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

The root vegetable table beet (Beta vulgaris subsp. vulgaris var. vulgaris), also known as red beet or beetroot, holds considerable nutritional and agricultural importance. However, comprehensive genomic resources for this species remain scarce. Researchers have now unveiled the chromosome-scale genome assembly RefTab-1, derived from the inbred table beet genotype W357B.

This assembly, constructed using PacBio and Hi-C data, measures 668.6 megabases with an N50 of 72 megabases. Remarkably, 96% of the assembly is anchored to nine pseudo-chromosomes.

The genome assembly is richly annotated, featuring 64% repetitive DNA, 24,863 protein-coding genes, and 10,405 non-coding RNA loci. Among these, a cluster of 5S rRNA genes is located on chromosome 4. Additionally, the genome underwent comprehensive methylation profiling via EM-seq, revealing substantial cytosine methylation in repeats, as well as context-specific methylation patterns in gene bodies and promoters.

The team proposes three terpene synthase candidate genes based on functional annotation and their spatial proximity to a genetic marker on chromosome 8, previously linked to geosmin concentration. This compound is responsible for table beet's characteristic earthy aroma. A comparative analysis with sugar beet highlights overall structural conservation, accompanied by a 9 megabase inversion on chromosome 9.

These high-quality genomic resources for table beet will greatly benefit genetic, epigenetic, and comparative studies within the Beta vulgaris genus, ultimately advancing beet biology and breeding programs.