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. 2025 Aug 11;12(1):1400.
doi: 10.1038/s41597-025-05779-y.

Chromosome-level genome assembly of the Phoxinus lagowskii

Han Zheng  1 , Peng Xie  2 , Xiaoyu Zheng  1 , Xufa Ma  1 , Kaijian Wei  1 , Rui Han  3
Affiliations

Chromosome-level genome assembly of the Phoxinus lagowskii

Han Zheng et al. Sci Data. .

Abstract

Phoxinus lagowskii is an economically important freshwater fish species native to China. In this study, a chromosome-level genome assembly of P. lagowskii was assembled using PacBio and Hi-C sequencing technologies. The total genome size was 1.22 Gb, with a contig N50 of 38.16 Mb. The final assembly comprised 25 chromosomes, with an anchor rate of 96.29%, resulting in a total anchored length of 1,173,227,270 bp. The genome completeness, as evaluated by the BUSCO assessment, was 94.2%. The genome contained 33,449 predicted protein-coding genes, and the BUSCO completeness for the gene set was 93.6%. A total of 76,416 proteins were predicted, of which 95.29% had functional annotations. Repetitive sequences in the genome totaled 626.50 Mb, representing 51.42% of the entire genome. This genome assembly of P. lagowskii provides significant insights into its biological traits, genetic diversity, and adaptive responses to environmental pressures. Moreover, it lays the groundwork for future genetic improvements in the aquaculture of this species.

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Conflict of interest statement

Competing interests: The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Characterization of assembled P. lagowskii genome. Circos plot of the P. lagowskii genome, with visualization of gene density (1), Transposon density (200 kb sliding window) (2), repetitive density (3), GC content (200 kb sliding window, red is the window higher than the average value of GC content in the whole genome, green is the opposite) (4), Collinear blocks (identified by the MCScanX program, based on the protein sequence as input) (5) in order from outside to inside.
Fig. 2
Fig. 2
Genome-wide Average Nucleotide Identity (ANI) clustering heatmap for six fish species. Color gradients (red to blue) represent ANI values ranging from high similarity (~100%) to low similarity (~93%). The hierarchical clustering dendrograms (left and top) group species based on ANI distances. Numerical values (%) are provided for each pairwise comparison.
Fig. 3
Fig. 3
K-mer depth distribution used to estimate the genome size of P. lagowskii.
Fig. 4
Fig. 4
Hi-C interaction heatmap of 25 chromosomes of P. lagowskii. The width of each column reflects the relative length of the corresponding chromosome, while the intensity of the red color indicates the contact density.
Fig. 5
Fig. 5
The genome synteny map among C. alburnus, P. lagowskii, and P. phoxinus.
Fig. 6
Fig. 6
BUSCO assessment results of P. lagowskii genome. C: complete BUSCOs, S: complete and single-copy BUSCOs, D: complete and duplicated BUSCOs, F: fragmented BUSCOs, M: missing BUSCOs, n: total BUSCO groups searched.
See this image and copyright information in PMC

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