Chromosome-scale phased genome assembly and annotations of Cardamine amara
The genus Cardamine (Brassicaceae) includes several well-established model species widely used in evolutionary biology, ecology, and developmental studies. While a chromosome-scale reference genome is available for C. hirsuta, its close relative C. amara, a widespread diploid with unique ecological and reproductive traits and a tendency toward polyploid formation, has lacked equivalent genomic resources. This gap has limited genomic investigation of an otherwise extensively studied system. Here, we present two chromosome-scale, haplotype-resolved genome assemblies for a diploid C. amara individual from Velký Reckov, Czech Republic, generated using 444-fold PacBio HiFi long-read coverage and 320-fold Hi-C data. The two haplomes span 211.96 Mb and 212.03 Mb, with scaffold N50s of 27.01 Mb and 26.41 Mb, respectively. Gene space completeness is exceptionally high in both assemblies (BUSCO =99.6%). Comparative genomic analyses confirmed a major pericentromeric inversion between C. amara and C. hirsuta and revealed large structural variants even between haplomes within this single heterozygous individual. These high-quality C. amara assemblies provide essential genomic references that will enable deeper insights into genome structure, evolution, and adaptation across the Cardamine genus.
The genus Cardamine (Brassicaceae) includes several well-established model species widely used in evolutionary biology, ecology, and developmental studies. While a chromosome-scale reference genome is available for C. hirsuta, its close relative C. amara, a widespread diploid with unique ecological and reproductive traits and a tendency toward polyploid formation, has lacked equivalent genomic resources. This gap has limited genomic investigation of an otherwise extensively studied system. Here, we present two chromosome-scale, haplotype-resolved genome assemblies for a diploid C. amara individual from Velký Reckov, Czech Republic, generated using 444-fold PacBio HiFi long-read coverage and 320-fold Hi-C data. The two haplomes span 211.96 Mb and 212.03 Mb, with scaffold N50s of 27.01 Mb and 26.41 Mb, respectively. Gene space completeness is exceptionally high in both assemblies (BUSCO =99.6%). Comparative genomic analyses confirmed a major pericentromeric inversion between C. amara and C. hirsuta and revealed large structural variants even between haplomes within this single heterozygous individual. These high-quality C. amara assemblies provide essential genomic references that will enable deeper insights into genome structure, evolution, and adaptation across the Cardamine genus.