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. 2025 Jun 16;12(1):1008.
doi: 10.1038/s41597-025-05373-2.

A chromosome-level genome assembly of the Bullacta exarata (Cephalaspidea: Haminoeidae)

Yongchao Zhao  1 , Yong Chi  2 , Ailing Wu  2   3 , Yiwo Wang  1 , Duo Li  1 , Yusheng Chen  1 , Shuyin Chen  1 , Hongjiu Ji  4 , Yangzhen Li  5
Affiliations

A chromosome-level genome assembly of the Bullacta exarata (Cephalaspidea: Haminoeidae)

Yongchao Zhao et al. Sci Data. .

Abstract

The mudsnail, Bullacta exarata, is an important marine food mollusk for both economic and aquaculture purposes. However, the scarcity of genomic information has hindered genetic research and breeding efforts. To address this gap, we developed a chromosome-level genome assembly utilizing short reads, HiFi long reads, and Hi-C sequencing data. The final assembly measures 836.77 Mb, with scaffold N50 and contig N50 values of 48.61 Mb and 1.00 Mb, respectively. Using Hi-C technology, 815.25 Mb (97.43%) of the contigs were anchored and arranged into 18 pseudochromosomes. A total of 358.66 Mb was identified as repeat elements, representing 42.86% of the genome. Furthermore, we predicted 85,914 non-coding RNAs and 17,996 protein-coding genes, with 93.48% of the protein-coding genes annotated. The BUSCO analysis indicated that the completeness of the genome assembly and annotation is 94.55% and 96.65%, respectively. Phylogenetic analysis clarified the evolutionary relationships between B. exarata and representative species in gastropoda. This high-quality reference genome for B. exarata serves as a valuable resource for aquaculture, fisheries, and ecological research.

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Conflict of interest statement

Competing interests: The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
The adult individual of B. exarata used in this study.
Fig. 2
Fig. 2
Genome size estimation summary using k-mer (21-mer) analysis.
Fig. 3
Fig. 3
The landscape of genome assembly and annotation of the B. exarata. (A) Hi-C interaction heat map of chromosomal level genome in B. exarata. (B) Chromosomal level genome feature distribution in B. exarata. Outer to inner tracks: (a) Length of chromosome, with each tick indicating a span of 1 Mb; (b) Coding gene density; (c) GC content distribution; (d) Repetitive sequence density; (e) DNA transposon density; (f) Density of Line elements; (g) LTR element density; (h) The interconnections within the circle represent syntenic gene pairs.
Fig. 4
Fig. 4
Venn diagram illustrating the outcomes of functional annotation for B. exarata across five databases.
Fig. 5
Fig. 5
Phylogenetic tree with estimated divergence times for B. exarata and other 14 species.
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