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Summary  We present draft genome assemblies of  Beta patula , a critically endangered wild beet endemic to the Madeira archipelago, and of the closely related  Beta vulgaris  ssp.  maritima  (sea beet). Evidence‐based reference gene sets for  B. patula  and sea beet were generated, consisting of 25 127 and 27 662 genes, respectively. The genomes and gene sets of the two wild beets were compared with their cultivated sister taxon  B. vulgaris  ssp.  vulgaris  (sugar beet). Large syntenic regions were identified, and a display tool for automatic genome‐wide synteny image generation was developed. Phylogenetic analysis based on 9861 genes showing 1:1:1 orthology supported the close relationship of  B. patula  to sea beet and sugar beet. A comparative analysis of the  Rz2  locus, responsible for rhizomania resistance, suggested that the sequenced  B. patula  accession was rhizomania susceptible. Reference karyotypes for the two wild beets were established, and genomic rearrangements were detected. We consider our data as highly valuable and comprehensive resources for wild beet studies,  B. patula  conservation management, and sugar beet breeding research.

Genomes of the wild beets Beta patula and Beta vulgaris ssp. maritima