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| Status |
Public on Dec 31, 2013 |
| Title |
Subtracted Diversity Array identifies novel molecular markers including retrotransposons for fingerprinting Echinacea species |
| Platform organism |
Echinacea |
| Sample organisms |
Echinacea pallida; Echinacea purpurea; Echinacea tennesseensis; Echinacea angustifolia; Echinacea paradoxa x Echinacea pallida; Echinacea angustifolia var. angustifolia; Echinacea angustifolia var. strigosa; Echinacea paradoxa var. neglecta; Echinacea paradoxa var. paradoxa |
| Experiment type |
Genome variation profiling by array
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| Summary |
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.
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| Overall design |
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 sequences. Five out of the eleven most discriminatory features matched to known retrotransposons.
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| Contributor(s) |
Olarte A, Pang E |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Feb 26, 2013 |
| Last update date |
Jan 01, 2014 |
| Contact name |
Nitin Mantri |
| E-mail(s) |
nitin.mantri@rmit.edu.au
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| Organization name |
RMIT University
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| Department |
School of Science
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| Street address |
Plenty Road
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| City |
Bundoora |
| State/province |
Victoria |
| ZIP/Postal code |
3083 |
| Country |
Australia |
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| Platforms (1) |
| GPL16782 |
RMIT University Echinacea-specific array |
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| Samples (27)
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| GSM1097417 |
Echinacea paradoxa var. neglecta PI631263, replicates 1 & 2 |
| GSM1097418 |
Echinacea paradoxa var. neglecta PI631264, replicates 1 & 2 |
| GSM1097419 |
Echinacea pallida PI631293, replicates 1 & 2 |
| GSM1097420 |
Echinacea purpurea PI633669, replicates 1 & 2 |
| GSM1097421 |
Echinacea purpurea cv. white purpurea, replicates 1 & 2 |
| GSM1097422 |
Echinacea angustifolia var. angustifolia PI631318, replicates 1 & 2 |
| GSM1097423 |
Echinacea pallida PI631290, replicates 1 & 2 |
| GSM1097424 |
Echinacea paradoxa var. paradoxa PI631321, replicates 1 & 2 |
| GSM1097425 |
Echinacea purpurea PI631313, replicates 1 & 2 |
| GSM1097426 |
Echinacea purpurea PI631308, replicates 1 & 2 |
| GSM1097427 |
Echinacea angustifolia var. strigosa PI631320, replicates 1 & 2 |
| GSM1097428 |
Echinacea tennesseensis, replicates 1 & 2 |
| GSM1097429 |
Echinacea pallida cv. Hula dancer, replicates 1 & 2 |
| GSM1097430 |
Echinacea paradoxa var. paradoxa PI631301, replicates 1 & 2 |
| GSM1097431 |
Echinacea pallida PI631275, replicates 1 & 2 |
| GSM1097432 |
Echinacea angustifolia var. angustifolia PI631272, replicates 1 & 2 |
| GSM1097433 |
Echinacea angustifolia var. angustifolia PI631285, replicates 1 & 2 |
| GSM1097434 |
Echinacea angustifolia var. strigosa PI631266, replicates 1 & 2 |
| GSM1097435 |
Echinacea pallida PI631296, replicates 1 & 2 |
| GSM1097436 |
Echinacea pallida PI631315, replicates 1 & 2 |
| GSM1097437 |
Echinacea purpurea cv. Purpurea, replicates 1 & 2 |
| GSM1097438 |
Echinacea purpurea plot 10009, replicates 1 & 2 |
| GSM1097439 |
Echinacea angustifolia PI631267, replicates 1 & 2 |
| GSM1097440 |
Echinacea paradoxa var. neglecta PI631265, replicates 1 & 2 |
| GSM1097441 |
Echinacea pallida plot 5, replicates 1 & 2 |
| GSM1097442 |
Echinacea angustifolia plot 9, replicates 1 & 2 |
| GSM1097443 |
Echinacea putative hybrid (E. paradoxa and E. pallida) PI631294, replicates 1 & 2 |
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| Relations |
| BioProject |
PRJNA192911 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE44683_RAW.tar |
2.7 Mb |
(http)(custom) |
TAR (of TXT) |
| Processed data included within Sample table |
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