 Kb and scaffold N50 of 486 Kb) 22 (Table 1). Among them, the genome is the most basic data that is essential for most multi-omics analyses. japonicus have been exploited, including the coding and noncoding RNA transcriptome 15, 16, 17, proteome 18, epigenome 19, genetic linkage map 20, 21 and genome 1, 22. With the deepening of research requirements and development of biological technologies, studies of the mechanisms on phenotype formation, physiological responses, and behavioral regulation is rapidly developing. Such research occurs in fisheries 8, 9, immunology 10, 11, food science and biological medicine 4, 5, ecological function 3, as well as biochemistry and molecular biology 12, 13, 14. japonicus were published between 2000 to 2021 7. japonicus is one of the most studied echinoderms, and a total of 1,358 research papers on A. japonicus are produced each year, with an estimated whole industrial chain value of about 15 billion dollars (Sea cucumber Industry Branch of China Fisheries Association, 2010–2022).įor the reasons listed above, A. In China alone, around 200,000 tons of adult A. Among approximately 60 species with exploitation value, Apostichopus japonicus is the most economically important species 6. In addition, sea cucumbers are important economic aquaculture species and have been deemed as one of the most valuable functional foods in the sea due to their nutritional and pharmacological properties 4, 5. Sea cucumbers play crucial roles in maintaining the health of the ocean floor by consuming dead plant and animal matter, which helps to keep the sediment in a balanced state 3. This adaptation has taken place over a long evolutionary history, which can be traced back to the early Cambrian era 2. Sea cucumbers have evolved special behaviors, including super regenerative capacity, aestivation, and anatomy, among others, to adapt to various oceanic environments. Evolutionary studies of sea cucumber are crucial for understanding the origin of chordates 1.
The sea cucumber belongs to Echinodermata, which occupy an important phylogenetic position together with their sister phylum, Hemichordata. 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. In total, 19,828 genes were annotated, and 97.2% of BUSCO genes were fully represented. A total of 99.9% of the assembly was anchored to 23 chromosomes. japonicus genome spanned 671.60 Mb with a contig N50 size of 17.20 Mb and scaffold N50 size of 29.65 Mb. japonicus using Pacbio HiFi long-reads and Hi-C sequencing data. In this study, we produced a high-quality chromosome-level genome of A. However, this genome assembly is fragmented and lacks relative position information of genes on chromosomes. The sea cucumber Apostichopus japonicus is the most economically valuable species of sea cucumber.
Sea cucumber is a morphologically diverse and ecologically important clade of echinoderms.
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