De novo transcriptome assembly, gene annotation, marker development, and miRNA potential target genes validation under abiotic stresses in Oenanthe javanica

Oenanthe javanica is an aquatic perennial herb with known medicinal properties and an edible vegetable with high vitamin and mineral content. The understanding of the biology of O. javanica is limited by the absence of information on its genome, transcriptome, and small RNA. In this study, transcriptome sequencing and small RNA sequencing were performed to annotate function genes, develop SSR markers and analyze potential target genes of miRNAs in O. javanica. All reads with total nucleotides number of 1,440,321,408 bp were assembled into 58,072 transcripts and 40,208 unigenes. A total of 1,233 SSRs were identified from O. javanica. Generated unigenes were aligned against seven databases and annotated with functions. A total of 29 potential targets were predicted. Expression of 10 miRNAs and their corresponding target genes under abiotic stresses (heat, cold, salinity, and drought) was validated. All ten miRNAs were confirmed to response to abiotic stresses. A pair of miRNA and its target gene was found. This study can serve as a valuable resource for future studies on O. javanica, which may focus on novel gene discovery, SSR development, gene mapping, and miRNA-affected processes and pathways. This can promote the development of the useful medicinal properties of O. javanica in medical science.