Transcriptome analysis of gall oak (Quercus infectoria): De novo assembly, functional annotation and metabolic pathways analysis

Gall oak (Quercus infectoria) is a native tree of Iran, whose gall extract is used to treat many diseases. The presence of abundant secondary metabolites with various bioactivities in this plant has made it medically important. Despite its medicinal value, due to the lack of genomic information, the biosynthetic pathways of these compounds in this species are still unknown. The current research was aimed at observing, characterizing, and investigating the biosynthetic pathways of these compounds in Q.infectoria. De novo transcriptome assembly was conducted using the RNA sequencing technique. A total of 89,335 unigenes were generated, of which 6928 unigenes showed differential expression in leaves compared to root tissue. Gene ontology examination of DEGs revealed GO-term enrichment was related to cellular processes and enzyme activity. KEGG enrichment analysis for DEGs showed that most unigenes were related to metabolic pathways and biosynthesis of secondary metabolites. Moreover, 39 families of transcription factors were identified, of which the C2H2, bZIP, bHLH, and ERF TFs had the highest frequency. In the absence of a reference genome, the overall study of transcriptome will provide a reference for future functional and comparative studies. Moreover, the data obtained from sequencing and de novo assembly can be a valuable scientific resource for Q.infectoria.

Automated summary

The current research achieved de novo transcriptome assembly of Gall oak using RNA sequencing technique, generating 89,335 unigenes, among which 6,928 unigenes showed significant differential expression between leaves and root tissues. Gene ontology examination revealed enrichment in cellular processes and enzyme activity. KEGG enrichment analysis displayed a high proportion of unigenes related to metabolic pathways and biosynthesis of secondary metabolites. Additionally, 39 families of transcription factors were identified, with C2H2, bZIP, bHLH, and ERF having the highest frequency. This transcriptome study provides a valuable reference for future functional and comparative studies in the absence of a reference genome and serves as a scientific resource for Q.infectoria.