|
| Status |
Public on May 31, 2012 |
| Title |
Cis- and trans- regulatory divergence between progenitor species determines gene-expression novelty in Arabidopsis allopolyploids |
| Organisms |
Arabidopsis thaliana; Arabidopsis arenosa; Arabidopsis suecica; Arabidopsis arenosa x Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Gene-expression divergence between species shapes morphological evolution, but the molecular basis is largely unknown. Here we show cis- and trans-regulatory elements and chromatin modifications on gene-expression diversity in genetically tractable Arabidopsis allotetraploids. In Arabidopsis thaliana and Arabidopsis arenosa, both cis and trans with predominant cis-regulatory effects mediate gene-expression divergence. The majority of genes with both cis- and trans-effects are subjected to compensating interactions and stabilizing selection. Interestingly, chromatin modifications correlate with cis - and trans -regulation. In F1 allotetraploids, Arabidopsis arenosa trans factors predominately affect allelic expression divergence. Arabidopsis arenosa trans factors tend to upregulate Arabidopsis thaliana alleles, whereas Arabidopsis thaliana trans factors up- or down-regulate Arabidopsis arenosa alleles. In resynthesized and natural allotetraploids, trans effects drive expression of both homoeologous loci into the same direction. We provide evidence for natural selection and chromatin regulation in shaping gene-expression diversity during plant evolution and speciation.
|
| |
|
| Overall design |
Examination of gene expression in 5 tetraploid Arabidopsis using mRNA-seq
|
| |
|
| Contributor(s) |
Shi X, Ng DW, Zhang C, Comai L, Ye W, Chen JZ |
| Citation(s) |
22805557, 25976351 |
| |
| Submission date |
Jun 02, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Z Jeffrey Jeffrey Chen |
| E-mail(s) |
[email protected]
|
| Phone |
512-475-9327
|
| Organization name |
The University of Texas at Austin
|
| Department |
Molecular Biosciences
|
| Lab |
Polyploidy, Hybrid Vigor, and Epigenetics
|
| Street address |
2506 Speedway NMS 3.122 Stop A500
|
| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78712-1597 |
| Country |
USA |
| |
|
| Platforms (4)
|
| GPL9062 |
Illumina Genome Analyzer (Arabidopsis thaliana) |
| GPL13676 |
Illumina Genome Analyzer (Arabidopsis arenosa) |
| GPL13677 |
Illumina Genome Analyzer (Arabidopsis arenosa x Arabidopsis thaliana) |
| GPL13678 |
Illumina Genome Analyzer (Arabidopsis suecica) |
|
| Samples (5)
|
|
| Relations |
| SRA |
SRP007110 |
| BioProject |
PRJNA141211 |
Less...
More...