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| Status |
Public on Sep 30, 2016 |
| Title |
Genomic data from pooled root and shoot tissue of Arabidopsis thaliana, Arabidopsis halleri and Arabidopsis lyrata |
| Platform organism |
Arabidopsis thaliana |
| Sample organisms |
Arabidopsis thaliana; Arabidopsis lyrata; Arabidopsis halleri |
| Experiment type |
Genome variation profiling by array
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| Summary |
Gene copy number variation (CNV) is a form of genetic polymorphism that contributes significantly to genome size and function but remains poorly characterized due to technological limitations. Inter-specific comparisons of CNVs in recently diverged plant species are crucial to uncover selection patterns underlying adaptation of a species to stressful environments. Especially given that gene amplifications have long been implicated in emergence of species-specific traits, we conducted a genome-wide survey to identify species-specific gene copy number expansions and deletions in the model extremophile species - Arabidopsis halleri that has diverged in evolutionarily recent time from Arabidopsis thaliana.
Cross-species cDNA array based comparative genomic hybridization was employed to compare and identify gene copy number variation in the two sister-species - the metallophyte Arabidopsis halleri and non-metallophyte Arabidopsis lyrata, both relative to Arabidopsis thaliana. We uncovered an unprecedented level of gene copy number polymorphism in Arabidopsis halleri, with a species-specific enrichment of metal homeostasis function in the genes found to be copy number expanded, thus indicating CNV as a mechanism that underlies the key physiological trait of metal hyperaccumulation and hypetolerance in A. halleri.
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| Overall design |
A total of 6 gDNA samples were hybridized to Affymetrix cDNA microarrays, two biological replicates for each of the three Arabidopsis species.
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| Contributor(s) |
Talke IN, Weber M, Clemens S, Eils R, Brors B, Singh V, Kraemer U |
| Citation(s) |
28155655 |
| |
| Submission date |
Nov 01, 2013 |
| Last update date |
Jun 12, 2017 |
| Contact name |
Vasantika Suryawanshi |
| E-mail(s) |
vsuryawanshi@lji.org
|
| Organization name |
La Jolla Institute of Immunology
|
| Lab |
Prof. Klaus Ley
|
| Street address |
9420 Athena Circle
|
| City |
La Jolla |
| State/province |
CALIFORNIA |
| ZIP/Postal code |
92037 |
| Country |
USA |
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| Platforms (1) |
| GPL198 |
[ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA226090 |
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