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. 2025 Jan 11;12(1):49.
doi: 10.1038/s41597-024-04349-y.

Chromosome-scale genome assembly of three-spotted seahorse (Hippocampus trimaculatus) with a unique karyotype

Ning Li #  1 , Xinhui Zhang #  2   3 , Xin Liu #  4 , Xueqiang Lin #  5 , Cancan Hu  6 , Jieming Chen  3 , Shengchao Wang  5 , Dong Zhang  4 , Shuguang Wei  7   8 , Qiong Shi  9   10   11
Affiliations

Chromosome-scale genome assembly of three-spotted seahorse (Hippocampus trimaculatus) with a unique karyotype

Ning Li et al. Sci Data. .

Abstract

Three-spotted seahorse (Hippocampi trimaculata) is a unique fish with important economic and medicinal values, and its total chromosome number is potentially quite different from other seahorse species. Herein, we constructed a chromosome-level genome assembly for this special seahorse by integration of MGI short-read, PacBio HiFi long-read and Hi-C sequencing techniques. A 416.57-Mb haplotypic genome assembly was obtained. Subsequently, 99.38% of its scaffold sequences were anchored onto 18 chromosomes, with identification of 29.1% repeat sequences in the assembled genome. Additional karyotype analysis validated the diploid chromosomes of 2n = 36, which are remarkably different from other seahorses' 2n = 42 or 44. The genome completeness (BUSCO score: 96.5%, CEGMA score: 97.87%) confirmed that this chromosome-scale assembly is indeed of high quality. Moreover, a total of 18,712 protein-coding genes were annotated, of which 96.36% could be predicted with functions. Based on construction of a phylogenetic tree, we estimated that Hippocampus and Syngnathoides diverged approximately 50.1 million years ago (Mya). Taken together, our genome data presented in this study provide a valuable genetic resource for numerical chromosome changes and in-depth evolutionary and functional investigations, as well as conservation and molecular breeding of this endangered teleost.

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Conflict of interest statement

Competing interests: The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Three-spotted seahorse and its whole-genome sequence distribution. (a) Image of the sequenced fish. (b) A K-mer (17-mer) distribution curve for estimation of the genome size of H. trimaculatus.
Fig. 2
Fig. 2
Hi-C heatmap, karyotype and chromosome-scale assembly of H. trimaculatus. (a) Genome-wide chromatin interactions at a 500-kb resolution. Color blocks represent the interactions, with various strengths from yellow (low) to red (high). (b) A karyotypic overview of H. trimaculatus. (c) Genomic repeat sequences and identified telomeres (marked by arrows) in the assembled genome of H. trimaculatus. Please note that identification of most telomeres also support the high quality of our chromosome-scale genome assembly for H. trimaculatus.
Fig. 3
Fig. 3
Phylogenetic relationships and divergence time estimation for H. trimaculatus and other eleven representative fish species. All nodes were supported by 100 cycles of bootstrap resampling. Blue numbers represent the estimated divergence times with a 95% confidence interval. Divergences used for the recalibration of time estimation are marked by red dots.
Fig. 4
Fig. 4
Genome synteny between H. trimaculatus and its reported relative H. abdominali.
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