Open Access Highly Accessed Open Badges Research

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

Laura M Zahn128, Xuan Ma123, Naomi S Altman24, Qing Zhang249, P Kerr Wall1102, Donglan Tian111, Cynthia J Gibas5, Raad Gharaibeh5, James H Leebens-Mack1122, Claude W dePamphilis12 and Hong Ma12367*

  • * Corresponding author: Hong Ma

  • † Equal contributors

Author Affiliations

1 Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA

2 The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA

3 The Intercollege Graduate Program in Cell and Developmental Biology, The Pennsylvania State University, University Park, PA 16802, USA

4 Department of Statistics, The Pennsylvania State University, University Park, PA 16802, USA

5 Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC 28223, USA

6 State Key Laboratory of Genetic Engineering and School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China

7 Institutes of Biomedical Sciences, Fudan University, 138 Yixueyuan Road, Shanghai 200032, China

8 Current address: American Association for the Advancement of Science, 1200 New York Avenue NW, Washington DC 20005, USA

9 Current address: 2367 Setter Run Lane, State College, PA 16802, USA

10 Current address: BASF Plant Science, 26 Davis Drive, Research Triangle Park, NC 27709, USA

11 Current address: Department of Entomology, The Pennsylvania State University, University Park, PA 16802, USA

12 Current address: Department of Plant Biology, University of Georgia, 120 Carlton Street, Athens, GA 30602, USA

For all author emails, please log on.

Genome Biology 2010, 11:R101  doi:10.1186/gb-2010-11-10-r101

Published: 15 October 2010



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.


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.