Open Access Highly Accessed Research article

Analysis of ripening-related gene expression in papaya using an Arabidopsis-based microarray

João Paulo Fabi1, Graham B Seymour2, Neil S Graham2, Martin R Broadley2, Sean T May2, Franco Maria Lajolo13, Beatriz Rosana Cordenunsi13 and João Roberto Oliveira do Nascimento13*

  • * Corresponding author: João Roberto Oliveira do Nascimento jronasci@usp.br

Author Affiliations

1 University of São Paulo, Department of Food Science and Experimental Nutrition, FCF, São Paulo, Brazil

2 Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leics, LE12 5RD, UK

3 University of São Paulo, – NAPAN – Food and Nutrition Research Center, São Paulo, Brazil

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BMC Plant Biology 2012, 12:242  doi:10.1186/1471-2229-12-242

Published: 21 December 2012

Additional files

Additional file 1:

Effect of Carica papaya genomic DNA (gDNA) hybridization on probe-pairs and probe-sets from the ATH1-121501 chip. This additional figure describes how different values of hybridization intensity threshold (masks) affect the probe-sets and probe-pairs retained after papaya genomic hybridization in A.thaliana commercial chip.

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Additional file 2:

Differentially expressed probe-sets identified in papaya fruit. This table is a full version (edited in Excel program) of Table 1 with crude data (19,286 probe-sets) and treated data (414 probe-sets). It describes the principal characteristics of probe-sets retained after threshold cut-off and comparison between ripe X unripe fruit, that includes systematic and common names of probe sets, normalized and raw values, fold time changes and p values, as well as GO identities for biological process, molecular function and cellular component.

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Additional file 3:

Hierarchical clustering of ATH1-121501 probe-sets hybridized with papaya RNA. This figure describes the hierarchical clustering of the 414 probe-sets identified by the XSpecies microarray technique, showing different clusters of gene expression.

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Additional file 4:

Differentially expressed probe-sets identified in papaya fruit. This table is a shorter version of Additional file 2, also edited in Excel program. However this table shows the probe-sets collected for generation of GO plot figure by names (Figure 1A and B) and also describes the parameters of Genespring software from statistical analyses.

Format: XLSX Size: 167KB Download file

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Additional file 5:

Ripening analysis from three different samples of papaya fruit. This table describes the main parameters that were used for classifying as unripe (green) and ripe (yellow) papayas. This includes respiration (CO2 production), ethylene production and pulp firmness.

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Additional file 6:

Differentially expressed probe-sets identified in papaya fruit. This table shows, in a reduced form, the probe-sets that were differentially expressed according to fold changes between ripe X unripe, but with a statistical p-value cut-off of 0.10, which returned 1,091 differentially expressed probe-sets.

Format: XLS Size: 108KB Download file

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Additional file 7:

Overview of cell function transcripts from tomatoes, grapes and papayas in response to ripening. This figure describes the cell function transcripts from tomato, grape and papaya fruits when analysed with the MapMan software.These values (and identities) were the same used to structure the Venn diagram in Figure 2.

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Additional file 8:

Differentially expressed transcription factors from papaya, tomato and grape. This table is a simplified version of Table 2 (edited in Excel program) and Figure 3. The table only returns the results from MapMan analysis of overview ripening regulation of papaya fruit, but there is no comparison of transcription factors between three species.

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Additional file 9:

Nucleotide sequences used in qPCR. This table describes the primers used in Real Time-PCR analyses.

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Additional file 10:

Standard curve calculation of Real Time-PCR primers. This table describes the efficiency values, as well the standard curves for all primers used in Real Time-PCR experiments.

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Additional file 11:

Genbank ID and sequences of proteins used for comparative biology analyses. This is compacted (zipped) file which contains all sequences of proteins used for generating the phylogenetic trees in order to analyse the comparative biology between different.

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