Comparative transcriptomics among floral organs of the basal eudicot Eschscholzia californica: a reference for comparison with core eudicots and basal angiosperms

Our results provide a foundation for comparative gene expression studies between eudicots and basal angiosperms. We identified whorl-specific gene expression patterns in Eschscholzia, and examined the floral expression of several gene families, such as MADS-box, bHLH and MYB. Interestingly, most homologs of genes important for flower development, except for MADS-box genes, show different expression patterns between Eschscholzia and Arabidopsis. Our comparative transcriptomics study highlights the unique evolutionary position of Eschscholzia compared with basal angiosperms and core eudicots. Custom microarrays targeting 6446 Eschscholzia floral unigenes were used to measure expression levels in eight tissues using an interwoven double-loop design for 16 arrays.