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Article|26 Oct 2022|OPEN
Gapless genome assembly of azalea and multi-omics investigation into divergence between two species with distinct flower color
Shuai Nie1 , Shi-Wei Zhao1 , Tian-Le Shi1 , Wei Zhao2 , Ren-Gang Zhang3 , Xue-Chan Tian1 , Jing-Fang Guo1 , Xue-Mei Yan1 , Yu-Tao Bao1 , Zhi-Chao Li1 , Lei Kong1 , Hai-Yao Ma1 , Zhao-Yang Chen1 , Hui Liu1 , Yousry A. El-Kassaby4 , Ilga Porth5 , Fu-Sheng Yang6,7 , , Jian-Feng Mao,1 ,
1National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
2Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, SE-901 87 Umeå, Sweden
3Department of Bioinformatics, Ori (Shandong) Gene Science and Technology Co., Ltd., Weifang 261322, China
4Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
5Départment des Sciences du Bois et de la Forêt, Faculté de Foresterie, de Géographie et Géomatique, Université Laval, Québec, QC, G1V 0A6, Canada
6State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
7University of Chinese Academy of Sciences, Beijing 100049, China
*Corresponding author. E-mail:,

Horticulture Research 10,
Article number: uhac241 (2023)
Views: 277

Received: 15 Aug 2022
Accepted: 17 Oct 2022
Published online: 26 Oct 2022


The genus Rhododendron (Ericaceae), with more than 1000 species highly diverse in flower color, is providing distinct ornamental values and a model system for flower color studies. Here, we investigated the divergence between two parental species with different flower color widely used for azalea breeding. Gapless genome assembly was generated for the yellow-flowered azalea, Rhododendron molle. Comparative genomics found recent proliferation of long terminal repeat retrotransposons (LTR-RTs), especially Gypsy, has resulted in a 125 Mb (19%) genome size increase in species-specific regions, and a significant amount of dispersed gene duplicates (13 402) and pseudogenes (17 437). Metabolomic assessment revealed that yellow flower coloration is attributed to the dynamic changes of carotenoids/flavonols biosynthesis and chlorophyll degradation. Time-ordered gene co-expression networks (TO-GCNs) and the comparison confirmed the metabolome and uncovered the specific gene regulatory changes underpinning the distinct flower pigmentation. B3 and ERF TFs were found dominating the gene regulation of carotenoids/flavonols characterized pigmentation in R. molle, while WRKY, ERF, WD40, C2H2, and NAC TFs collectively regulated the anthocyanins characterized pigmentation in the red-flowered R simsii. This study employed a multi-omics strategy in disentangling the complex divergence between two important azaleas and provided references for further functional genetics and molecular breeding.