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Figure S1. Experimental setup and flower development in B. napus (a-d) and the CMS-line (e-h), respectively. Arrows connect the samples that were co-hybridised to microarrays. Arrows pointing in different directions indicate dye-swap experiments. Black and red arrows represent independent biological repetitions. (a) A mature B. napus flower. The inset shows a close-up of the reproductive floral organs. (b) B. napus inflorescence containing flower buds up to stage 3 (S3). The inset shows a flower bud at stage 4. (c) Stage 6 flower bud from B. napus, where whorls 3 and 4 are depicted (w3 and w4). (d) B. napus flower bud at early stage 8. (e) A mature flower from the CMS-line. The inset shows a close-up of a carpelloid stamen. An arrowhead points to an ovule-like structure. (f) Inflorescence from the CMS-line containing flower buds up to stage 4 (S4). (g) Stage 6 flower bud from the CMS-line, where whorls 1, 3 and 4 are depicted (w1, w3 and w4). (h) CMS flower bud at late stage 8 when petal primordia start to appear. In (c), (d), (g), and (h), sepals were removed for a better visibility of the inner whorl organs. In (b) and (f), the succession of flower bud initiation is indicated by numbers. Abbreviations: Se ? Sepal; Pe ? Petal; St ? Stamen; A ? Anther; C ? Carpel; Cl ? Carpelloid stamen. Figure S2. Shows the phylogeny of the A. thaliana multicopper oxidase, type 1 gene family. Included in the analysis is also the pollen specific multi-copper oxidase type 1 gene from B. napus. Locus names and trivial names (were applicable) are indicated. Full-length nucleotide sequences were obtained from the A. thaliana database. The tree presented is the one most parsimonious tree (length 21324) found in a heuristic search (CI=0.299, HI=0.701,RI= 0.492). Figure S3. Shows the phylogeny of the A. thaliana pectinesterase gene family. Locus names are indicated. Full-length nucleotide sequences were obtained from the A. thaliana database. The tree presented is a strict consensus of the two most parsimonious trees (length 32611) found in a heuristic search (CI=0.219, HI=0.781,RI= 0.454). Figure S4. Shows the phylogeny of the A. thaliana glycoside hydrolase 28 gene family. Locus names are indicated. Full-length nucleotide sequences were obtained from the A. thaliana database. The tree presented is a strict consensus of the four most parsimonious trees (length 24999) found in a heuristic search (CI=0.230, HI=0.770, RI= 0.525). References Albani, D., Sardana, R., Robert, L.S., Altosaar, I., Arnison, P.G. and Fabijanski, S.F. (1992) A Brassica napus gene family which shows sequence similarity to ascorbate oxidase is expressed in developing pollen. Molecular characterization and analysis of promoter activity in transgenic tobacco plants. Plant J, 2, 331-342. Zimmermann, P., Hirsch-Hoffmann, M., Hennig, L. and Gruissem, W. (2004) GENEVESTIGATOR. Arabidopsis Microarray Database and Analysis Toolbox. Plant Physiol, 136, 2621-2632. Table S1. Elements with significant expression changes Table S2. Description of the genes discussed in this study Phylogenetic trees. Results and experimental procedures used for generating polygenetic trees. Microarray protocol. The protocol used for microarray experiments. Primers. The sequences of the primers used in this study.

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TPJ_2975_sm_FiguresS1toS4.zip1722KSupporting info item
TPJ_2975_sm_Phylogenetic_trees_Methods_Primers.zip10KSupporting info item
TPJ_2975_sm_TableS1.xls319KSupporting info item
TPJ_2975_sm_TableS2.xls85KSupporting info item

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