Chromosome-level genome assembly of Sinocyclocheilus jii based on PacBio HiFi and Hi-C sequencing

Abstract

Sinocyclocheilus jii, a cavefish species endemic to China, belongs to the genus Sinocyclocheilus within the family Cyprinidae. Species within this genus exhibit significant morphological differentiation, making it not only the most species-rich genus within Cyprinidae in China but also the most diverse group of cavefishes worldwide. However, the limited availability of genomic resources has limited investigations into the genetic basis of trait variations, phylogenetic relationships, and adaptive evolution in this genus. In this study, we assembled a chromosome-level reference genome for S. jii by integrating PacBio HiFi long reads, Illumina short reads, and Hi-C sequencing data. Flow cytometry was used to estimate the genome size prior to assembly, providing a key step in technical validation. The final genome assembly spans 1.75 Gb with a contig N50 of 35.0 Mb. Using Hi-C sequencing data, the assembled scaffolds were successfully anchored to 50 chromosomes. The completeness of the chromosome-level assembly was estimated at 98.9% by BUSCO analysis. Genome annotation identified 855.5 Mb of repetitive sequences and predicted a total of 52,867 protein-coding genes, of which 51,932 genes were functionally annotated. This study presents a high-quality chromosome-level genome assembly and annotation of S. jii, providing a fundamental genomic resource for future phylogenetic and evolutionary studies.

Fig. 1

Morphological characters of the Sinocyclocheilus jii. (Image: Hongfu Yang/Source: Unpublished photograph, 2024; Reproduced with permission from Mr. Hongfu Yang).

Fig. 2

Genome size and karyotype of Sinocyclocheilus jii. (A) Diagram of C value. Flow cytometry-based genome size estimation of S. jii, with chicken blood used as internal reference. (B) Karyotype analysis diagram of Sinocyclocheilus jii. Chromosome number: 2n = 100.

Fig. 3

Hi-C contact map of the Sinocyclocheilus jii genome. The blocks represent the contacts between one location and another.

Fig. 4

Genomic features of the Sinocyclocheilus jii genome. From inner to outer tracks: (A) GC content across the genome; (B) distribution of DNA TEs across the genome; (C) distribution of RNA TEs across the genome; (D) gene density across the genome; (E) Sinocyclocheilus jii chromosomes.

Fig. 5

The functional annotation of Sinocyclocheilus jii using different databases.

Fig. 6

K-mer distribution of whole-genome sequencing reads of Sinocyclocheilus jii. (a,b,c,d) correspond to k-mer values of 21, 25, 27 and 31, respectively.