Open Access Highly Accessed Research article

A spatial dissection of the Arabidopsis floral transcriptome by MPSS

Jason A Peiffer14, Shail Kaushik1, Hajime Sakai2, Mario Arteaga-Vazquez35, Nidia Sanchez-Leon3, Hassan Ghazal16, Jean-Philippe Vielle-Calzada3 and Blake C Meyers1*

Author Affiliations

1 Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA

2 DuPont Crop Genetics, Wilmington, DE 19880, USA

3 National Laboratory of Genomics for Biodiversity and Department of Genetic Engineering, CINVESTAV Campus, Guanajuato, Irapuato, Mexico

4 Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14850, USA

5 Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA

6 University Mohammed I, Laboratory of Genetics and Biotechnology, Faculty of Sciences, Oujda and Pluridisciplinary Faculty of Nador, Morocco

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BMC Plant Biology 2008, 8:43  doi:10.1186/1471-2229-8-43

Published: 21 April 2008



We have further characterized floral organ-localized gene expression in the inflorescence of Arabidopsis thaliana by comparison of massively parallel signature sequencing (MPSS) data. Six libraries of RNA sequence tags from immature inflorescence tissues were constructed and matched to their respective loci in the annotated Arabidopsis genome. These signature libraries survey the floral transcriptome of wild-type tissue as well as the floral homeotic mutants, apetala1, apetala3, agamous, a superman/apetala1 double mutant, and differentiated ovules dissected from the gynoecia of wild-type inflorescences. Comparing and contrasting these MPSS floral expression libraries enabled demarcation of transcripts enriched in the petals, stamens, stigma-style, gynoecia, and those with predicted enrichment within the sepal/sepal-petals, petal-stamens, or gynoecia-stamens.


By comparison of expression libraries, a total of 572 genes were found to have organ-enriched expression within the inflorescence. The bulk of characterized organ-enriched transcript diversity was noted in the gynoecia and stamens, whereas fewer genes demonstrated sepal or petal-localized expression. Validation of the computational analyses was performed by comparison with previously published expression data, in situ hybridizations, promoter-reporter fusions, and reverse transcription PCR. A number of well-characterized genes were accurately delineated within our system of transcript filtration. Moreover, empirical validations confirm MPSS predictions for several genes with previously uncharacterized expression patterns.


This extensive MPSS analysis confirms and supplements prior microarray floral expression studies and illustrates the utility of sequence survey-based expression analysis in functional genomics. Spatial floral expression data accrued by MPSS and similar methods will be advantageous in the elucidation of more comprehensive genetic regulatory networks governing floral development.