Abstract
BackgroundWe 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.ResultsBy 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.ConclusionThis 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.
Highlights
We have further characterized floral organ-localized gene expression in the inflorescence of Arabidopsis thaliana by comparison of massively parallel signature sequencing (MPSS) data
To further characterize floral development, we have constructed MPSS signature libraries from cDNA of wild type, ap1, ap3, ag, sup ap1 inflorescences during the first twelve stages of development [27] as well as differentiated ovule, root, and leaf tissues
The number of genes enriched within each floral organ has likely been underestimated in order to reduce our false discovery rate; the relative trends in transcript diversity that we identified were maintained even under relaxed filtering parameters based merely on gene presence (>0 transcripts per million assayed (TPM)) or absence (0 TPM)
Summary
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, apetala, apetala, agamous, a superman/apetala double mutant, and differentiated ovules dissected from the gynoecia of wild-type inflorescences. An interesting subset of these mutants is the group of homeotic floral phenotypes In these mutants, the organs of a single whorl of the inflorescence are duplicated within another distinct whorl at the expense of the organs typically present. The organs of a single whorl of the inflorescence are duplicated within another distinct whorl at the expense of the organs typically present The premise for these mutations is explained in the classic "ABC model" of floral development for Arabidopsis [1,2]. In vivo interactions of homologous petunia MADS-box proteins involved in a putative ovule-defining quaternary complex were observed [5]
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