Azaleas (Ericaceae) comprise one of the most diverse ornamental plants, renowned for their
cultural and economic importance. We present a chromosome-scale genome assembly for
Rhododendron simsii, the primary ancestor of azalea cultivars. Genome analyses unveil the
remnants of an ancient whole-genome duplication preceding the radiation of most Ericaceae,
likely contributing to the genomic architecture of flowering time. Small-scale gene duplications
contribute to the expansion of gene families involved in azalea pigment biosynthesis.
We reconstruct entire metabolic pathways for anthocyanins and carotenoids and their
potential regulatory networks by detailed analysis of time-ordered gene co-expression networks.
MYB, bHLH, and WD40 transcription factors may collectively regulate anthocyanin
accumulation in R. simsii, particularly at the initial stages of flower coloration, and with WRKY
transcription factors controlling progressive flower coloring at later stages. This work provides
a cornerstone for understanding the underlying genetics governing flower timing and
coloration and could accelerate selective breeding in azalea.