Rhododendron genus is famous with important ecology impacts, ornamental values, and high medicine values. To obtain a comprehensive overview of anthocyanin regulatory networks, RNA-seq and de novo assembly of five Rhododendron species flower tissues were performed, generating 159,408 unigenes with an average length of 490 bp and an N50 of 552 bp. In particular, 106,766 unigenes could be annotated. Flavonoid biosynthesis was the most abundant KEGG pathway. Genes controlling flower color varied in different species: transcripts involving in carotenoid biosynthesis and isoflavonoid biosynthesis highly expressed in Rhododendron molle G. Don possessing yellow color flower; genes involved in flavone and flavonol biosynthesis showed higher abundance in Rhododendron fortune Lindl. with light pink flowers; transcripts of unigenes participated in flavonoid biosynthesis exhibited higher levels in Rhododendron mariesii Hemsl. with pink color; unigenes involved in anthocyanin biosynthesis showed higher mRNA levels in Rhododendron simsii Planch. with red color; genes involved in carotenoid biosynthesis and flavonoid biosynthesis showed higher expression levels in Rhododendron pulchrum Sweet with purplish red flowers. The five species were clustered into two main groups: group 1 (R. fortune and R. mariesii) and group 2 (R. simsii, R. molle and R. pulchrum) based on expression levels of differentially expressed genes (DEGs). In particular, R. molle showed a closer relationship with R. simsii. This study will provide rich genetic information for further mechanism analysis of flower color variation and genetic improvement of flower color in Rhododendron species.

杜鹃属植物以重要的生态影响、观赏价值和较高的药用价值而闻名。为了全面了解花青素调控网络，对五种杜鹃花的花组织进行了RNA-seq 和从头组装，产生了 159,408 个平均长度为 490 bp 和 N50 为 552 bp 的 unigenes。特别是，可以注释 106,766 个 unigenes。黄酮类生物合成是最丰富的 KEGG 途径。不同物种控制花色的基因不同：涉及类胡萝卜素生物合成和异黄酮生物合成的转录本在杜鹃花中高表达。参与黄酮和黄酮醇生物合成的基因在杜鹃花财富Lindl。带着淡粉色的花朵；参与黄酮类生物合成的unigenes 转录本在Rhododendron mariesii Hemsl 中表现出更高的水平。粉红色; 参与花青素生物合成的unigenes在杜鹃花中显示出更高的 mRNA 水平。红色; 参与类胡萝卜素生物合成和类黄酮生物合成的基因在具有紫红色花朵的杜鹃花中表现出更高的表达水平。五个种聚为两个主要的组：组1（R.财富和R. mariesii）和组2（R. simsii，R. MOLLE和R. pulchrum) 基于差异表达基因 (DEG) 的表达水平。特别是，R. molle与R. simsii表现出更密切的关系。本研究将为进一步分析杜鹃花花色变异的机制及花色遗传改良提供丰富的遗传信息。