Transcriptomics

Dataset Information

303

Transcription profiling by high throughput sequencing of 5 tetraploid Arabidopsis


ABSTRACT: 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. Examination of gene expression in 5 tetraploid Arabidopsis using mRNA-seq

ORGANISM(S): Arabidopsis thaliana  

SUBMITTER: Danny W Ng   Luca Comai  Changqing Zhang  Xiaoli Shi  Jeffrey Z Chen  Z. Jeffrey Chen  Wenxue Ye 

PROVIDER: E-GEOD-29687 | ArrayExpress | 2012-05-31

SECONDARY ACCESSION(S): SRP007110GSE29687PRJNA141211

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Cis- and trans-regulatory divergence between progenitor species determines gene-expression novelty in Arabidopsis allopolyploids.

Shi Xiaoli X   Ng Danny W-K DW   Zhang Changqing C   Comai Luca L   Ye Wenxue W   Chen Z Jeffrey ZJ  

Nature communications 20120717


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 compen  ...[more]

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