Within and between whorls: comparative transcriptional profiling of Aquilegia and Arabidopsis

Abstract

Background: The genus Aquilegia is an emerging model system in plant evolutionary biology predominantly because of its wide variation in floral traits and associated floral ecology. The anatomy of the Aquilegia flower is also very distinct. There are two whorls of petaloid organs, the outer whorl of sepals and the second whorl of petals that form nectar spurs, as well as a recently evolved fifth whorl of staminodia inserted between stamens and carpels.

Methodology/principal findings: We designed an oligonucleotide microarray based on EST sequences from a mixed tissue, normalized cDNA library of an A. formosa x A. pubescens F2 population representing 17,246 unigenes. We then used this array to analyze floral gene expression in late pre-anthesis stage floral organs from a natural A. formosa population. In particular, we tested for gene expression patterns specific to each floral whorl and to combinations of whorls that correspond to traditional and modified ABC model groupings. Similar analyses were performed on gene expression data of Arabidopsis thaliana whorls previously obtained using the Ath1 gene chips (data available through The Arabidopsis Information Resource).

Conclusions/significance: Our comparative gene expression analyses suggest that 1) petaloid sepals and petals of A. formosa share gene expression patterns more than either have organ-specific patterns, 2) petals of A. formosa and A. thaliana may be independently derived, 3) staminodia express B and C genes similar to stamens but the staminodium genetic program has also converged on aspects of the carpel program and 4) staminodia have unique up-regulation of regulatory genes and genes that have been implicated with defense against microbial infection and herbivory. Our study also highlights the value of comparative gene expression profiling and the Aquilegia microarray in particular for the study of floral evolution and ecology.

Figure 1. A. formosa pre-anthesis flower and fruit development.

A A. formosa pre-anthesis flower. B Left: A. formosa pre-anthesis flower with stamens removed to expose staminodia. Middle and right: Early and later stages of fruit development, respectively. The sepals, petals and stamens dehisce while the staminodia remain attached to the receptacle and surround the carpels during fruit development.

Figure 2. Differentially expressed genes in Aquilegia floral whorls and whorl combinations.

A Floral diagram of an Aquilegia flower showing one whorl of five petaloid sepals, one whorl of five petals, four whorls of 10 stamens, one whorl of 10 staminodia and one whorl of five carpels. B Twelve contrasts were tested for differential expression, comparing each whorl against all others (1–5) and combinations of whorls against the remaining whorls (6–12). See text for details. C Numbers of down (downward arrow) and up (upward arrow) regulated genes for each of the 12 contrasts. First line shows number of differentially expressed genes with the corresponding permutation-based false discovery rate in brackets. Bold numbers below state the number of genes that have their highest absolute D statistic under that contrast and are being considered specifically expressed in the context of this study. Note that contrast 11 is reverse to contrast 6 and therefore yields similar numbers but with opposite regulation patterns.