De novo full length transcriptome analysis and gene expression profiling reveal the regulation of phenylethanol glycosides biosynthesis in Cistanche tubulosa

Background: Cistanche as a famous tonic Chinese traditional medicine, is known as "desert ginseng". Its dried fleshy stem is a crucial tonic in Chinese traditional medicine, and the main active pharmacodynamic components are phenylethanol glycosides. Cistanche tubulosa is more suitable for cultivation and extracting active ingredients because it produces higher level of phenylethanol glycosides than C. deserticola . The molecular regulation of the phenylethanol glycosides is not clear, partially due to the lack of genomic and transcriptomic resources in C. tubulosa . Results In this study, we performed the full-length transcriptome sequencing and gene expression profiling of C. tubulosa using PacBio combined with BGISEQ-500 RNA-seq technology. Totally, 237,772 unique transcripts were obtained, the transcript lengths ranging from 199 bp to 31,857 bp, and the N50 length was 1,797 bp. Among the unique transcripts, 188,135 (79.12%) transcripts were annotated. Interestingly, 1080 transcripts were annotated as 22 enzymes related to PhGs biosynthesis. We measured the content of echinacoside, acteoside and total PhGs at two development stages, and found that the content of PhGs was 46.74% of dry matter in young fleshy stem (YS1) and then decreased to 31.22% at the harvest stage (HS2). To compare with YS1, 13,631 genes were up-regulated, and 15,521 genes were down regulated in HS2. Many differentially expressed genes (DEGs) were identified to be involved in phenylpropanoid biosynthesis pathway, phenylalanine metabolism pathway and tyrosine metabolism pathway between YS1 and HS2. Conclusions Based on these results, we proposed a potential model for phenylethanol biosynthesis regulation. This is the first report of transcriptome study of C. tubulosa which provided the foundation for understanding of PhGs biosynthesis regulation.