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

Key message Using Pacbio and Hi-C technology, we obtained the whole genome assembly of Carex rigescens and established its transformation system , providing new insights into the study of Carex rigescens . Abstract 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 obtained a high-quality genome assembly of C. rigescens using Illumina, PacBio and Hi-C technologies. Sequences totaling 582.39 Mb in length can be anchored to 60 chromosomes. The genome has 59,761 genes with functional annotations (91.28%), and a total of 30.30% of the genome was occupied by repetitive sequences. Evolutionary analysis reveals that one WGD event had occurred in C. rigescens and 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. It also lays the foundation for the acquisition of transgenic C. rigescens.