Transcriptomic and proteomic data in developing tomato fruit

Abstract

Transcriptomic and proteomic analyses were performed on three replicates of tomato fruit pericarp samples collected at nine developmental stages, each replicate resulting from the pooling of at least 15 fruits. For transcriptome analysis, Illumina-sequenced libraries were mapped on the tomato genome with the aim to obtain absolute quantification of mRNA abundance. To achieve this, spikes were added at the beginning of the RNA extraction procedure. From 34,725 possible transcripts identified in the tomato, 22,877 were quantified in at least one of the nine developmental stages. For the proteome analysis, label-free liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) was used. Peptide ions, and subsequently the proteins from which they were derived, were quantified by integrating the signal intensities obtained from extracted ion currents (XIC) with the MassChroQ software. Absolute concentrations of individual proteins were estimated for 2375 proteins by using a mixed effects model from log₁₀-transformed intensities and normalized to the total protein content. Transcriptomics data are available via GEO repository with accession number GSE128739. The raw MS output files and identification data were deposited on-line using the PROTICdb database (http://moulon.inra.fr/protic/tomato_fruit_development) and MS proteomics data have also been deposited to the ProteomeXchange with the dataset identifier PXD012877. The main added value of these quantitative datasets is their use in a mathematical model to estimate protein turnover in developing tomato fruit.

Keywords: Absolute quantification; Pericarp; Protein turnover; Proteomics; Time-series; Tomato fruit development; Transcriptomics.

Fig. 1

Experimental setup. (A) The nine stages of samples with corresponding physiological phases of the tomato fruit development (Solanum lycopersicum cv. ‘Moneymaker’). (B) Description of the analyzed tissue, the pericarp, composed of endocarp, mesocarp and exocarp in tomato fruit at the last stage of development.

Fig. 2

Hierarchical clustering analysis of (A) transcript and (B) protein concentrations from tomato at nine developmental stages. The hierarchical clustering analysis was performed using Pearson's correlation on mean centered and scaled data. Hierarchical clustering analysis was performed using plyr, gplots and reshape2 packages from R studio (R 3.3.2; http://www.rstudio.com/).

Fig. 3

Principal component analysis of (A) transcriptomics and (B) proteomics data (fmol.gFW⁻¹). Data were mean centered and scaled. Developmental stages and replicates were distinguished by colors and shapes. Principal component analysis was performed using factoextra and gplots packages from R studio (R 3.3.2; http://www.rstudio.com/).