Additional file 1 - A summary of array-based methods used on the studies of herbal plants.

Sources of Probes Array method Species assessed Substrate Results DNA based on Allocasia nacrorrhiza, Datura innoxia, D. metel, Dried Silicon- Spacer D. innoxia, D. metel and T. giganteum were Oligonucleotide D. tatula, Pinellia cordata, P. ternata, materials and based region of 5S- differentiated based on the differences of the microarray P. pedatisecta and Typhonium giganteum. fresh leaves microarray rRNA gene hybridizations [17]. Dendrobium chrysanthum, D. chrysotoxum, Using the fluorescence-labeled ITS2 D. crystallinum, D. densiflorum, D. falconeri, Fresh, Internal sequences as probes, the presence of D. Gene-based probe D. fimbriatum, D. jenkinsii, D. lindleyi, medicinal Microarray transcribed nobile in a Chinese medicinal formulation microarray D. loddigesii, D. lohohense, D. moniliforme, formulation; (glass) spacer 2 gene containing nine herbal components was D. moschatum, D. nobile, D. pendulum, leaves, stems detected [6]. D. primulinum. Fragments Fourteen species-specific probes from five Suppression Stems of from pair- Dendrobium auriantiacum, D. nobile closely related Dendrobium species were Subtraction commercially Array wise D. chrysotoxum, D. fimbriatum and used on the array. Various commercial Hybridization- available (nylon) subtraction D. officinale. Dendrobium samples and unrelated samples based array samples of genomic were successfully identified [27]. DNA 72 samples of Dendrobrium spp. containing Fragments 21 samples of D.officinale Kimura et Migo, Suppression from pair- Dendrobium aurantiacum Kerr, D. officinale 11 samples of D.chrysotoxum Lindl. and 40 Subtraction Array wise Kimura et Migo, D.nobile Lindl., D. Fresh leaves samples of other Dendrobrium spp. were Hybridization- (nylon) subtraction chrysotoxum Lindl. and D. fimbriatum Hook. screened using this array. This array could based array of genomic successfully identify the species used to DNA generate the probes [21]. This array was prepared using a partial genomic library from total genomic DNA of PstI digested 23 E. grandis trees, of which 22 were full Diversity Array Microarray Eucalyptus grandis Fresh leaves genomic siblings. 27% of the 384 fragments screened Technology (glass) DNA were found to be polymorphic and allowed identification of all the 17 full-sibling individuals tested [19]. Aconitum carmichaeli, A. pendulum, Alocasia macrorrhiza, Corton tiglium, Datura inoxia, D. Multiple toxic plant species were metel, D. tatula, Dysosma versipellis, Spacer Silicon- successfully identified by parallel Oligonucleotide Euphorbia kansui, Hyoscyamus niger, Pinellia region of Fresh leaves based genotyping. Datura inoxia, D. metel, D. array cordata, P. pedatisecta, P. ternate, 5S-rRNA microarray tatula were identified based on the Rhododendron molle, Stellera chamaejasme, gene differences in fluorescent intensities [15]. Strychnos nux-vomica, Typhonium divaricatum, T. giganteum. Aconitum napellus Herb., Arabidopsis thaliana L., A. absinthium L., A. vulgaris L., Atropa belladonna L., Capsicum annuum var. glabriusculum L. (Dunal) Heiser & Pickersgill, Caulophyllum thalictroides L. Michx., Citrus The genes for cytochrome P450 enzymes aurantium L., Datura metel L., Digitalis lanata were cloned and sequenced for probes Oligonucleotide Microarray Cytochrome Ehrh., Echinacea angustifolia, DC., Ephedra Fresh leaves design in MLPA assays for identification. array (glass) P450 gene viridis Coville, Glycyrrhiza uralensis Fisch. ex The probes can detect the presence of their DC., Hypericum perforatum L., Lawsonia cognate genomic DNA [26]. inermis L., Lobelia inflata L., Mentha pulegium L., Symphytum officinale L., Tanacetum vulgare L., Teucrium canadense L., T. chamaedrys L., Tussilago farfara L. Fragments A dendrogram of the relatedness of six Suppression Dendrobium aurantiacum Kerr, D. officinale from pair- Dendrobium species was produced Subtraction Kimura et Migo, D. nobile Lindl., D. Array wise according to their polymorphic profiles. The Fresh leaves Hybridization- chrysotoxum Lindl., D. fimbriatum Hook. and (nylon) subtraction results revealed that the SSH-based array based array D. densiflorum Lindl. et Wall. of genomic was effective for profiling genomic DNA DNA polymorphisms and dendrograms [14]. Subtracted A population of 28 angiosperm species Fresh leaves Microarray Fragments Pooled genomic DNA of 5 non-angiosperm Diversity Array (including 25 medicinal herbs) representing the (glass) from species was subtracted from pooled genomic six main clades in angiosperms subtracting DNA of 49 angiosperm species to obtain pooled 376 probes. Species representing the six genomic angiosperm clades (Asterids, Rosids, DNA Caryophyllids, Ranunculids, Monocots and Eumagnoliids) could be differentiated using the SDA. A polymorphism rate of 68% was obtained for the probes used [24]. P. ginseng C. A. Meyer, P. japonicus C. A. 33 probes corresponding to the species- Meyer (Japanese ginseng), P. quinquefolius L. specific nucleotide substitutions observed at (American ginseng), P. notoginseng (Burk.) F. 11 sites in the 18S rRNA gene sequence Oligonucleotide Dried leaf or Microarray 18S rRNA H. Chen, P. japonicus C. A. Meyer var. were used on the array. This array allowed microarray roots (glass) gene angustifolius (Seem.) C. Y. Wu et Feng, P. successful authentication of all the Panax stipuleanatus H. T. Tsai et K. M. Feng, P. plants, drugs and derived health foods tested pseudoginseng Wall. [18]. This array could correctly genotype species Fragments that were not used for initial DNA pooling from 34 species belonging to six angiosperm clades to generate probes. All species tested Subtracted Microarray subtracting and seven different families Fresh leaves correctly clustered at the family level, but Diversity Array (glass) pooled minor discrepancies were observed when the genomic fingerprinting was performed at the species DNA level [20].