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. 2025 Jun 18;12(1):1025.
doi: 10.1038/s41597-025-05367-0.

Telomere-to-telomere genome assembly of Phoxinus lagowskii

Yanfeng Zhou #  1 , Chunhai Chen #  2 , Dian Fang  1 , Chenhe Wang  2 , Yajuan Peng  2 , Binhu Wang  2 , Minying Zhang  1 , Yang You  1 , Yixin Liu  3 , Guoping Deng  4 , Jianbo Jian  5   6 , Dongpo Xu  7
Affiliations

Telomere-to-telomere genome assembly of Phoxinus lagowskii

Yanfeng Zhou et al. Sci Data. .

Abstract

As an important economic and ecological fish, Amur minnow (Phoxinus lagowskii) plays a significant role in food products as well as evolutionary, ecological research. However, a high-quality chromosome-level genome of P. lagowskii is not currently available. In this study, we report a T2T (Telomere-to-telomere) genome for P. lagowskii with chromosome-level. The finally assembled genome size is 1.04 G, with a contig N50 of 41.7 Mb, comprising 25 chromosomes. The transposable elements constituted 512.40 Mb (49.22%) of the assembled P. lagowskii genome, with DNA transposons 25.02% being the predominant repeat type. A total of 2,4610 protein-coding genes were predicted in P. lagowskii genome, with 99.96% of these genes being functionally annotated. The identification of telomeres, BUSCO assessment, mapping coverage, and sequencing depth collectively demonstrated the high quality of the genome assembly. The T2T genomic information serves as an invaluable resource for studies in evolution, comparative genomics, fish breeding applications, 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 characteristics of P. lagowskii. (a)The picture of the P. lagowskii. (b) The genomescope plot of the P. lagowskii genome survey. (c) The circos plot of the P. lagowskii T2T genome. a: gene density in 1-Mb sliding windows; b: GC content in non-overlapping 1 Mb windows; c: percentage of tandem repeats in 1 Mb sliding windows; d: percentage of interspersed repeats in 1 Mb sliding windows; e: the heatmap of telomeric locations; f: the position of centromeres; g: the length of chromosomes in the size of Mb.
Fig. 2
Fig. 2
Hi-C intra-chromosomal interaction map in P. lagowskii with 500 Kb.
Fig. 3
Fig. 3
Functional annotation of P. lagowskii protein-coding genes. (a) Venn diagram of functional annotation of the P. lagowskii genome. (b) The functional annotation statistics in seven databases.
Fig. 4
Fig. 4
Genome evaluation of P. lagowskii. (a) GC content and depth distribution of HiFi reads in P. lagowskii genome. (a) BUSCO assessment of P. lagowskii and P. Phoxinus genomes.
Fig. 5
Fig. 5
The sequence comparison between P. lagowskii and P. Phoxinus genomes.
Fig. 6
Fig. 6
The synteny comparison of P. lagowskii to Phoxinus Phoxinus using protein-coding gene synteny.
See this image and copyright information in PMC

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