School of Applied Sciences, Health Innovations Research Institute, RMIT University, Melbourne, Victoria, Australia.
PLoS One. 2013 Aug 5;8(8):e70347. doi: 10.1371/journal.pone.0070347. Print 2013.
Echinacea, native to the Canadian prairies and the prairie states of the United States, has a long tradition as a folk medicine for the Native Americans. Currently, Echinacea are among the top 10 selling herbal medicines in the U.S. and Europe, due to increasing popularity for the treatment of common cold and ability to stimulate the immune system. However, the genetic relationship within the species of this genus is unclear, making the authentication of the species used for the medicinal industry more difficult. We report the construction of a novel Subtracted Diversity Array (SDA) for Echinacea species and demonstrate the potential of this array for isolating highly polymorphic sequences. In order to selectively isolate Echinacea-specific sequences, a Suppression Subtractive Hybridization (SSH) was performed between a pool of twenty-four Echinacea genotypes and a pool of other angiosperms and non-angiosperms. A total of 283 subtracted genomic DNA (gDNA) fragments were amplified and arrayed. Twenty-seven Echinacea genotypes including four that were not used in the array construction could be successfully discriminated. Interestingly, unknown samples of E. paradoxa and E. purpurea could be unambiguously identified from the cluster analysis. Furthermore, this Echinacea-specific SDA was also able to isolate highly polymorphic retrotransposon sequences. Five out of the eleven most discriminatory features matched to known retrotransposons. This is the first time retrotransposon sequences have been used to fingerprint Echinacea, highlighting the potential of retrotransposons as based molecular markers useful for fingerprinting and studying diversity patterns in Echinacea.
紫锥菊原产于加拿大草原和美国的草原各州，在美国和欧洲，它作为一种民间药物已有很长的历史，用于治疗普通感冒和刺激免疫系统。然而，该属内物种的遗传关系尚不清楚，这使得用于医药行业的物种鉴定更加困难。我们报告了一种新型的紫锥菊物种差减多样性阵列（SDA）的构建，并展示了该阵列用于分离高度多态性序列的潜力。为了选择性地分离紫锥菊特异性序列，在一组二十四种紫锥菊基因型和一组其他被子植物和非被子植物之间进行了抑制性消减杂交（SSH）。共扩增和排列了 283 个消减基因组 DNA（gDNA）片段。27 种紫锥菊基因型，包括 4 种未用于阵列构建的基因型，可以成功区分。有趣的是，从聚类分析中可以明确鉴定出未知的 E. paradoxa 和 E. purpurea 样本。此外，这种紫锥菊特异性 SDA 还能够分离出高度多态性的逆转录转座子序列。11 个最具区分性的特征中有 5 个与已知的逆转录转座子匹配。这是首次使用逆转录转座子序列来鉴定紫锥菊，突出了逆转录转座子作为基于分子标记的潜力，可用于鉴定和研究紫锥菊的多样性模式。
