The ornamental value of the lotus flower is largely determined by its color. To further understand the regulatory mechanism underlying the anthocyanin pigmentation, digital gene expression analyses through RNA-seq were performed on the early developmental stages of leaf and flower buds during the coloration process in lotus cultivar ‘Yehonglian’ (with red flowers). A total of 13022 differentially expressed genes (DEGs) were identified with the largest number of DEGs being enriched in the biosynthesis of secondary metabolites, especially the flavonoid biosynthesis pathway. Further analysis revealed that 47 DEGs were involved in anthocyanin biosynthesis pathway and one anthocyanin-3-O-glucosyltransferase (UFGT) coding gene may be the key player in anthocyanin biosynthesis during the development of lotus flower and leaf buds. Additionally, 5 MYB, 2 bHLH, and 1 WD-repeat gene may be the candidate transcription factors that regulate anthocyanin biosynthesis. This study characterized potential candidate genes involved in anthocyanin biosynthesis and might provide new insights into the coloration mechanisms of lotus.

莲花的观赏价值很大程度上取决于它的颜色。为了进一步了解花青素色素沉着的调控机制，通过RNA-seq对荷花品种'野红莲'（红色花朵）着色过程中叶和花芽的早期发育阶段进行了数字基因表达分析。共鉴定出 13022 个差异表达基因 (DEGs)，其中最多的 DEGs 富集在次生代谢物的生物合成中，尤其是黄酮类生物合成途径。进一步分析表明，47个DEGs参与花青素生物合成途径和1个花青素-3-O-葡萄糖基转移酶（UFGT）) 编码基因可能是莲花和叶芽发育过程中花青素生物合成的关键参与者。此外，5个MYB、2个bHLH和1个WD-repeat基因可能是调控花青素生物合成的候选转录因子。这项研究表征了参与花青素生物合成的潜在候选基因，并可能为莲花的着色机制提供新的见解。