Comparative transcriptomics among floral organs of the basal eudicot Eschscholzia californica as reference for floral evolutionary developmental studies

Using a recently generated expressed sequence tag (EST) set, we have designed an oligonucleotide microarray for the basal eudicot Eschscholzia californica (California poppy). We performed microarray experiments with an interwoven-loop design in order to characterize the E. californica floral transcriptome and to identify differentially expressed genes in flower buds with pre-meiotic and meiotic cells, four floral organs at pre-anthesis stages (sepals, petals, stamens and carpels), developing fruits, and leaves.Our results provide a foundation for comparative gene expression studies between eudicots and basal angiosperms. We identified whorl-specific gene expression patterns in E. californica and examined the floral expression of several gene families. Interestingly, most E. californica homologs of Arabidopsis genes important for flower development, except for genes encoding MADS-box transcription factors, show different expression patterns between the two species. Our comparative transcriptomics study highlights the unique evolutionary position of E. californica compared with basal angiosperms and core eudicots.The eudicots are believed to have originated approximately 130 million years ago [1]. They include about 70% of all flowering plant species and consist of core eudicots [2-4], which include the groups containing Arabidopsis thaliana and Antirrhinum majus, and species that branched earlier from these groups and are at basal positions within the eudicot clade. The earliest branching lineage of the eudicots, the Ranunculales, contains the Papaveraceae (poppy) family, of which Eschscholzia californica (California poppy) is a member [3]. The core eudicots commonly have stable (that is, canalized) flower architecture (Figure 1a); by contrast, the basal eudicots exhibit a wider range of floral patterns [5] (see examples in Figure 1a). Comparing the morphology and the underlying mechanisms of flower development between the core and basal eudicots may help us better u