Metabolome and transcriptome profiling reveals quality variation and underlying regulation of three ecotypes for Cistanche deserticola

Cistanche deserticola is a plant used both as food and medicine. We are interested in understanding how C. deserticola responds to environmental conditions. Samples were collected from three ecotypes grown in saline–alkali land, grassland and sandy land. Transcriptome and metabolome analysis were performed by using RNA-seq and LC–ESI–MS/MS. Among 578 metabolites identified, 218, 209 and 215 compounds were found differentially produced among the three ecotypes. Particularly, 2′-acetylacteoside, belonging to phenylethanoid glycosides (PhGs) is the most significantly differentially produced with a VIP > 0.5 and fold change > 2, representing a potential chemical marker to distinguish the three ecotypes. RNA-Seq analysis revealed 52,043 unigenes, and 947, 632 and 97 of them were found differentially expressed among the three ecotypes. Analysis of the correlation between the metabolome profiles and transcriptome profiles among three ecotypes identified that the 12 key genes related to PhGs biosynthesis were differentially expressed. Particularly, the expression of PAL , ALDH and GOT genes were significantly up-regulated in saline–alkali land compared to the other two. In summary, we found PhGs content was higher in saline–alkali land compared with other ecotypes. This is likely due to the up-regulation of the PhGs biosynthetic genes in response to the saline–alkali conditions.