Objective  Transcriptome of Stellaria yunnanensis root was sequenced and genes associated with the flavonoid biosynthesis identified.

  Method  Transcriptome of S. yunnanensis root was sequenced using the high-throughput Illumina Novaseq 6 000. Functional annotation of the unigenes were conducted and genes related to the biosynthesis identified.

  Result   There were 34 137 unigenes found with an average length of 1 093.58 bp. They annotated to 6 functional databases, including NR, egg NOG, Pfam, Swiss-Prot, GO, and KEGG, that numbered 22 369 in total. There were 21 510 unigenes annotated in NR database, which had high homology with Beta vulgaris, Chenopodium quinoa, and Spinacia oleracea of Chenopodiaceae, while 19 980 from 19 414 unigenes in egg NOG in 23 categories, and 69 356 from 19 942 unigenes in GO in 3 major functional categories of cellular components, molecular functions, and, especially, biological processes with 14, 16, and 23 subcategories, respectively. Of the unigenes, 6 505 were enriched in 131 pathways in KEGG with the largest proportion related to the metabolism pathways, 80 associated with the flavonoid biosynthesis encoding 16 key enzymes, and 724 annotated as transcription factors.

  Conclusion  The high-throughput transcriptome sequencing and gene function annotation on the S. yunnanensis roots were successfully performed. Several unigenes related to the flavonoid synthesis were identified. The information would facilitate further studies on the key genes and mechanisms in the formation of medicinal important functional ingredient in the plant.