Genome and methylome of the root crop table beet (Beta vulgaris)

Table beet (Beta vulgaris subsp. vulgaris var. vulgaris), also known as red beet, garden beet, or beetroot, is an important crop with both nutritional and agricultural value, yet high-quality genomic resources for this taxon are limited. We present the chromosome-scale genome assembly RefTab-1 based on PacBio and Hi-C data of the inbred table beet genotype W357B. The assembly has a size of 668.6 Mbp and an N50 of 72 Mbp, with 96% of the assembly anchored to nine pseudo-chromosomes. We annotated 64% repetitive DNA, 24,863 protein-coding genes, and 10,405 non-coding RNA loci including a 5S rRNA cluster on chromosome 4. Genome-wide methylation profiling using EM-seq revealed high levels of cytosine methylation in repeats and context-specific methylation in gene bodies and promoters. We propose three terpene synthase candidate genes based on functional annotation and based on their location near a genetic marker on chromosome 8 previously associated with geosmin concentration, responsible for the earthy aroma of table beet. Comparative analysis with sugar beet indicated overall structural conservation and a 9 Mbp inversion on chromosome 9. These high-quality resources for table beet will enhance genetic, epigenetic, and comparative studies in Beta vulgaris, advancing beet biology and breeding programs.