Abstract

Background Euphorbia maculata is a herbaceous plant in China, known for its medicinal properties. The main active components of E. maculata are flavonoids. However, the biosynthesis mechanism of flavonoids in E. maculata remains poorly understood due to the limited availability of genetic information. In order to explore the flavonoid biosynthesis mechanism of this species, we carried our study. Results A total of 20,238 non-redundant transcript isoforms were acquired with an N50 length of 2,994 bp and an average length of 2,766.82 bp. Of these isoforms, 20,069 (99.16%) were successfully annotated in NR, Swissprot, KOG, GO, and KEGG databases. Additionally, 20,085 coding sequences (CDSs), 117 long noncoding RNAs (LncRNAs), and 971 transcription factors (TFs) were identified from the full-length transcriptome data. The RNA-Seq data was then analyzed using the full-length transcriptome as a reference sequence, revealing 27 differentially expressed genes (DEGs) involved in phenylpropanoid pathway in E. maculata . These included 15 PAL , 5 C4H , 4 4CL , and 3 CHS genes. The expression levels of these DEGs were found to vary in the leaf and stem across five different periods, with the majority of phenylpropanoid pathway genes being upregulated in the stem compared to the leaf at the same period. Protein-protein interaction (PPI) analysis revealed that the bHLH , HD-ZIP , bZIP , MYB , FAR1 , and AP2 may regulate the expression of 5 C4H and 3 CHS . Furthermore, through analyzing the correlation between the expression levels of DEGs and the accumulation of flavonoids in various tissues of E. maculata at different stages, we found that 2 PAL , 2 C4H , 1 4CL , and 2 CHS may play a crucial role in regulating flavonoid biosynthesis in this species. Conclusions Our study enriched the genomic resources and revealed candidate genes involved in phenylpropanoid pathway in E. maculata . These findings provide candidate gene resources for further investig