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Background   Gastrodia elata  Blume (Orchidaceae) is an important Chinese medicine with several functional components. In the life cycle of  G. elata , the orchid develops a symbiotic relationship with two compatible mycorrhizal fungi  Mycena  spp. and  Armillaria mellea  during seed germination to form vegetative propagation corm and vegetative growth to develop tubers, respectively. Gastrodin (p-hydroxymethylphenol-beta-D-glucoside) is the most important functional component in  G. elata , and gastrodin significantly increases from vegetative propagation corms to tubers. To address the gene regulation mechanism in gastrodin biosynthesis in  G. elata , a comparative analysis of  de novo  transcriptome sequencing among the vegetative propagation corms and tubers of  G. elata  and  A. mellea  was conducted using deep sequencing.    Results  Transcriptome comparison between the vegetative propagation corms and juvenile tubers of  G. elata  revealed 703 differentially expressed unigenes, of which 298 and 405 unigenes were, respectively up-regulated (fold-change ≥ 2,  q -value < 0.05, the trimmed mean of M-values (TMM)-normalized fragments per kilobase of transcript per Million mapped reads (FPKM) > 10) and down-regulated (fold-change ≤ 0.5,  q -value <0.05, TMM-normalized FPKM > 10) in juvenile tubers. After Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, 112 up-regulated unigenes with KEGG Ortholog identifiers (KOids) or enzyme commission (EC) numbers were assigned to 159 isogroups involved in seventy-eight different pathways, and 132 down-regulated unigenes with KOids or EC numbers were assigned to 168 isogroups, involved in eighty different pathways. The analysis of the isogroup genes from all pathways revealed that the two unigenes TRINITY_DN54282_c0_g1 (putative monooxygenases) and TRINITY_DN50323_c0_g1 (putative glycosyltransferases) might participate in hydroxylation and glucosylation in the gastrodin biosynthetic pathway.    Conclusions  The gene expression of the two unique unigenes encoding monooxygenase and glycosyltransferase significantly increases from vegetative propagation corms to tubers, and the molecular basis of gastrodin biosynthesis in the tubers of  G. elata  is proposed.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-2508-6) contains supplementary material, which is available to authorized users.

Comparative transcriptome analysis of Gastrodia elata (Orchidaceae) in response to fungus symbiosis to identify gastrodin biosynthesis-related genes