A telomere-to-telomere chromosome-scale genome assembly of glass catfish (Kryptopterus vitreolus)

Abstract

Glass catfish (Kryptopterus vitreolus) is commonly distributed in several Asian countries, such as Thailand, Malaysia, and Indonesia. It is renowned for its near-transparent appearance, which has drawn considerable attention for biomedical research and the tropical ornamental fish industry. Here, we successfully constructed the first telomere-to-telomere (T2T) chromosome-scale genome assembly for glass catfish, by integration of PacBio HiFi, Nanopore ONT ultra-long, and Hi-C sequencing technologies. The haplotypic assembly covers approximately 687.7 Mb in length, featuring a high contig N50 of 21.3 Mb. This assembly was then anchored into 32 chromosomes, presenting a complete set of 64 telomeres and 32 centromeres. It was predicted with 252.4 Mb of repetitive sequences and annotated with a total of 24,696 protein-coding genes. Subsequent BUSCO analysis revealed high genome completeness (up to 96.4%). This high-quality T2T genome assembly not only provides a valuable genetic resource for investigating the molecular mechanisms underlying transparency, but also supports in-depth studies on functional genomics, genetic diversity, and selective breeding for this economically important fish species.

Fig. 1

A chromosomal heatmap derived from Hi-C data. A total of 32 chromosomes (blue boxes) were successfully anchored.

Fig. 2

A Circos image of the 32 anchored chromosomes within the assembled haplotypic genome. Data from the outside to the inside include the length and number of each chromosome, gene density distribution (bin = 0.1 Mb), GC content (bin = 0.1 Mb), repetitive sequence density (bin = 0.1 Mb), and a fish photo (in the center).

Fig. 3

Localization of telomeres and centromeres and the distribution pattern of repetitive sequences in the assembled genome of glass catfish. Arrows represent the complete set of 64 telomeres at both ends of the 32 chromosomes. One centromer is localized within each chromosome. Repetitive sequences are marked with different colors (a ruler in the top right is provided as the density reference).