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. 2025 Oct 10:10:560.
doi: 10.12688/wellcomeopenres.25028.1. eCollection 2025.

The genome sequence of the Panther Danio, Danio aesculapii Kullander & Fang, 2009

Kerstin Howe  1 , Braedan McCluskey  2 , Zoltan Varga  3 , Bill Trevarrow  4 , Shane A McCarthy  1   5 , Sarah Pelan  1 , Jonathan M D Wood  1 , Michelle Smith  6 , Karen Oliver  6
Affiliations

The genome sequence of the Panther Danio, Danio aesculapii Kullander & Fang, 2009

Kerstin Howe et al. Wellcome Open Res. .

Abstract

We present a genome assembly from a female specimen of Danio aesculapii (the Panther Danio; Chordata; Actinopteri; Cypriniformes; Cyprinidae). The genome sequence is 1,381.5 megabases in span. Most of the assembly is scaffolded into 25 chromosomal pseudomolecules. Gene annotation of this assembly on Ensembl identified 23,884 protein coding genes.

Keywords: Cypriniformes; Danio aesculapii; Panther Danio; chromosomal; genome sequence.

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Conflict of interest statement

No competing interests were disclosed.

Figures

Figure 1.
Figure 1.. Image of Danio aesculapii (not the specimen used for genome sequencing).
Photograph by Andrewbogott.
Figure 2.
Figure 2.. Genome assembly of Danio aesculapii, fDanAes4.1: metrics.
The BlobToolKit Snailplot shows N50 metrics and BUSCO gene completeness. The main plot is divided into 1,000 size-ordered bins around the circumference with each bin representing 0.1% of the 1,381,485,597 bp assembly. The distribution of sequence lengths is shown in dark grey with the plot radius scaled to the longest sequence present in the assembly (74,595,647 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 sequence lengths (55,996,547 and 46,123,639 bp), respectively. The pale grey spiral shows the cumulative sequence count on a log scale with white scale lines showing successive orders of magnitude. The blue and pale-blue area around the outside of the plot shows the distribution of GC, AT and N percentages in the same bins as the inner plot. A summary of complete, fragmented, duplicated and missing BUSCO genes in the actinopterygii_odb10 set is shown in the top right. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/GCA_903798145.1/dataset/CAIGQR01/snail.
Figure 3.
Figure 3.. Genome assembly of Danio aesculapii, fDanAes4.1: BlobToolKit GC-coverage plot.
Scaffolds are coloured by phylum. Circles are sized in proportion to scaffold length. Histograms show the distribution of scaffold length sum along each axis. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/GCA_903798145.1/dataset/CAIGQR01/blob.
Figure 4.
Figure 4.. Genome assembly of Danio aesculapii, fDanAes4.1: BlobToolKit cumulative sequence plot.
The grey line shows cumulative length for all scaffolds. Coloured lines show cumulative lengths of scaffolds assigned to each phylum using the buscogenes taxrule. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/GCA_903798145.1/dataset/CAIGQR01/cumulative.
Figure 5.
Figure 5.. Genome assembly of Danio aesculapii, fDanAes4.1: Hi-C contact map of the fDanAes4.1 assembly, visualised using HiGlass.
Chromosomes are shown in order of size from left to right and top to bottom. An interactive version of this figure may be viewed at https://genome-note-higlass.tol.sanger.ac.uk/l/?d=NqfPyxSZSEC7xRCzeZhxYA
See this image and copyright information in PMC

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