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bioRxiv · 10.64898/2026.09.07.749830

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

Holzweber, T.·Dorn, K. M.·Rasaki, L. A.·Dohm, J. C.·Himmelbauer, H.
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Abstract

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.

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Holzweber, T., Dorn, K. M., Rasaki, L. A., Dohm, J. C., Himmelbauer, H.. 2026-09-11. Genome and methylome of the root crop table beet (Beta vulgaris). https://doi.org/10.64898/2026.09.07.749830

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