Objective  Transcriptomes of Acorus gramineus tissues were applied to molecularly differentiating flavonoid synthesis genes in the organs.

  Methods  The high-throughput sequencing technology was employed to obtain the transcriptomes of the genes in 7 organs of A, gramineus. Thereby, the functions of unigenes were annotated, the flavonoid biosynthesis pathway deciphered, the differentially expressed genes (DEGs) in the pathway screened, and an expression analysis performed.

  Results  A total of 39.91 to 42.97 M of high-quality data were secured with 5.98–6.45 Gb bases, more than 94.05% Q30 bases, and a GC content of 47.81%–50.32%. From the GO database, 62506 were annotated to classify the 18616 unigenes into 3 functional groups that included cellular components, molecular functions, and biological processes corresponding to 6, 14, and 21 subcategories, respectively. Numerous genes were distributed in the subcategories, such as cellular anatomical entities, connections, catalytic activities, and cellular processes. There were 10124 unigenes enriched in the 5 major categories and 19 subclasses of the KEGG database. From which, 4 flavonoid biosynthesis pathways, 14 key enzymes, and 63 DEGs were screened. The transcriptomes in 7 tissues of A. gramineus obtained in this study led to the identification of 63 DEGs involved in 4 flavonoid biosynthesis pathways. These genes differed in expressions in the organs indicating their diversified roles in the flavonoid biosynthesis in A. gramineus

  Conclusion  The research results have enriched the genetic information of A. gramineus and provided a reference for further elucidating the functional genes involved in the biosynthesis of flavonoids in A. gramineus.