Abstract
A chromosome-level genome assembly of Bohadschia ocellata, a member of the Holothuriidae family, was constructed through the integration of MGI DNBSEQ-T7 short-read sequencing, PacBio HiFi long-read sequencing, and Hi-C genomic scaffolding technology. After optimization to eliminate redundant sequences, the genome assembly was precisely anchored to 23 chromosomes, resulting in a total size of 909.18 Mb. The N50 of its contig and scaffold sequences were 12.00 Mb and 38.97 Mb, respectively, confirming that the assembly was highly continuous. According to Merqury and BUSCO evaluations, the genome assembly reached a QV of 64.44 and completeness of 94.40%. From this assembly, 31,277 protein-coding genes were identified, which were 98.10% complete based on BUSCO assessment of the predicted proteome. Functional annotations were obtained from at least one database for more than 99% of these genes. This high-quality B. ocellata genome assembly from the current study could offer valuable information for further genetic and evolutionary studies of this sea cucumber species.
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Data availability
All sequencing and assembly data generated in this study have been deposited in public repositories. Raw sequencing data including BGI short-reads, PacBio HiFi long-reads, Hi-C reads and RNA-seq data are available at NCBI Sequence Read Archive database under the number SRP58693854 (https://identifiers.org/ncbi/insdc.sra:SRP586938). The whole genome shotgun project has been deposited in the DDBJ/ENA/GenBank under the accession number JBOCEH00000000055 (https://identifiers.org/ncbi/insdc:JBOCEH000000000). Additionally, the genome assembly, gene annotation and functional annotation are available in the Figshare repository65 (https://doi.org/10.6084/m9.figshare.29124434.v1) or Baiduyun66 (https://pan.baidu.com/s/10DBoB_GQQhThYBiloGInsA?pwd=wmhs).
Code availability
All commands and workflows used for data processing were executed in accordance with the respective software manuals and protocols, with the relevant settings and parameters detailed below:
SOAPnuke (v2.1.4): Employed to filter out low-quality reads from MGI raw sequencing data using the software’s default configurations.
SMRT Link (v13.1): Employed to process and filter PacBio raw sequencing data using default configurations.
Jellyfish (v2.3.0): Utilized to count 21-mers for estimating genome size and heterozygosity.
GenomeScope (v2.0.0): Utilized to process the K-mer frequency histogram for estimating genome size, heterozygosity, and repeat content using default configurations.
Hifiasm (v0.19.8-r603): Utilized to assemble the PacBio HiFi data after reads comparison and self-correct using built-in configurations.
Bwa (v0.7.17-r1188): Utilized to map the MGI short read data onto the draft assembly using built-in configurations.
Pilon (v1.23): Utilized to correct residual errors with Bwa alignment result using built-in configurations.
Purge_dups (v1.2.5): Utilized to reduce redundant haplotigs and determine heterozygosity for the draft genome under a configuration of -j 80 -s 80.
ALLHiC (v1.1): Utilized to assign and orient scaffolds using Hi-C reads into chromosome-level assemblies.
Merqury (v1.3): Utilized to assess k-mer coverage and QV value for the qualification of the assembled genome using best-fit K-mer = 19.
BUSCO (v5.7.1): Utilized to estimate genomic coverage using the metazoa_odb10 data collection.
Circos (v0.69): Utilized to display chromosomal structure and visualize the distribution of gene regions, repeat sequences, SNP percentage and NGS sequencing depth.
RepeatMasker (v4.09): Utilized to annotate transposable elements using built-in configurations.
EDTA: Utilized to annotate de-novo transposable elements using built-in configurations.
Barrnap (v0.9): Utilized to identify ribosomal RNAs (rRNAs) using built-in configurations.
tRNAscan-SE (v2.0.11): Utilized to search for transfer RNAs (tRNAs) sing built-in configurations.
Infernal (v1.1.4): Utilized to identify microRNAs (miRNAs) and small nuclear RNAs (snRNAs) using built-in configurations.
Braker (v3.0.8): Utilized to integrate gene prediction results with 9 selected proteomes and RNAseq reads from tissues with parameters set to gff3, threads 48, prot_seq = pep.fasta, bam = bams and UTR = on.
HISAT2 (v2.2.1): Utilized to map transcriptomic data for genome annotation using built-in configurations.
StringTie (v2.1.7): Utilized to assemble the transcripts for the prediction of gene structures using built-in configurations.
MAKER3 (v3.01.03): Utilized to combine outputs from various prediction modes into the final gene collection using built-in configurations.
BLAST (v2.11.0 +): Employed for synteny analysis and functional annotation of predicted genes using the BLASTP module with an E-value threshold of 1e–⁵.
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Acknowledgements
This study was graciously supported by grants from the National Natural Science Foundation of China (W2512089 to A.Y., and 42176132 and 32573487 to T.C.), the Research on breeding technology of candidate species for Guangdong modern marine ranching (2024-MRB-00-001 to T.C.), and the Guangdong Province Project (2024A1515011418 to T.C.).
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Chunhua Ren, Chaoqun Hu, Ting Chen, and Aifen Yan planned and conceptualized the research. Qianying Huang, Xuan Wang, Zhou Qin, Hua Ge, Yingxin Lin, Junyan Wang, Yun Yang, Da Huo, Xiaoli Zhang and Xiangxing Zhu acquired and processed the samples. Zhou Qin and Dingding Fan constructed the genome and performed annotations. Qianying Huang, Xuan Wang, Zhou Qin and Dingding Fan analysed gene functions. Qianying Huang, Xuan Wang, Zhou Qin, Dingding Fan and Ting Chen conducted bioinformatic analyses. Zhenyu Xie, Chang Chen, Haipeng Qin, Dongsheng Tang, Chunhua Ren, Chaoqun Hu, Aifen Yan, and Ting Chen offered experimental materials and computational resources. Qianying Huang, Xuan Wang, Dingding Fan, Aifen Yan and Ting Chen composed the manuscript. Ting Chen and Aifen Yan and carried out revisions. All authors have reviewed and consented to the final version of the manuscript.
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Huang, Q., Wang, X., Qin, Z. et al. Chromosome-level genome assembly and annotation of the tropical sea cucumber Bohadschia ocellate. Sci Data (2025). https://doi.org/10.1038/s41597-025-06453-z
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DOI: https://doi.org/10.1038/s41597-025-06453-z
