Analysis of the Prunellae Spica transcriptome under salt stress

Prunella vulgaris L. is a moderately salt tolerant plant commonly found in China and Europe, whose spica (Prunellae Spica) has been used as a traditional medicine. The scant transcriptomic and genomic resources of Prunellae Spica have greatly hindered further exploration of the underlying salt tolerance mechanism of this species. To clarify the genetic basis of its salt tolerance, high-throughput sequencing of mRNAs was employed for de novo transcriptome assembly differential expression analysis of Prunellae Spica under salt stress. 118,664 unigenes were obtained by assembling pooled reads from all libraries with 68,119 sequences annotated. A total of 3857 unigenes were differentially expressed under low, medium and high salt stress, including 2456 up-regulated and 1401 down-regulated DEGs, respectively. Gene ontology analysis revealed that salt stress-related categories involving 'catalytic activity', 'binding', 'metabolic process' and 'cellular process' were highly enriched. KEGG pathway annotation showed that the DEGs from different salt stress treatment groups were mainly enriched in the pathways of translation, signal transduction, carbohydrate metabolism, energy metabolism, lipid metabolism and amino acid metabolism, accounting for over 60% of all DEGs. Finally, it showed that the results of quantitative real-time polymerase chain reaction (qRT-PCR) analysis for 10 unigenes that randomly selected were significantly consistent with RNA-seq data, which further assisted in the selection of salt stress-responsive candidate genes in Prunellae Spica. This study represents a significant step forward in understanding the salt tolerance mechanism of Prunellae Spica, and also provides a significant transcriptomic resource for future work.