Gastrodia elata, a kind of perennial herb of Orchidaceae, is traditional Chinese herbal medicine. The growth cycle of G.elata is generally about 3 years, including development stages of seed, protocorm, juvenile tuber, immature tuber, mature tuber and scape. The G.elata is a typical heterotrophic plant, which has a symbiotic relationship with at least two fungi during its life cycle: One is Mycena that offers nutrition for the seed germinations of G.elata, the other is A. mellea that offeres nutrition and energy for the vegetative propagation corms of G.elata development into tubers. As one of an important medicinal plant, G.elata has many chemical ingredients, such as gastrodins, 4-hydroxybenzyl alcohols, vanillyl alcohols, vanillins, polysaccharides, sterols and orgnic acids et al. G.elata has important functions such as sedation, anti-convulsions, anti-aging and lowering blood pressure and also has effects on immune and cardiovascular system, its pharmacological action makes it widely used in clinical.
Gastrodia elata genomic data was derived from National Genomics Data Center (NGDC) of China (Accession number:GWHAAEX00000000). We collected the transcriptome data of 39 samples, and 27 samples data of them from Sequence Read Archive (Accession number:SRP064423,SRP108465 and SRP118053) in NCBI and 12 samples data (Accession number:SRP279888) were generated by our group, then we constructed a G. elata gene function analysis platform (GelFAP). The platform includes co-expression network, gene families, KEGG pathways and analysis tools, such as blast, motif search and GSEA.
We applied PCC algorithm to construct co-expression network through integration of 39 samples of RNA-seq data.
We combined several analysis tools such as iTAK, blast, HMM, interProScan, Pfam to classify the proteins into different families:
cytochrome P450 families, transcription regulators, kinase proteins, ubiquitin proteasome system, carbohydrate-active enzymes and EAR motif-containing proteins. In addition,GO terms were predicted by interProScan. Enzymes and metabolism pathways were annotated by KOALA from KEGG database.
In GelFAP, co-expression networks of genes can be browsed from gene families or metabolism pathways and functional annotation. Moreover, Blast, cis-element enrichment and Gene Sets analysis tools were provided to explore potential function of group genes.