Structure and Evolution of the Mesohexaploid Radish (Raphanus sativus L.) Genome

Radish (Raphanus sativus L.) is an agronomically important root vegetable crop and its origin and phylogenetic position in the tribe Brassiceae is controversial. Here we present a comprehensive analysis of the radish genome based on the fully-sequenced and annotated chromosome sequences. The radish genome was sequenced and assembled into 426.2 Mb spanning >98% of the gene space, of which 344.0 Mb were integrated into nine chromosome pseudomolecules. Approximately 36% of the genome was repetitive sequences and 46,514 protein-coding genes were predicted and annotated. Comparative mapping of the tPCK-like ancestral genome revealed that the radish genome has intermediate characteristics between the Brassica A/C and B genomes in the triplicated segments, suggesting an internal origin from the genus Brassica. The evolutionary characteristics shared between radish and other Brassica species provided genomic evidences that the current form of 9 chromosomes in radish was reconstructed from 12 chromosomes. Overall, this study provides a reference genome sequence of radish as well as novel insight into evolution of the mesohexaploid genomes in the tribe Brassiceae.