Two-Axis Metabolomic Organization in the Cistanche deserticola Succulent Stem

Cistanche deserticola is a holoparasitic medicinal plant that has lost the ability to photosynthesize and grows entirely underground, so its reduced genome might suggest weak tissue-level metabolic partitioning. Using untargeted metabolomics of 132 samples from 22 plants, with each stem divided by tissue type (outer fraction vs. internal tissues) and longitudinal position (upper, middle, lower), we found a clear two-axis organization. Tissue type accounted for the smallest proportion of variance (15.2%) yet yielded the clearest discrimination: phenylethanoid glycosides (PhGs) and flavonoids were enriched in the outer fraction, whereas iridoids and primary metabolites predominated in internal tissues; along the stem, the upper part was an active metabolic zone and the lower part a sugar sink. The decline in PhG abundance with plant size occurred predominantly within tissues, with anatomical dilution contributing only 18.6%. Pathway-resolved mapping showed that the downstream steps of PhG assembly (acylation, rhamnosylation, hydroxylation, glucosylation) are progressively enriched in the outer fraction, so the discarded outer fraction is consistent with a possible site of biosynthesis, rather than merely a storage site, for acteoside and echinacoside. This stable organization likely reflects developmental canalization, indicating that gene loss does not eliminate tissue-level metabolic specialization.