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. 2025 Apr 21;12(1):668.
doi: 10.1038/s41597-025-04790-7.

Chromosome-level genome assembly and annotation of Chinese herring (Ilisha elongata)

Bingjian Liu #  1   2 , Xinyi Niu #  1   2 , Chi Zhang #  3 , Sixu Zheng  1   2 , Luxiu Gao  1   2 , Mingzhe Han  1 , Taobo Feng  1 , Jinghua Wu  1 , Chaoxuan Jiang  1 , Shuaishuo Kang  1 , DongDong Xu  4 , Yifan Liu  5   6
Affiliations

Chromosome-level genome assembly and annotation of Chinese herring (Ilisha elongata)

Bingjian Liu et al. Sci Data. .

Abstract

The Chinese herring (Ilisha elongata) is a commercially and scientifically significant fish species. In this study, we conducted high-precision whole-genome sequencing using two high-throughput platforms: second-generation MGI and third-generation PacBio. Hi-C technology assisted in assembling the contig sequences onto 24 chromosomes, resulting in a high-quality chromosome-level genome map with excellent continuity and coverage. The completed genome size was approximately 815 Mb, with a contig N50 of 4.82 Mb, scaffold N50 of 32.61 Mb, and a chromosome mounting rate of 95.32%. SNP and InDel purity rates were 0.003% and 0.012%, respectively, and the genome assembly completeness was 96.68%, assessed by BUSCO. Repetitive sequences were annotated via ab initio and homology predictions, identifying 295.7 Mb of repetitive sequences, constituting 35.08% of the genome. A total of 26,381 protein-coding genes were predicted, with 24,596 functionally annotated.

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Conflict of interest statement

Competing interests: The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
2D statistical chart of the quality and length of the third-generation PacBio sequencing results of I. elongata genome.
Fig. 2
Fig. 2
Frequency and depth distribution plot of the I. elongata genome surveyed through genome analysis.
Fig. 3
Fig. 3
Hi-C interaction heatmap of I. elongata chromosome genome.
Fig. 4
Fig. 4
Circle map of I. elongata genome at the chromosome level. From outside to inside: (A) Chromosome length, (B) GC content distribution, (C) Second-generation sequencing depth distribution, (D) Third-generation sequencing depth distribution, (E) Gene density distribution, (F) Distribution of long tandem repeat sequences.
Fig. 5
Fig. 5
BUSCO evaluation results of I. elongata genome at the chromosome level.
See this image and copyright information in PMC

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