School of Applied Sciences, Health Innovations Research Institute, RMIT University, Melbourne, Victoria, Australia.
PLoS One. 2012;7(4):e34873. doi: 10.1371/journal.pone.0034873. Epub 2012 Apr 9.
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.
Asterids 是主要的植物类群之一，包含许多具有商业重要性的药用物种。药用植物产业的主要关注点之一是由于草药植物的鉴定错误导致的掺假/污染。本研究报告了一种能够鉴定 Asterids 类群中重要药用物种的微阵列的构建和验证。
方法/主要发现：从 67 种 Asterid 物种的混合基因组 DNA 中减去 104 种非 Asterid 被子植物和非被子植物物种的混合基因组 DNA。随后，使用 283 个减去的 DNA 片段构建了 Asterid 特异性阵列。Asterid 特异性阵列的验证显示出高（99.5%）的减去效率。在该类群内的 20 个科和 9 个目中代表 25 种 Asterid 物种（主要是药用植物）被杂交到阵列上，以显示其物种鉴别能力。所有这些物种都可以通过它们的杂交模式成功地进行区分。为一些商业上重要的物种，如茶、咖啡、蒲公英、蓍草、益母草、金银花、缬草、野芹菜和马黛茶，鉴定了一些物种特异性探针。通过测序对 37 个多态性探针进行了表征。大量的探针是新的物种特异性探针，而其中一些探针来自叶绿体区域，包括 atpB、rpoB 和 ndh 等基因，这些基因已被广泛用于植物的指纹分析和系统发育分析。
结论/意义：差减多样性阵列技术在鉴定具有很少或没有基因组信息的物种方面非常高效。Asterid 特异性阵列可以鉴定所有 25 种评估的物种，包括三种未用于构建阵列的物种。本研究验证了使用叶绿体基因进行植物物种的条形码（指纹）分析。此外，该方法还可以检测到几个新的基因座，可以用来解决植物系统发育和指纹分析中的现有差异。
