Chromosome-level genome assembly of a parent species of widely cultivated azaleas

Yves Van de Peer,Rengang Zhang ,Yousry A. El‐Kassaby ,Na An,Quanzheng Yun ,Ilga Porth,Shanshan Zhou ,Jian‐Feng Mao ,Yu-Tao Bao,Nathaniel R. Street ,Zhao Wang ,Kai‐Hua Jia ,Hui Liu,Tian-Le Shi,Yang Fang ,Xiaoru Wang ,Chanaka Mannapperuma,Xue Tian ,Jing‐Fang Guo ,Xinzhu Wang ,Shuai Nie

doi:10.1038/s41467-020-18771-4

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.

Highlights

Azaleas (Ericaceae) comprise one of the most diverse ornamental plants, renowned for their cultural and economic importance
The assembly is slightly larger than the estimated genome size, which may be due to high heterozygosity (~1.78%, estimated with K-mer frequency, see Supplementary Note 1 for details)
After mapping the Illumina reads to the final assembly, single nucleotide polymorphisms (SNPs) were identified with SAMtools[9] and obtained a SNP heterozygosity level of ~1.07% and a single base error rate of ~0.0054% was obtained

Summary

Introduction

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. This work provides a cornerstone for understanding the underlying genetics governing flower timing and coloration and could accelerate selective breeding in azalea. We unravel the metabolic co-expression network of flower pigmentation and identified the structural genes, and their potential regulators, of flower coloring through time-ordered comparative transcriptome analyses. The availability of this reference genome sequence and information on the molecular basis and the genetic mechanisms governing flower color in Rhododendron present valuable resources for the development of consumer-oriented selective breeding novelties of azalea

Methods

Results

Conclusion