A high-quality chromosome-level genome assembly of the Chinese medaka Oryzias sinensis

Abstract

Oryzias sinensis, also known as Chinese medaka or Chinese ricefish, is a commonly used animal model for aquatic environmental assessment in the wild as well as gene function validation or toxicology research in the lab. Here, a high-quality chromosome-level genome assembly of O. sinensis was generated using single-tube long fragment read (stLFR) reads, Nanopore long-reads, and Hi-C sequencing data. The genome is 796.58 Mb, and a total of 712.17 Mb of the assembled sequences were anchored to 23 pseudo-chromosomes. A final set of 22,461 genes were annotated, with 98.67% being functionally annotated. The Benchmarking Universal Single-Copy Orthologs (BUSCO) benchmark of genome assembly and gene annotation reached 95.1% (93.3% single-copy) and 94.6% (91.7% single-copy), respectively. Furthermore, we also use ATAC-seq to uncover chromosome transposase-accessibility as well as related genome area function enrichment for Oryzias sinensis. This study offers a new improved foundation for future genomics research in Chinese medaka.

Fig. 1

(A) Global genome landscape of Chinese medaka. From inner to outer circles: Density of genes with 500 kbp windows, ranging from 0 to 50; Density of TE with 500 kbp windows, ranging from 0 to 600; Density of TRF with 500 kbp windows, ranging from 0 to 450; Distributions of GC content with 500 kbp windows. (B) Hi-C interaction heat map and scatter plot of genome assembly GC content and sequencing depth.

Fig. 2

ATAC-seq peaks result from related genes’ functional enrichment. (A) GO enrichment; (B) KEGG enrichment.