Transcriptome-wide identification of genes related to fatty acid biosynthesis in the medicinal plant Salvia miltiorrhiza.

Salvia miltiorrhiza is an important medicinal plant that is commonly used in the treatment of cardiovascular diseases and neuro-asthenic insomnia. How to increase the production of its active components is an active area of research. Since the fatty acid biosynthesis pathway is linked to the production of its active components, here we performed a systematic identification of the genes involved in fatty acid biosynthesis based on RNA-Seq data from three different types of tissues of S. miltiorrhiza. First, 76 fatty acid biosynthesis-related genes were identified based on sequence similarity to known genes, which were classified into 29 gene families. Second, multiple sequence alignment and phylogenetic analyses were performed for members of each protein family. One of these families, the Acyl Carrier Protein (ACP) family is the important cofactor protein involved in fatty acid biosynthesis, demonstrated significant variations among the sequences from different species. Third, qRT-PCR was used to validate the expression levels for 49 genes. It is found that the expression profiles obtained using qRT-PCR were consistent with those obtained from the RNA-Seq results for 36 genes (74%). Forth, hierarchical clustering analysis of the 76 genes based on their gene expression profiles across the tissues revealed eight major clusters. Last, detailed examination showed that 28 genes were significantly differentially expressed among the tissues. These tissue-specific genes might serve as the switches for the regulation of fatty acid biosynthesis in S. miltiorrhiza. In summary, the current study has identified and characterized 76 novels genes involved in the fatty acid biosynthesis pathway in S. miltiorrhiza, laying the foundation for their future detailed functional characterization.