Arabidopsis lyrata
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA195607 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR800644.fastq.gz | Fastqsanger.gz | |||
| SRR800645.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 2 of 2 |
Similar Datasets
Project description:Understanding transcriptional changes associated with the transition to selfing in Arabidopsis thaliana
| PRJNA195608 | ENA
Project description:African genomes illuminate the early history and transition to selfing in Arabidopsis thaliana
2017-12-29 | PRJEB24044 | EVA
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 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.
2013-04-02 | GSE45676 | GEO
Project description:Deep sequencing of the 5' ends of uncapped, polyA-enriched mRNA from two biological replicate samples from Arabidopsis thaliana inflorescences, as well as two biological replicates of Arabidopsis lyrata inflorescences. These data were used to experimentally identify sliced microRNA targets from the two species.
2010-04-22 | GSE20451 | 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. 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:Arabidopsis thaliana and Arabidopsis lyrata are two closely related Brassicaceae species, which are used as models for plant comparative biology. They differ by lifestyle, predominant mating strategy, ecological niches and genome organization. In order to explore molecular basis of specific traits, we performed RNA-sequencing of vegetative rosettes from both species. Additionally, we sequenced apical meristems and inflorescences of A. lyrata that allow for intra-specific transcriptome comparison in several major developmental stages. Please view also related dataset GSE69077 (RNA-sequencing of heat stressed A. lyrata and A. thaliana plants).
2015-08-01 | GSE69222 | GEO
Project description:Deep sequencing of the 5' ends of uncapped, polyA-enriched mRNA from two biological replicate samples from Arabidopsis thaliana inflorescences, as well as two biological replicates of Arabidopsis lyrata inflorescences. These data were used to experimentally identify sliced microRNA targets from the two species. Two biological replicate samples of the 5' ends of uncapped, polyA+ RNAs from both A. thaliana and A. lyrata
2010-04-22 | E-GEOD-20451 | biostudies-arrayexpress
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