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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

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



Papaya (Carica papaya L.) is a commercially important crop that produces climacteric fruits with a soft and sweet pulp that contain a wide range of health promoting phytochemicals. Despite its importance, little is known about transcriptional modifications during papaya fruit ripening and their control. In this study we report the analysis of ripe papaya transcriptome by using a cross-species (XSpecies) microarray technique based on the phylogenetic proximity between papaya and Arabidopsis thaliana.


Papaya transcriptome analyses resulted in the identification of 414 ripening-related genes with some having their expression validated by qPCR. The transcription profile was compared with that from ripening tomato and grape. There were many similarities between papaya and tomato especially with respect to the expression of genes encoding proteins involved in primary metabolism, regulation of transcription, biotic and abiotic stress and cell wall metabolism. XSpecies microarray data indicated that transcription factors (TFs) of the MADS-box, NAC and AP2/ERF gene families were involved in the control of papaya ripening and revealed that cell wall-related gene expression in papaya had similarities to the expression profiles seen in Arabidopsis during hypocotyl development.


The cross-species array experiment identified a ripening-related set of genes in papaya allowing the comparison of transcription control between papaya and other fruit bearing taxa during the ripening process.

Oligo-chip; Heterologous microarray; Papaya ripening; Quantitative gene expression; Whole genome shotgun; Transcript profiling