De novo transcriptome provides insights into the growth and adaptation of the endangered terrestrial orchid Dactylorhiza hatagirea in the alpine desert of western Himalaya

Dactylorhiza hatagirea is a critically-endangered, terrestrial orchid of alpine Himalayas. The plant is acclaimed for medicinal properties but little is known about its secondary metabolite profile or cues regulating their biosynthesis. De novo transcriptome analysis was therefore undertaken to gain basic understanding on these aspects, while circumventing the acute limitation of plant material availability. 65,384 transcripts and finally, 37,371 unigenes were assembled de novo from a total of 236 million reads obtained from shoot, tuber and leaves of the plant. Dominance of differentially expressing genes (DEGs) related to cold stress response and plant hormone signal transduction; and those involved in photosynthesis, stress response, sugar metabolism and secondary metabolite synthesis provided insights into carbohydrate partitioning during the plant’s adaptation at natural habitat. DEGs of glucomannan, ascorbic acid, resveratrol and stilbene biosynthesis revealed the secondary metabolite profile of D. hatagirea. Expression analysis of 15 selected genes including those of shikimic acid and phenylpropanoid pathways; and temperature and tissue specific differential expression of ROMT and GRP78 genes in clonal plants indicated adaptive preparation and maximum secondary metabolite biosynthesis gene expression at 15 ºC, a temperature representative of average day temperature before winter.