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Background  Molecular genetic studies of floral development have concentrated on several core eudicots and grasses (monocots), which have canalized floral forms. Basal eudicots possess a wider range of floral morphologies than the core eudicots and grasses and can serve as an evolutionary link between core eudicots and monocots, and provide a reference for studies of other basal angiosperms. Recent advances in genomics have enabled researchers to profile gene activities during floral development, primarily in the eudicot  Arabidopsis   thaliana  and the monocots rice and maize. However, our understanding of floral developmental processes among the basal eudicots remains limited.    Results  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.    Conclusions  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.

genome biology

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