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Subtracted Diversity Array identifies novel molecular markers including retrotransposons for fingerprinting Echinacea species

ABSTRACT: 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 relationships within the species of this genus are unclear, which makes difficult the authentication of the species used for the medicinal industry. 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.

ORGANISM(S): Echinacea angustifolia var. strigosa Echinacea paradoxa var. paradoxa Echinacea paradoxa var. neglecta Echinacea angustifolia Echinacea Echinacea purpurea Echinacea pallida Echinacea angustifolia var. angustifolia Echinacea tennesseensis Echinacea paradoxa x Echinacea pallida

PROVIDER: GSE44683 | GEO | 2013/12/31

SECONDARY ACCESSION(S): PRJNA192911

REPOSITORIES: GEO

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Project description:The SOS response to DNA damage in bacteria is a well-known component of the complex transcriptional responses to genotoxic environmental stresses such as exposure to reactive oxygen species, alkylating agents, and many of the antibiotics targeting DNA replication. However, bacteria such as Bacillus subtilis also respond to conditions that perturb DNA replication via a transcriptional response mediated by the replication initiation protein DnaA. In addition to regulating the initiation of DNA replication, DnaA directly regulates the transcription of specific genes. Conditions that perturb DNA replication can trigger the accumulation of active DnaA, activating or repressing transcription of genes in the DnaA regulon. We report here that simply growing B. subtilis in LB medium altered DnaA-dependent gene expression in a manner consistent with the accumulation of active DnaA, and that this was part of a general transcriptional response to manganese limitation. The SOS response to DNA damage was not induced under these conditions. One of the genes positively regulated by DnaA in Bacillus subtilis encodes a protein that inhibits the initiation of sporulation, Sda. Sda expression was induced as cells entered stationary phase in LB but not in LB supplemented with manganese, and induction of Sda inhibited sporulation-specific gene expression and the onset of spore morphogenesis. In the absence of Sda, manganese-limited cells initiated spore development but failed to form mature spores. These data highlight that DnaA-dependent gene expression may influence the response of bacteria to a range of environmental conditions, including conditions that are not obviously associated with genotoxic stress. Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays).

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Subtracted Diversity Array identifies novel molecular markers including retrotransposons for fingerprinting Echinacea species

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