Chromosome-level genome assembly of Oxyria digyna

Abstract

Oxyria digyna is a perennial herb widely distributed across Arctic and Alpine regions, representing one of the oldest extant Arctic plant lineages. Despite its ecological and evolutionary importance, no chromosome-scale reference genome has been published as a research paper to date. Here, we present two high-quality chromosome-level genome assemblies of O. digyna generated using high-fidelity long-read sequencing data and long-read–based chromatin conformation capture sequencing data. Our final phased genome assemblies span 548.60 Mb and 540.00 Mb with scaffold N50 values of 77.17 Mb and 76.59 Mb, respectively. Karyotyping confirmed a chromosome number of 2n = 14, which matches the number of chromosome-scale scaffolds in our final genome assemblies. Also, Telomere-to-telomere continuity was achieved for three chromosomes in one haplotype. The assemblies exhibit high completeness and accuracy, with BUSCO scores exceeding 95% and QV values above 57. Gene annotation identified 20,794 genes, including 19,500 protein-coding genes. Pan-genome analysis incorporating publicly available assemblies revealed 3.17 million variant loci, including 84,360 structural variants. This chromosome-level genome provides a valuable resource for studying Arctic plant adaptation, genome evolution, and genetic mechanisms underlying environmental resilience.