Research article
Computational annotation of genes differentially expressed along olive fruit development
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* Corresponding author: Pietro Tonutti pietro.tonutti@sssup.it
1 Department of Environmental Agronomy and Crop Science, University of Padova, Viale dell'Università 16, 35020 Legnaro (Padova), Italy
2 CNR - Istituto di Genetica Vegetale - Research Division of Perugia, Via Madonna Alta 130, 06128 Perugia, Italy
3 Scuola Superiore Sant'Anna - Pisa, Piazza Martiri della Libertà 33, 56127 Pisa, Italy
BMC Plant Biology 2009, 9:128 doi:10.1186/1471-2229-9-128
Published: 24 October 2009Additional files
Additional file 1:
RT-PCR validation. Results of the validation of 42 genes analyzed by quantitative Real-Time PCR and grouped according to eight different subgroups of expression patterns among the three fruit developmental stages.
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Additional file 2:
List of enzyme names and codes. List of enzyme names, codes and library of the 89 gene sequences tested by quantitative Real-Time PCR.
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Additional file 3:
KEGG map. KEGG pathway for starch and sucrose metabolism (Map:00500) (A) combined with glycolysis and gluconeogenesis (Map:00010) (B). Box colors: blue and green correspond to up-regulated genes between olive stages 1 and 2, and 2 and 3, respectively, whereas red and yellow correspond to down-regulated genes between olive stages 1 and 2, and 2 and 3, respectively; gray indicates transiently regulated genes from stage 1 to stage 3.
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Additional file 4:
KEGG map. KEGG pathway related to fatty acid biosynthesis (Map:00061) (A) and metabolism (Map:00071) (B). Box colors: blue and green correspond to up-regulated genes between olive stages 1 and 2, and 2 and 3, respectively, whereas red and yellow correspond to down-regulated genes between olive stages 1 and 2, and 2 and 3, respectively; gray indicates transiently down-regulated genes while violet indicates constantly and down-regulated genes from stage 1 to stage 3.
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Additional file 5:
Secondary metabolism enzymes. List of enzymes involved in the biosynthesis and metabolism of secondary metabolites, such as steroids, phenylpropanoids, flavonoids, alkaloids and specific products like caffeine, limonene and pinene.
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Additional file 6:
MAPMAN map. Overview MAPMAN metabolism map showing several constantly and transiently up- and down-regulated genes related to cell wall synthesis and breakdown, fatty acid biosynthesis and lipid breakdown, starch and sucrose metabolism, glycolysis, Calvin cycle and the secondary metabolism (e.g., terpenoids, flavonoids, phenols). Signal colors: blue and green correspond to up-regulated genes between olive stages 1 and 2, and 2 and 3, respectively, whereas red and yellow correspond to down-regulated genes between olive stages 1 and 2, and 2 and 3, respectively; cyan and violet indicate, respectively, constantly up-regulated and down-regulated genes from olive stage 1 to stage 3; gray and orange indicate, respectively, transiently down- and up-regulated genes.
Format: JPEG Size: 2.6MB Download file
Additional file 7:
List of specific primers used for RT-PCR analysis. List of specific primers designed on the selected key genes for the validation of their expression patterns by Real-Time PCR analysis.
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