Chromosome-level genome assembly and annotation of Japanese anchovy (Engraulis japonicus)

This dataset comprises raw sequencing reads (PacBio HiFi long reads, Illumina short reads, Hi-C data, and RNA-Seq from brain, ovary, heart, muscle, and liver), the chromosome-level genome assembly (1.42 Gb across 24 pseudochromosomes), repeat annotations (54.9% of the genome), gene predictions (24,405 protein-coding genes), and functional annotations (97.15% of genes annotated). The assembly achieves 94.07% completeness (BUSCO) and provides critical resources for population genomics and evolutionary studies of Engraulis japonicus.