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

Bian C 1 , Li D 2 , Wang Y 2 , He Z 2 , Chen WT 3 , Chong CM 4 Show all authors , Zhou H 5 , Shi Q 6

Affiliations 

  • 1 Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518057, China. bianchao@szu.edu.cn
  • 2 Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518057, China
  • 3 School of Life Sciences, Jiaying University, Meizhou, Guangdong, 514015, China
  • 4 State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, 999078, China
  • 5 Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518116, China
  • 6 Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518057, China. shiqiong@genomics.cn
Sci Data, 2025 Mar 23;12(1):483.
PMID: 40122884 DOI: 10.1038/s41597-025-04841-z

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.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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