Temporal and spatial domain-specific transcriptomic analysis of a vital reproductive meristem in Arabidopsis thaliana

Abstract

BackgroundPlant meristems are analogous to animal stem cell niches as they maintain a pool of undifferentiated cells that divide and differentiate to give rise to organs. The carpel margin meristem is a vital, multi-potent structure located in the medial domain of the Arabidopsis thaliana gynoecium, the female floral reproductive organ. The carpel margin meristem generates ovules that upon fertilization become seeds. The molecular mechanisms that specify this meristematic region and regulate its organogenic potential are poorly understood. Here, we present an analysis of the transcriptional profile of the medial domain of the Arabidopsis gynoecium highlighting the developmental stages that immediately proceed ovule initiation, the earliest stages of seed development.\n\nResultsUsing a floral synchronization system and a SHATTERPROOF2 domain-specific reporter, paired with fluorescence-activated cell sorting and RNA sequencing, we assayed the transcriptome of the gynoecial medial domain with temporal and spatial precision. This analysis reveals a set of genes that are differentially expressed within the SHATTERPROOF2 expression domain that marks portions of the developing medial domain. Many members of this gene set have been shown previously to function during the development of medial domain-derived structures, including the ovules, thus validating our approach. Other uncharacterized members including differentially expressed cis-natural antisense transcripts, are potential novel regulators of medial domain development. Members of the REPRODUCTIVE MERISTEM (REM) family of transcriptional regulators were enriched in the SHATTERPROOF2-expressing cell population including a previously unrecognized REM family member. Finally, the analysis transcriptional isoforms in the medial domain identified genes that may exhibit \"isoform switching\" behavior during gynoecial development.\n\nConclusionsThis data set provides genome-wide transcriptional insight into the development of the gynoecial medial domain that contains the carpel margin meristem, a vital reproductive structure that gives rise to the ovules in Arabidopsis thaliana.