GEO DataSets

(Submitter supplied) Hybrid seed failure arising from wide crosses between plant species is a recurring obstacle in plant breeding, impeding the transfer of desirable traits. This postzygotic reproductive barrier primarily occurs in the endosperm, a dosage-sensitive tissue that nurtures the embryo and functions analogously to the placenta in mammals. Here, we show that the endosperm in incompatible seeds loses DNA methylation and chromatin condensation, resembling the endosperm of seeds depleted for maternal RNA Polymerase IV (PolIV) function. more...

Organism:

Capsella grandiflora x Capsella rubella; Capsella bursa-pastoris; Capsella rubella; Capsella rubella x Capsella grandiflora; Capsella grandiflora; Capsella orientalis; Capsella orientalis x Capsella rubella; Capsella bursa-pastoris x Capsella grandiflora

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

8 related Platforms

81 Samples

Download data: TXT

(Submitter supplied) We used RNA-seq to profile gene expression changes during flg22 activated pattern-triggered immunity in multiple Brassicaceae including Capsella rubella, Cardamine hirsuta and Eutrema salsugineum as well as in multiple Arabidopsis thaliana accessions. This allows comparative transcriptomics within and across species to investigate the evolution of stress-responsive transcrption changes in these species.

Organism:

Arabidopsis thaliana; Capsella rubella; Cardamine hirsuta; Eutrema salsugineum

Type:

Expression profiling by high throughput sequencing

5 related Platforms

102 Samples

Download data: TXT

(Submitter supplied) Whether, and to what extent, phenotypic evolution follows predictable genetic paths, remains an important question in evolutionary biology. Convergent evolution of similar characters provides a unique opportunity to address this question. The transition to selfing and the associated changes in flower morphology are among the most prominent examples of repeated evolution in plants. Yet, to date no studies have directly compared the extent of similarities between convergent adaptations to selfing. more...

Organism:

Capsella orientalis; Capsella grandiflora; Capsella rubella

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16879 GPL23964 GPL19953

27 Samples

Download data: TXT

(Submitter supplied) In Arabidopsis thaliana, DNA-dependent RNA polymerase IV (Pol IV) is required for the formation of transposable element (TE)-derived small RNA (sRNA) transcripts. These transcripts are processed by DICER-LIKE3 into 24-nt small interfering RNAs (siRNAs) that guide RNA-directed DNA methylation. In the pollen grain, Pol IV is also required for the accumulation of 21/22-nt epigenetically activated siRNAs (easiRNAs), which likely silence TEs via post-transcriptional mechanisms. more...

Organism:

Arabidopsis thaliana; Capsella rubella

Type:

Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other; Methylation profiling by high throughput sequencing

Platforms:

GPL17639 GPL25199 GPL19580

32 Samples

Download data: TXT

(Submitter supplied) Genome-wide identification of imprinted genes in C. rubella.

Organism:

Capsella rubella

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL19953

6 Samples

Download data: CSV

(Submitter supplied) In plants, CG DNA methylation is prevalent in the transcribed regions of constitutively expressed genes (“gene body methylation; gbM”), but the origin and function of gbM remain unknown. Here we report the discovery that Eutrema salsugineum, has lost gbM from its genome, the first known instance for a flowering plant. Of all known DNA methyltransferases, only CHROMOMETHYLTRANSFERASE 3 (CMT3) is missing from E. more...

Organism:

Brassica oleracea; Eutrema salsugineum; Arabidopsis thaliana; Capsella rubella; Brassica rapa; Arabidopsis lyrata

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Third-party reanalysis

10 related Platforms

44 Samples

Download data: BED, TSV

(Submitter supplied) We described in this work the reproductive barrier between Capsella rubella and Capsella grandiflora leading to hybrid seed inviability. The transcriptome revealed a similar response to the one observed in interploidy hybrid seeds.

Organism:

Capsella rubella; Capsella grandiflora x Capsella rubella; Capsella grandiflora

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19955 GPL16879 GPL19953

8 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Arabidopsis lyrata; Arabidopsis thaliana; Capsella grandiflora; Capsella rubella

Type:

Expression profiling by high throughput sequencing

5 related Platforms

22 Samples

Download data: FPKM_TRACKING

(Submitter supplied) We compare RNA expression and polymorphism patterns between C. rubella and its outcrossing progenitor C. grandiflora. There is a clear shift in the expression of genes associated with flowering phenotypes; a similar shift is seen in the related genus Arabidopsis, where self-fertilization evolved about 1 million years ago.

Organism:

Capsella grandiflora; Capsella rubella

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16878 GPL16877 GPL16879

18 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Arabidopsis lyrata; Arabidopsis thaliana; Capsella rubella

Type:

Non-coding RNA profiling by high throughput sequencing

4 related Platforms

12 Samples

Download data: FNA, GFF3, QUAL

(Submitter supplied) Deep sequencing of small RNA from three closely related brassicaceae A. thaliana, A. lyrata and Capsella rubella was done to systematically analyze the evolution of MIRNA genes and their targets.

Organism:

Capsella rubella; Arabidopsis lyrata

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL10143 GPL10142

8 Samples

Download data: FNA, GFF3, QUAL, TXT