Abstract
By the integration of MGI short-read sequencing, PacBio HiFi long-read sequencing, and Hi-C techniques, we constructed a chromosome-scale genome assembly for Holothuria fuscocinerea, a highly abundant and widely distributed sea cucumber species in the family Holothuriidae. The assembly was anchored into 23 pseudochromosomes with a total size of 1.556 Gb after redundancy removal, demonstrating contig and scaffold N50 values of 5.18 Mb and 63.82 Mb, respectively, indicative of high contiguity. Genome quality assessment using Merqury and BUSCO analyses yielded a QV score of 60.4087 and a BUSCO completeness rate of 97.8%, confirming high assembly quality with minimal gaps. Among the 29,878 protein coding genes, 95 percent obtained functional annotations from at least one database. This high-resolution genome resource is expected to advance research on H. fuscocinerea and the Holothuroidea class, providing insights for population management, evolutionary studies, and genetics research.
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Data availability
The following sites store all the data generated in this study available for downloading. The BioProject PRJNA125024973 of NCBI has been created to store raw data acquired in various sequencings and the final H. fuscocinerea genome assembled into 23 chromosomes. Additionally, the accession number JBNFMV00000000074 of DDBJ/ENA/GenBank store the genome assembly. The Figshare database75 hosts all data generated from genome assembly, gene annotation and functional annotations at the link: https://figshare.com/s/6c5acac389a19d8c8386.
Code availability
The following packages, under their established procedures and guidelines, were applied to compute and analyze the data in this study. The workflows and scripts were not altered unless otherwise specified. No custom code was used in this study for data processing, curation, or validation. All analyses were performed using publicly available tools as described in the Methods section. The detailed list of parameters of each software is as follows:
SOAPnuke (v2.1.4): Applied to remove low-quality reads from MGI sequencing raw reads using built-in configurations.
SMRT Link (v13.1): Applied to transform and filter PacBio sequencing raw data using built-in configurations.
Jellyfish (v2.3.0): Applied to count K-mers for assessment of genome size and heterozygosity with a K-mer size of 21.
GenomeScope (v2.0.0): Applied to process the K-mer histogram for the assessment of genome size, heterozygosity and repetitive component using built-in configurations.
Hifiasm (v0.19.8-r603): Applied to assemble the PacBio HiFi data after reads comparison and self-correct using built-in configurations.
Bwa (v0.7.17-r1188): Applied to map the MGI short read data onto the draft assembly using built-in configurations.
Pilon (v1.23): Applied to correct residual errors with Bwa alignment result using built-in configurations.
Purge_dups (v1.2.5): Applied to reduce redundant haplotigs and determine heterozygosity for the draft genome under a configuration of -j 80 -s 80.
ALLHiC (v1.1): Applied to assign and orient scaffolds using Hi-C reads into chromosome-level assemblies.
Merqury (v1.3): Applied 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): Applied to estimate genomic coverage using the metazoa_odb10 data collection.
Circos (v0.69): Applied to display chromosomal structure and visualize the distribution of gene regions, repeat sequences, SNP percentage and NGS sequencing depth.
RepeatMasker (v4.09): Applied to annotate transposable elements using built-in configurations.
EDTA: Applied to annotate de-novo transposable elements using built-in configurations.
Barrnap (v0.9): Applied to identify ribosomal RNAs (rRNAs) using built-in configurations.
tRNAscan-SE (v2.0.11): Applied to search for transfer RNAs (tRNAs) sing built-in configurations.
Infernal (v1.1.4): Applied to identify microRNAs (miRNAs) and small nuclear RNAs (snRNAs) using built-in configurations.
Braker (v3.0.8): Applied 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): Applied to map transcriptomic data for genome annotation using built-in configurations.
StringTie (v2.1.7): Applied to assemble the transcripts for the prediction of gene structures using built-in configurations.
MAKER3 (v3.01.03): Applied to combine outputs from various prediction modes into the final gene collection using built-in configurations.
BLAST (v2.11.0+): Applied for synteny analysis and functional annotation of predicted genes with blastp module set to e-value = 1e^-5.
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Acknowledgements
This study was graciously supported by grants from the National Natural Science Foundation of China (42176132 and 32573487 to T.C., and W2512089 to L.S. and A.Y.), the Research on breeding technology of candidate species for Guangdong modern marine ranching (2024-MRB-00-001 to T.C.), the Science and Technology Program of Nansha District (NSJL202103 to C.H.),, the National Key R & D Program of China (2022YFD2401301 to C.H.), the Guangdong Province Project (2024A1515011418 to T.C., 2024A1515010899 to X.J.).
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Chunhua Ren, Chaoqun Hu, Aifen Yan, and Ting Chen planned and conceptualized the research. Xuan Wang, Qianying Huang, Zhou Qin, Wenjie Pan, Jiasheng Huang, Zepeng Zhang, Hua Ge, Jingxuan Liang, Jianfeng Xu, and Yi Zhang acquired and processed the samples. Zhou Qin and Dingding Fan constructed the genome and performed annotations. Xuan Wang, Qianying Huang, Zhou Qin and Dingding Fan analysed gene functions. Xuan Wang, Qianying Huang, Zhou Qin, Dingding Fan and Ting Chen conducted bioinformatic analyses. Chunhua Ren, Peng Luo, Xiao Jiang, Lina Sun, Hongyan Sun, Chaoqun Hu, Aifen Yan, and Ting Chen offered experimental materials and computational resources. Xuan Wang, Qianying Huang, Dingding Fan, Aifen Yan and Ting Chen composed the manuscript. Chunhua Ren, Chaoqun Hu, Aifen Yan, and Ting Chen carried out revisions. All authors have reviewed and consented to the final version of the manuscript.
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Wang, X., Huang, Q., Qin, Z. et al. Chromosome-level genome assembly and annotation of the tropical sea cucumber Holothuria fuscocinerea. Sci Data (2026). https://doi.org/10.1038/s41597-026-06609-5
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DOI: https://doi.org/10.1038/s41597-026-06609-5
