Polyploid genome assembly of Cardamine chenopodiifolia

<i>Cardamine chenopodiifolia</i> is an amphicarpic plant in the Brassicaceae family. Plants develop two fruit types, one above and another below ground. This rare trait is associated with octoploidy in <i>C. chenopodiifolia</i>. The absence of genomic data for <i>C. chenopodiifolia</i> currently limits our understanding of the development and evolution of amphicarpy. Here, we produced a chromosome-scale assembly of the <i>C. chenopodiifolia</i> genome using high-fidelity long read sequencing with the Pacific Biosciences platform. We assembled 32 chromosomes and two organelle genomes with a total length of 597.2 Mb and an N50 of 18.8 Mb. Genome completeness was estimated at 99.8%. We observed structural variation among homeologous chromosomes, suggesting that <i>C. chenopodiifolia</i> originated via allopolyploidy, and phased the octoploid genome into four sub-genomes using orthogroup trees. This fully phased, chromosome-level genome assembly is an important resource to help investigate amphicarpy in <i>C. chenopodiifolia</i> and the origin of trait novelties by allopolyploidy.