Evaluation of the transcriptome of valerian (Valeriana officinalis) to identify genes involved in terpenoids biosynthesis pathway

The Valerian plant (Valeriana officinalis) contains compounds that can be used to treat nerve disorders, epilepsy, and sleep disorders. Terpenes (sesquiterpenoids) are the major group of compounds in this plant, whose biosynthesis pathway is poorly understood. Due to the lack of genomic sequence, studies based on de novo transcriptome assembly are important to elucidate more genes of the terpenoid biosynthetic pathway in this valuable medicinal plant. To reconstruct de novo assembly of RNA-Seq data from previously published SRR data for V. officinalis, Trinity and rnaSPAdes were used in this study. The primary assemblies were then analyzed using additional tools, such as CAP3 and CD-HIT-EST, in an attempt to determine the most effective de novo assembly. Based on the results of quality assessment tools such as rnaQUST, SeqKit statistics, and BUSCO, the combination of CAP3 and CD-HIT tools successfully produced an optimal assembly for Trinity (T-CAP-CD). A total of 57.78% of T-CAP-CD assembly genes were annotated in three subgroups (BP, MF, CC) with the highly accurate plant-specific Hayai-Annotation Plants annotation tool. The reconstruction of the KEGG pathway revealed 30 ortholog genes in the terpenoid biosynthetic backbone pathway and 8 ortholog genes in the sesquiterpenoid biosynthesis pathway. By performing homology search of T-CAP-CD transcriptome against PlantTFDB v.5, the most frequent transcription factor families were identified as bHLH (9.5 %), NAC (7.3 %), and MYB (6.6 %), respectively.