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

Abstract

BackgroundPapaya (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.ResultsPapaya 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.ConclusionThe 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.

Physiological Degradation of Pectin in Papaya Cell Walls: Release of Long Chains Galacturonans Derived from Insoluble Fractions during Postharvest Fruit Ripening

“…In this way, the present study aimed to investigate the correlations between 16 genes of cell wall-related enzymes identified in previous works ( Fabi et al, 2009 , 2010 , 2012 ) and the changes in the monosaccharide composition of polysaccharides from the water-soluble, chelate-soluble, and ASFs of the cell wall during papaya ripening. As expected for other fleshy fruits, papaya WSF would correspond to the most soluble polysaccharides, including pectins, whereas the OSF would represent less soluble polysaccharides, mainly pectins that are tightened together by calcium bridges.…”

“…The softening of papaya fruit pulp is an ethylene-dependent process likely resulting from the action of several cell wall-related enzymes on the polysaccharide components of the plant cell wall and middle lamella. Previous works had indeed identified a critical subset of genes involved in cell-wall disassembly ( Fabi et al, 2009 , 2010 , 2012 ). However, despite the relevance of this process to fruit quality, the role played by each enzyme, the polysaccharides affected, and the time course of the structural changes are not clear.…”

Integrated Network Analysis Identifies Fight-Club Nodes as a Class of Hubs Encompassing Key Putative Switch Genes That Induce Major Transcriptome Reprogramming during Grapevine Development

“…The identification of MYBA1, MYBA2, and MYBA3, already well characterized for their direct and crucial role during the transition to berry ripening (Kobayashi et al, 2004;Walker et al, 2007), strongly supports the robustness of our approach and allows us to propose other transcription factors as potential regulators of the metabolic shift during berry development. Interestingly, we identified four NAC proteins (NAC33 and NAC60, also identified as switch genes in the atlas transcriptome, and NAC11 and NAC13) whose regulatory role in organ development has been proposed in many plant species (Raman et al, 2008;Fabi et al, 2012;Hendelman et al, 2013), including grapevine (Sun et al, 2012;Wang et al, 2013). We also identified two MYB proteins, eight zing-finger proteins (three shared with the atlas switch genes), two WRKY proteins, one bHLH protein, one Agamous-like MADS box protein, and three LATERAL ORGAN BOUNDARIES (LOB) proteins (two shared with the atlas switch genes).…”

“…ZFWD proteins contain a C3H-type zinc finger and seven WD40 repeats, and a role in development has been suggested based on their structural similarity to the Arabidopsis thaliana CONSTITUTIVE PHOTOMORPHOGENESIS1 and PLEIOTROPIC REGULATORY LOCUS1 proteins, which regulate photomorphogenesis (Németh et al, 1998;Torii et al, 1998), whereas NAC transcription factors have been shown to regulate vegetative and reproductive development in Arabidopsis (Raman et al, 2008), tomato (Hendelman et al, 2013), papaya (Carica papaya) (Fabi et al, 2012), and grapevine (Sun et al, 2012;Wang et al, 2013), suggesting a broad role as master regulators of fruit ripening. The parameters z g and K p represent a normalized measure of intramodule communication and the mode of communication between nodes in different modules, respectively.…”

Isolation of ripening-related genes from ethylene/1-MCP treated papaya through RNA-seq

“…To better understand the mechanisms of papaya fruit ripening, numerous studies have focused on the analysis of transcript, protein , and metabolite levels in papaya fruits. Using an Arabidopsis thaliana microarray, 414 ripening-related genes were identified, and some transcription factors were found in papaya fruit [ 11 ]. Twenty-seven protein spots showing differences in abundance during papaya ripening were successfully identified using the 2-DE analysis [ 9 ].…”