Chromosome-scale assembly of Capsella orientalis, maternal progenitor of cosmopolitan hybrid C. bursa-pastoris. Chromosome-scale assembly of Capsella orientalis, maternal progenitor of cosmopolitan hybrid C. bursa-pastoris

The genus Capsella serves as a model for understanding speciation, hybridization, and genome evolution in plants. Here, we present a chromosome-scale genome assembly of Capsella orientalis, the maternal progenitor of a cosmopolitan allotetraploid C. bursa-pastoris. Using nanopore sequencing and data on chromatin contacts (HiC) we assembled the genome into eight pseudo-chromosomes with high contiguity, evidenced by a BUSCO completeness score of 99.3%. Comparative analysis with C. rubella and C. bursa-pastoris revealed overall synteny, except for 2 Mb inversion on chromosome 4 of C. rubella. Comparative genome analysis highlighted the conservation of gene content and structural integrity in the C. orientalis-derived subgenome of C. bursa-pastoris, with exception of a 1.8 Mb region absent in O-subgenome but present in C. orientalis. The genome annotation includes 27,889 protein-coding genes, with most exhibiting one-to-one orthology with Arabidopsis thaliana. Notably, 2,258 genes showed no similarity to A. thaliana ones. These results establish a robust genomic resource for C. orientalis, facilitating future studies on polyploid evolution, gene regulation, and species divergence within Capsella. This assembly is being updated. The actual version can be found at: https://doi.org/10.6084/m9.figshare.28081604.v1