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Sci Data
2024 Nov 18;111:1245. doi: 10.1038/s41597-024-03985-8.
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Chromosome-level genome assembly and annotation of the tropical sea cucumber Stichopus monotuberculatus.
Chen T
,
Yang Y
,
Wang X
,
Qin Z
,
Xie Z
,
Fan D
,
Ren C
,
Sun H
,
Luo P
,
Jiang X
,
Long H
,
Chen C
,
Pan W
,
E Z
,
Huang J
,
Huang Q
,
Xu J
,
Zhang Z
,
Cheng C
,
Yu S
,
Wang Y
,
Jiang F
,
Yan A
,
Hu C
.
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In this study, a chromosome-level genome of the tropical sea cucumber Stichopus monotuberculatus was generated by a combination of Nanopore long-read, Illumina short-read, and Hi-C sequencing technologies. The final assembly was 810.54 Mb in length, with contig N50 and scaffold N50 values of 10.15 Mb and 35.36 Mb, respectively. This assembly comprised 23 pseudo-chromosomes, covering 99.82% of the genome. Completeness analysis using BUSCO indicated that 97.8% of the metazoan conserved genes were presented in their entirety. A total of 29,596 protein-coding genes were predicted, with functional annotations available for 94.43% of these genes. The high-quality genome assembly produced in this study may provide an essential foundation for future researches on resource conservation and genetic breeding of S. monotuberculatus.
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39557846
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42176132 National Natural Science Foundation of China (National Science Foundation of China), 2024A1515011418 Guangdong Science and Technology Department (Science and Technology Department, Guangdong Province), 2024A1515010899 Guangdong Science and Technology Department (Science and Technology Department, Guangdong Province), 2022YFD2401301 Ministry of Science and Technology of the People & apos;s Republic of China (Chinese Ministry of Science and Technology)
Fig. 1. S. monotuberculatus and its genomics feature. (a) Appearance and global distribution of S. monotuberculatus; (b) 21-mer seq frequency distribution in the S. monotuberculatus genome; (c) Hi-C contact heatmap of the S. monotuberculatus genome.
Fig. 2. Circos plot depicting the features of the S. monotuberculatus genome. From inner to outer circles: chromosomes, gene densities, repeat sequences, SNP percentage, and NGS sequencing depth. Average values for these features are 0.600, 0.200, 0.019 and 173, respectively. The windows size for all circles was 500k bp.
Fig. 3. Prediction and annotation of repetitive element (a) and Noncoding RNA (b).
Fig. 4. Prediction and annotation of gene, and gene family analysis. (a) Prediction and annotation of gene; (b) Venn diagram of common and unique gene family in 4 sea cucumbers; (c) Phylogenetic and gene family evolution analysis among 9 echinoderm species. The scale below represents the divergence time. The number of expanded (+green) and contracted (−red) gene families were shown alongside the species.
