Chromosome-level genome assembly and annotation of the Spinibarbus caldwelli

• Published in: Scientific data 2024-08, Vol.11 (1), p.933-9, Article 933
• Main Authors: Wu, Lina, Gu, Sui, Wen, Ping, Wu, Lisheng, Li, Leibin, Guo, Shaopeng, Ding, Shaoxiong
• Format: Article
• Language: English
• Subjects: 631/208; 704/158; Animals; Annotations; China; Chromatin; Chromosomes; Data Descriptor; Earth science; Fishing; Gene mapping; Genetic structure; Genome; Genomes; Germplasm; Humanities and Social Sciences; Molecular Sequence Annotation; multidisciplinary; Science; Science (multidisciplinary); Smicridea caldwelli; SMRT protein; Software; Spinibarbus
• ISSN: 2052-4463; 2052-4463
• DOI: 10.1038/s41597-024-03796-x

Spinibarbus caldwelli is an important freshwater economic fish in China. Owing to uncontrolled fishing, wild resources of S. caldwelli have decreased rapidly and may be on the verge of extinction. In this study, utilizing single-molecule real-time (SMRT) sequencing technology and chromatin interaction mapping (Hi-C) technologies, we assembled the first chromosome-scale genome for S. caldwelli about 1.77 Gb in size, with a contig N50 length of 11.83 Mb and scaffold N50 length of 33.91 Mb. In total 1.72 Gb (97.01%) of the contig sequences were anchored onto fifty chromosomes with the longest scaffold being 56.20 Mb. Furthermore, proximately 49.41% of the genome was composed of repetitive elements. In total, 49,377 protein-coding genes were predicted, of which 47,724 (96.65%) genes have been functionally annotated. The high-quality chromosome-level reference genome and annotation are vital for supporting basic genetic studies and will be contribute to genetic structure, functional elucidation, evolutionary inquiry, and germplasm conservation for S. caldwelli .