Patterns of gene expression during Arabidopsis flower development from the time of initiation to maturation

Abstract

BackgroundThe formation of flowers is one of the main model systems to elucidate the molecular mechanisms that control developmental processes in plants. Although several studies have explored gene expression during flower development in the model plant Arabidopsis thaliana on a genome-wide scale, a continuous series of expression data from the earliest floral stages until maturation has been lacking. Here, we used a floral induction system to close this information gap and to generate a reference dataset for stage-specific gene expression during flower formation.ResultsUsing a floral induction system, we collected floral buds at 14 different stages from the time of initiation until maturation. Using whole-genome microarray analysis, we identified 7,405 genes that exhibit rapid expression changes during flower development. These genes comprise many known floral regulators and we found that the expression profiles for these regulators match their known expression patterns, thus validating the dataset. We analyzed groups of co-expressed genes for over-represented cellular and developmental functions through Gene Ontology analysis and found that they could be assigned specific patterns of activities, which are in agreement with the progression of flower development. Furthermore, by mapping binding sites of floral organ identity factors onto our dataset, we were able to identify gene groups that are likely predominantly under control of these transcriptional regulators. We further found that the distribution of paralogs among groups of co-expressed genes varies considerably, with genes expressed predominantly at early and intermediate stages of flower development showing the highest proportion of such genes.ConclusionsOur results highlight and describe the dynamic expression changes undergone by a large number of genes during flower development. They further provide a comprehensive reference dataset for temporal gene expression during flower formation and we demonstrate that it can be used to integrate data from other genomics approaches such as genome-wide localization studies of transcription factor binding sites.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1699-6) contains supplementary material, which is available to authorized users.

Genetic and Biochemical Mechanisms of Pollen Wall Development

“…Transcriptomic profiling will definitely expand our knowledge about the genes involved in this specific process. Unfortunately, currently-available microarray and RNA-seq data are mainly for flowers, anthers, or pollen grains [37][38][39][40]. However, these studies indicated that functions of pollen-enriched genes and differentially expressed genes in the male-sterile mutants are mainly relative to two pathways: cell wall and cytoskeletal remodeling [37,40], highlighting possible roles for these genes in pollen wall development.…”

Floral Organogenesis: When Knowing Your ABCs Is Not Enough

“…These studies yielded a comprehensive view of gene expression during flower formation. However, because the available data did not always provide detailed information on when and where genes are expressed, additional studies conducted in recent years have aimed at increasing the spatio-temporal resolution of the gene expression map for flower development (Jiao and Meyerowitz, 2010;Wuest et al, 2010;Mantegazza et al, 2014;Chen et al, 2015;Ryan et al, 2015;Villarino et al, 2016). To this end, a wide range of methods, such as laser capture microdissection Mantegazza et al, 2014) or fluorescence-activated cell sorting, in combination with a flower synchronization system Villarino et al, 2016), was used.…”

Post-embryonic hourglass patterns mark ontogenetic transitions in plant development

“…S2). We then combined the transcriptomic information with previously generated gene age information (Drost et al 2015). Based on an age assignment approach called phylostratigraphy (DomazetLošo et al 2007) ( Supplementary Fig.…”

“…Because no new organs are established during the two postembryonic phase transitions assessed here, our results also support the aforementioned conjecture that transcriptomic hourglass patterns are not specifically associated with organogenic processes. To directly test this, we performed phylotranscriptomic analyses of a flower development data set we previously generated (Ryan et al 2015). Flower development follows floral transition and is dominated by the formation of different show a clear antagonistic behavior in their expression ( Fig.…”