Chromosome-level genome assembly, annotation, evolutionary analysis, and establishment of transformation systems in...

Using PacBio and Hi-C technologies, we generated a chromosome-level whole-genome assembly of Carex rigescens and established its genetic transformation system, which provides novel insights into the research of this species. Carex rigescens is an important turfgrass species and grass for ecological restoration, but the lack of genomic resources in the genus Carex has hindered its genetic improvement. In this study, C. rigescens was determined to be diploid (2n = 60) by flow cytometry and chromosome visualization. We generated a high-quality genome assembly of C. rigescens via a combination of Illumina, PacBio, and Hi-C technologies, with 300 Mb of sequences anchored to 30 chromosomes. This genome contains 59,761 functionally annotated protein-coding genes (91.28%), and repetitive sequences account for 33.28% of the total genome length. Evolutionary analysis reveals that one WGD event had occurred in C. rigescens and that an LTR burst in C. rigescens occurred around 0.04 Mya. We also performed WOX gene family analysis, including its localization and classification on the chromosomes of C. rigescens, as well as the analysis of cis-acting elements in the CrWOX14 promoter. The first efficient regeneration and transformation system was established. These findings provide new insights into the characterization and evolution of the genomes of the genus Carex and provide a reference for comparative genetic and genomic studies of the genus Carex. They also lay the foundation for the acquisition of transgenic C. rigescens.