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. 2025 Mar 18;12(1):452.
doi: 10.1038/s41597-025-04800-8.

Chromosome-scale assembly of the Xenocypris davidi using PacBio HiFi reads and Hi-C technologies

Tiezhu Yang #  1   2 , Liangjie Zhao #  1   2 , Chaoqun Su  1   2 , Xusheng Guo  3   4   5 , Xinliang Peng  6   7 , Shijie Yang  8 , Gaoyou Yao  1   2
Affiliations

Chromosome-scale assembly of the Xenocypris davidi using PacBio HiFi reads and Hi-C technologies

Tiezhu Yang et al. Sci Data. .

Abstract

Xenocypris davidi is a benthic fish species widely distributed in the water systems south of the Yellow River in China, playing a significant role in aquatic ecosystems. Despite its ecological and economic importance, genomic resources for X. davidi are limited, hindering a comprehensive understanding of its evolutionary adaptations and genetic improvements. This study presents the first chromosome-level genome assembly of X. davidi, utilizing PacBio long-reads, Illumina short reads, and Hi-C sequencing data. The genome assembly spans 1.05 Gb with a scaffold N50 length of 33.99 Mb, and 95.12% of the genome sequence was successfully anchored onto 24 pseudochromosomes. We identified 27,360 protein-coding genes, of which 26,672 were functionally annotated. This genome sequence provides a valuable resource for exploring the molecular basis of agronomic traits in X. davidi and will facilitate its genetic enhancement.

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Conflict of interest statement

Competing interests: The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
A circus plot of 24 chromosomes of X. davidi. The tracks from outside to inside are: 24 chromosomes, the distributions of transposable element and bar plot for gene density profile.
Fig. 2
Fig. 2
Hi-C chromatin interaction heatmap of the X. davidi assembly.
Fig. 3
Fig. 3
Comparisons of the genomic elements of closely related species.
Fig. 4
Fig. 4
Gene prediction and functional annotation of the X. davidi genome. (A) Venn diagram of the gene set prediction. (B) Venn diagram of functional annotation based on different databases.
See this image and copyright information in PMC

References

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    1. Li, C. et al. Effects of Different Levels of Bee Pollen in Feed on Reproductive Performance of Xenocypris davidi Bleeker. Agricultural Science and Technology20, 48–52 (2019).

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