Chromosome-level genome assembly of a parent species of widely cultivated azaleas
Fu‐Sheng Yang, Shuai Nie, Hui Liu, Tian‐Le Shi, Xue‐Chan Tian, Shanshan Zhou, Yu-Tao Bao, Kai‐Hua Jia, Jing‐Fang Guo, Wei Zhao, Na An, Rengang Zhang, Quanzheng Yun, Xinzhu Wang, Chanaka Mannapperuma, Ilga Porth, Yousry A. El‐Kassaby, Nathaniel R. Street, Xiaoru Wang, Yves Van de Peer, Jian‐Feng Mao
Abstract
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.