Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Understanding transcriptional changes associated with the transition to selfing in Arabidopsis thaliana

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Stephen Wright

PROVIDER: E-GEOD-45685 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Publications

The Capsella rubella genome and the genomic consequences of rapid mating system evolution.

Slotte Tanja T Hazzouri Khaled M KM Ågren J Arvid JA Koenig Daniel D Maumus Florian F Guo Ya-Long YL Steige Kim K Platts Adrian E AE Escobar Juan S JS Newman L Killian LK Wang Wei W Mandáková Terezie T Vello Emilio E Smith Lisa M LM Henz Stefan R SR Steffen Joshua J Takuno Shohei S Brandvain Yaniv Y Coop Graham G Andolfatto Peter P Hu Tina T TT Blanchette Mathieu M Clark Richard M RM Quesneville Hadi H Nordborg Magnus M Gaut Brandon S BS Lysak Martin A MA Jenkins Jerry J Grimwood Jane J Chapman Jarrod J Prochnik Simon S Shu Shengqiang S Rokhsar Daniel D Schmutz Jeremy J Weigel Detlef D Wright Stephen I SI

Nature genetics 20130609 7

The shift from outcrossing to selfing is common in flowering plants, but the genomic consequences and the speed at which they emerge remain poorly 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 report a C. rubella reference genome sequence and compare RNA expression and polymorphism patterns between C. rubella and its outcrossing progenitor Capsella grandiflora. We found a c ...[more]

PMID: 23749190

Similar Datasets

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.

Dataset Information

Understanding transcriptional changes associated with the transition to selfing in Arabidopsis thaliana

Publications

The Capsella rubella genome and the genomic consequences of rapid mating system evolution.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets