Chromosome-scale haplome 2 genome assembly and annotation of Cardamine amara
The genus Cardamine (Brassicaceae) includes several model species widely used in evolutionary, ecological, and developmental studies. Although a chromosome-scale reference genome exists for C. hirsuta, comparable resources for its close relative C. amara have been lacking, limiting genomic research in this studied system. Here, we present the chromosome-scale, haplotype-resolved genome assembly and annotation of haplome 2 from a diploid C. amara individual collected in Velky Reckov, Czech Republic. The assembly, generated using 444-fold PacBio HiFi long-read coverage and 320-fold Hi-C data, spans 212.03 Mb with a scaffold N50 of 26.41 Mb and BUSCO completeness = 99.6 %. Comparative analyses revealed a major pericentromeric inversion relative to C. hirsuta and extensive structural variation between haplomes within this heterozygous individual. This high-quality haplome 2 assembly provides an essential genomic reference for exploring genome structure, evolution, and adaptation across the Cardamine genus.