Gapless genome assembly of azalea and multi-omics investigation into divergence between two species with distinct flower color

作者：Shuai Nie, Shiwei Zhao, Tian‐Le Shi, Wei Zhao, Rengang Zhang, Xue‐Chan Tian, Jing‐Fang Guo, Xuemei Yan, Yu-Tao Bao, Zhichao Li, Lei Kong, Hai-Yao Ma, Zhaoyang Chen, Hui Liu, Yousry A. El‐Kassaby, Ilga Porth, Fu‐Sheng Yang, Jian‐Feng Mao · 发表于：Horticulture Research · 年份：2022 · DOI：10.1093/hr/uhac241 · 被引用次数：65 · 研究领域：Plant biochemistry and biosynthesis、Plant Gene Expression Analysis、Genomics and Phylogenetic Studies

Abstract 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 bre...