Background Asterids is one of the major plant clades comprising of many commercially important medicinal species. One of the major concerns in medicinal plant industry is adulteration/contamination resulting from misidentification of herbal plants. This study reports the construction and validation of a microarray capable of fingerprinting medicinally important species from the Asterids clade. Methodology/Principal Findings Pooled genomic DNA of 104 non-asterid angiosperm and non-angiosperm species was subtracted from pooled genomic DNA of 67 asterid species. Subsequently, 283 subtracted DNA fragments were used to construct an Asterid-specific array. The validation of Asterid-specific array revealed a high (99.5%) subtraction efficiency. Twenty-five Asterid species (mostly medicinal) representing 20 families and 9 orders within the clade were hybridized onto the array to reveal its level of species discrimination. All these species could be successfully differentiated using their hybridization patterns. A number of species-specific probes were identified for commercially important species like tea, coffee, dandelion, yarrow, motherwort, Japanese honeysuckle, valerian, wild celery, and yerba mate. Thirty-seven polymorphic probes were characterized by sequencing. A large number of probes were novel species-specific probes whilst some of them were from chloroplast region including genes like atpB, rpoB, and ndh that have extensively been used for fingerprinting and phylogenetic analysis of plants. Conclusions/Significance Subtracted Diversity Array technique is highly efficient in fingerprinting species with little or no genomic information. The Asterid-specific array could fingerprint all 25 species assessed including three species that were not used in constructing the array. This study validates the use of chloroplast genes for bar-coding (fingerprinting) plant species. In addition, this method allowed detection of several new loci that can be explored to solve existing discrepancies in phylogenetics and fingerprinting of plants.
References
[1]
Bremer K, Friis E, Bremer B (2004) Molecular phylogenetic dating of asterid flowering plants shows early Cretaceous diversification. Systematic Biology 53: 496.
[2]
APG (2009) An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Botanical Journal of the Linnean Society 161: 105–121.
[3]
Leonti M, Casu L, Sanna F, Bonsignore L (2009) A comparison of medicinal plant use in Sardinia and Sicily–De Materia Medica revisited? Journal of ethnopharmacology 121: 255–267.
[4]
Moerman DE (1996) An analysis of the food plants and drug plants of native North America. Journal of ethnopharmacology 52: 1–22.
[5]
Leonti M, Sticher O, Heinrich M (2003) Antiquity of medicinal plant usage in two Macro-Mayan ethnic groups (Mexico). Journal of ethnopharmacology 88: 119–124.
[6]
Barthelson RA, Sundareshan P, Galbraith DW, Woosley RL (2006) Development of a comprehensive detection method for medicinal and toxic plant species. Am J Bot 93: 566–574.
[7]
Chan K (2003) Some aspects of toxic contaminants in herbal medicines. Chemosphere 52: 1361–1371.
[8]
Zhou J, Qi L, Li P (2008) Quality control of Chinese herbal medicines with chromatographic fingerprint. Chinese Journal of Chromatography 26: 153–159.
[9]
Rao L, Usha Rani P, Deshmukh P, Kumar P, Panguluri S (2007) RAPD and ISSR fingerprinting in cultivated chickpea (Cicer arietinum L.) and its wild progenitor Cicer reticulatum Ladizinsky. Genetic resources and crop evolution 54: 1235–1244.
[10]
Kapteyn JaS JE (2002) The use of RAPDs for assessment of identity, diversity, and quality of Echinacea. Trends in new crops and new uses. In: Janick J, Whipkey A, editors. 509–513 ASHS Press, Alexandria, VA.
[11]
Techen N, Crockett S, Khan I, Scheffler B (2004) Authentication of Medicinal Plants Using Molecular Biology Techniques to Compliment Conventional Methods. Current Medicinal Chemistry 11: 1391–1401.
[12]
Henry RJ (2001) Plant genotyping : the DNA fingerprinting of plants. Wallingford: CABI Pub. xiii. 325 p.
[13]
Jaccoud D, Peng K, Feinstein D, Kilian A (2001) Diversity arrays: a solid state technology for sequence independent denotyping. Nucleic Acids Res 29:
[14]
Vizcaíno N, Cloeckaert A, Verger J-M, Grayon M, Fernández-Lago L (2000) DNA polymorphism in the genus Brucella. Microbes and Infection 2: 1089–1100.
[15]
James KE, Schneider H, Ansell SW, Evers M, Robba L, et al. (2008) Diversity arrays technology (DArT) for pan-genomic evolutionary studies of non-model organisms. PloS one 3: e1682.
[16]
Li TX, Wang JK, Bai YF, Lu ZH (2006) Diversity suppression-subtractive hybridization array for profiling genomic DNA polymorphisms. J Int Plant Biol 48: 460–467.
[17]
Jayasinghe R, Kong S, Coram TE, Kaganovitch J, Xue CCL, et al. (2007) Construction and validation of a prototype microarray for efficient and high throughput genotyping of angiosperms. Plant Biotechnology Journal 5: 282–289.
[18]
Jayasinghe R, Niu LH, Coram TE, Kong S, Kaganovitch J, et al. (2009) Effectiveness of an innovative prototype subtracted diversity array (SDA) for fingerprinting plant species of medicinal importance. Planta Med 75: 1180–1185.
[19]
Bremer B, Bremer K, Heidari N, Erixon P, Olmstead RG, et al. (2002) Phylogenetics of asterids based on 3 coding and 3 non-coding chloroplast DNA markers and the utility of non-coding DNA at higher taxonomic levels. Molecular Phylogenetics and Evolution 24: 274–301.
[20]
deKochko A, Akaffou S, Andrade AC, Campa C, Crouzillat D, et al. (2010) Advances in Coffea Genomics. Advances in Botanical Research 53: 23–63.
[21]
Niu LH, Mantri N, Li CG, Xue C, Pang E (2011) Array-based techniques for fingerprinting medicinal herbs. Chinese Medicine 6: 18.
[22]
Lezar S, Myburg A, Berger D, Wingfield M, Wingfield B (2004) Development and assessment of microarray-based DNA fingerprinting in Eucalyptus grandis. TAG Theoretical and Applied Genetics 109: 1329–1336.
[23]
Yang S, Pang W, Ash G, Harper J, Carling J, et al. (2006) Low level of genetic diversity in cultivated pigeonpea compared to its wild relatives is revealed by diversity arrays technology. TAG Theoretical and Applied Genetics 113: 585–595.
[24]
Heller-Uszynska K, Uszynski G, Huttner E, Evers M, Carlig J, et al. (2010) Diversity Arrays Technology effectively reveals DNA polymorphism in a large and complex genome of sugarcane. Molecular Breeding 1–19.
[25]
Olmstead RG, Kim KJ, Jansen RK, Wagstaff SJ (2000) The phylogeny of the Asteridae sensu lato based on chloroplast ndhF gene sequences. Molecular Phylogenetics and Evolution 16: 96–112.
[26]
Albach DC, Soltis PS, Soltis DE, Olmstead RG (2001) Phylogenetic analysis of asterids based on sequences of four genes. Annals of the Missouri Botanical Garden 88: 163–212.
[27]
Coelho M, Da Mota FF, Carneiro NP, Marriel IE, Paiva E, et al. (2007) Diversity of Paenibacillus spp. in the rhizosphere of four sorghum (Sorghum bicolor) cultivars sown with two contrasting levels of nitrogen fertilizer assessed by rpoB-based PCR-DGGE and sequencing analysis. Journal of Microbiology and Biotechnology 17: 753.
[28]
Tsui CKM, Daniel HM, Robert V, Meyer W (2008) Re examining the phylogeny of clinically relevant Candida species and allied genera based on multigene analyses. FEMS yeast research 8: 651–659.
[29]
Kim W, Kim JY, Cho SL, Nam SW, Shin JW, et al. (2008) Glycosyltransferase-a specific marker for the discrimination of Bacillus anthracis from the Bacillus cereus group. Journal of Medical Microbiology 57: 279.
