Ontology highlight
ABSTRACT:
PROVIDER: PRJEB24044 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| africa_and1001.EVA.vcf.gz | Vcf | |||
| africa_and1001.EVA.vcf.gz.tbi | Vcf |
Items per page: 5 1 - 2 of 2 |
Similar Datasets
Project description:African genomes illuminate the early history and transition to selfing in Arabidopsis thaliana
2017-12-29 | PRJEB24044 | EVA
Project description:African genomes illuminate the early history and transition to selfing in Arabidopsis thaliana
| PRJEB19780 | ENA
Project description:Convergent evolution, the independent evolution of similar traits in different species under similar environmental pressures, is widespread across many taxa. In plants, a key example is the repeated evolution of floral traits associated with the transition from outcrossing to self- fertilization, often resulting in the “selfing syndrome” (e.g., reduced flower size, loss of scent, and altered reproductive strategies). However, potentially overlooked changes concern the pollen coat, which plays a role in different aspects of outcrossing strategy. To investigate this, we compared pollen morphology and proteomes between selfing and outcrossing species in the 2 Arabidopsis and Capsella genera, representing three independent selfing transitions. Pollen coat area diminished with the age of the selfing transition, with significant reductions in A. thaliana and Capsella rubella, but not in A. lyrata (recent transition, no selfing syndrome). Moreover, differentially expressed pollen coat proteins, primarily related to pathogen response, were shared across selfer-outcrosser contrasts more than expected by chance. However, similar functions appeared in random outcrosser-outcrosser comparisons, suggesting additional drivers beyond mating system transitions. Overall, our findings reveal convergent evolution of pollen coat morphology and protein composition following selfing transitions, while highlighting pathogen response as a key factor driving the fast evolution of pollen coat protein independently of the mating system.
2026-04-08 | PXD061508 | Pride
Project description:RNA-seq reads from the selfing species Arabidopsis thaliana were produced from flowers to study the consequences of the transition from the ancestral state (outcrossing) to the derived state (selfing). This was done in the context of examining another species in the Arabidopsis genus (A. lyrata) and another species pair (Capsella rubella versus Capsella grandiflora, which are selfing and outcrossing, respectively). These samples were generated to complement part of this larger study. Briefly, the shift from outcrossing to selfing is common in flowering plants, but neither the genomic consequences nor the speed with which they appear are well understood. An excellent model for understanding the evolution of self fertilization is provided by Capsella rubella, which became self-compatible <200,000 years ago. We present a reference genome for the species, and 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. DNA sequence polymorphisms distinguishing the two Capsella species reveal rapid genome-wide relaxation of purifying selection in C. rubella but without a concomitant change in transposable element abundance. Overall, we document that the transition to selfing may be typified by shifts in expression for genes that function in pollen and flower development, along with a measurable reduction of purifying selection.
2013-04-02 | GSE45685 | GEO
Project description:RNA-seq reads from the outcrossing species Arabidopsis lyrata were produced from flowers to study the consequences of the transition from the ancestral state (outcrossing) to the derived state (selfing) that is observed in the sister species Arabidopsis thaliana. This was done in the context of examining another species pair (Capsella rubella versus Capsella grandiflora, which are selfing and outcrossing, respectively). These samples were generated to complement part of this larger study. Briefly, the shift from outcrossing to selfing is common in flowering plants, but neither the genomic consequences nor the speed with which they appear are well understood. An excellent model for understanding the evolution of self fertilization is provided by Capsella rubella, which became self-compatible <200,000 years ago. We present a reference genome for the species, and 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. DNA sequence polymorphisms distinguishing the two Capsella species reveal rapid genome-wide relaxation of purifying selection in C. rubella but without a concomitant change in transposable element abundance. Overall, we document that the transition to selfing may be typified by shifts in expression for genes that function in pollen and flower development, along with a measurable reduction of purifying selection.
2013-04-02 | GSE45676 | GEO
Project description:RNA-seq reads from the selfing species Arabidopsis thaliana were produced from flowers to study the consequences of the transition from the ancestral state (outcrossing) to the derived state (selfing). This was done in the context of examining another species in the Arabidopsis genus (A. lyrata) and another species pair (Capsella rubella versus Capsella grandiflora, which are selfing and outcrossing, respectively). These samples were generated to complement part of this larger study. Briefly, the shift from outcrossing to selfing is common in flowering plants, but neither the genomic consequences nor the speed with which they appear are well understood. An excellent model for understanding the evolution of self fertilization is provided by Capsella rubella, which became self-compatible <200,000 years ago. We present a reference genome for the species, and 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. DNA sequence polymorphisms distinguishing the two Capsella species reveal rapid genome-wide relaxation of purifying selection in C. rubella but without a concomitant change in transposable element abundance. Overall, we document that the transition to selfing may be typified by shifts in expression for genes that function in pollen and flower development, along with a measurable reduction of purifying selection. As part of a cross-species comparison of gene expression, RNA-seq data was generated in biological replication (2 replicates) from Arabidopsis thaliana at the floral stage. In total, two samples (biological replicates) were used. The reference strain was used for the experments (strain Col-0). Resulting data about gene expression was used as part of a larger study. The Capsella rubella and Capsella grandiflora data are included in GEO Series GSE45518.
2013-04-02 | E-GEOD-45685 | biostudies-arrayexpress
Project description:RNA-seq reads from the outcrossing species Arabidopsis lyrata were produced from flowers to study the consequences of the transition from the ancestral state (outcrossing) to the derived state (selfing) that is observed in the sister species Arabidopsis thaliana. This was done in the context of examining another species pair (Capsella rubella versus Capsella grandiflora, which are selfing and outcrossing, respectively). These samples were generated to complement part of this larger study. Briefly, the shift from outcrossing to selfing is common in flowering plants, but neither the genomic consequences nor the speed with which they appear are well understood. An excellent model for understanding the evolution of self fertilization is provided by Capsella rubella, which became self-compatible <200,000 years ago. We present a reference genome for the species, and 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. DNA sequence polymorphisms distinguishing the two Capsella species reveal rapid genome-wide relaxation of purifying selection in C. rubella but without a concomitant change in transposable element abundance. Overall, we document that the transition to selfing may be typified by shifts in expression for genes that function in pollen and flower development, along with a measurable reduction of purifying selection. As part of a cross-species comparison of gene expression, RNA-seq data was generated in biological replication (2 replicates) from Arabidopsis lyrata at the floral stage. In total, two samples (biological replicates) were used. The reference strain was used for the experments (strain MN47). Resulting data about gene expression was used as part of a larger study. The Capsella rubella and Capsella grandiflora data are included in GEO Series GSE45518.
2013-04-02 | E-GEOD-45676 | biostudies-arrayexpress
Project description:Understanding transcriptional changes associated with the transition to selfing in Arabidopsis thaliana
| PRJNA195608 | ENA
Project description:Arabidopsis thaliana is a well-established model system for the analysis of the basic physiological and metabolic pathways of plants. The presented model is a new semi-quantitative mathematical model of the metabolism of Arabidopsis thaliana. The Petri net formalism was used to express the complex reaction system in a mathematically unique manner. To verify the model for correctness and consistency concepts of network decomposition and network reduction such as transition invariants, common transition pairs, and invariant transition pairs were applied. Based on recent knowledge from literature, including the Calvin cycle, glycolysis and citric acid cycle, glyoxylate cycle, urea cycle, sucrose synthesis, and the starch metabolism, the core metabolism of Arabidopsis thaliana was formulated. Each reaction (transition) is experimentally proven. The complete Petri net model consists of 134 metabolites, represented by places, and 243 reactions, represented by transitions. Places and transitions are connected via 572 edges.
2020-04-09 | MODEL1801090001 | BioModels
Project description:Understanding transcriptional changes associated with the transition to selfing in Arabidopsis thaliana by using outgroup data
| PRJNA195607 | ENA