Chromosome-Scale Assembly of Capsella orientalis, Maternal Progenitor of Cosmopolitan Allotetraploid 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 (Hi-C), we assembled the genome into eight pseudo-chromosomes with high contiguity, evidenced by a benchmarking universal single-copy orthologs (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 the exception of a 1.8 Mb region absent in O subgenome but present in C. orientalis. The genome annotation includes 27,675 protein-coding genes, with most exhibiting one-to-one orthology with Arabidopsis thaliana. Notably, 2,155 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.