Abstract
BackgroundGastrodia 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.ResultsTranscriptome 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.ConclusionsThe 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 materialThe online version of this article (doi:10.1186/s12864-016-2508-6) contains supplementary material, which is available to authorized users.
Highlights
Gastrodia elata Blume (Orchidaceae) is an important Chinese medicine with several functional components
Gastrodia elata is a rootless and leafless achlorophyllous orchid that grows in a symbiotic relationship with two compatible mycorrhizal fungi, Mycena spp. and Armillaria mellea, during seed germination and vegetative growth, respectively [1,2,3]
next generation sequencing (NGS) platforms, such as the Illumina/Solexa Genome Analyzer and the Roche 454 GS FLX, have been widely used in recent years for the high-throughput sequencing of various organisms [59, 60]. Using these techniques for de novo transcriptome sequencing, expressed sequence tag (EST) databases have been successfully obtained for several medicinal herbs, including American ginseng [48], Salvia miltiorrhiza [61], sweet wormwood [62], Euphorbia fischeriana [63], Taxus [64], and other crops, such as chili pepper [65], maize [66], Curcuma longa [67], chestnut [68], Eucalyptus tree [69], olive [70], Camellia sinensis [71], sweet potato [72], Arabidopsis [73], and Phalaenopsis [74]
Summary
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. Gastrodia elata is a rootless and leafless achlorophyllous orchid that grows in a symbiotic relationship with two compatible mycorrhizal fungi, Mycena spp. and Armillaria mellea, during seed germination and vegetative growth, respectively [1,2,3]. Once vegetative propagation corms have been established from seed germination, G. elata undergoes vegetative growth through an established symbiotic association with the compatible mycorrhizal fungi, A. mellea (Fig. 1c), to yield juvenile tubers (Fig. 1d) [1, 6, 17]. The hyphae of A. mellea develop well in the cortical layers of G. elata tubers [1, 20,21,22]; the cells in the pith of tubers digest the invaded hyphae to obtain nutrition and energy [1]
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