Comparative transcriptional profiling analysis of olive ripe-fruit pericarp and abscission zone tissues shows expression differences and distinct patterns of transcriptional regulation

Ruben Parra,Isabel M Sanchez-Calle,Miguel A Paredes,Maria C Gomez-Jimenez

doi:10.1186/1471-2164-14-866

Abstract

BackgroundIn fleshy fruit, abscission of fully ripe fruit is a process intimately linked to the ripening process. In many fruit-tree species, such as olive (Olea europaea L. cv. Picual), there is a coupling of the full ripening and the activation of the abscission-zone (AZ). Although fully ripe fruit have marked physiological differences with respect to their AZs, dissimilarities in gene expression have not been thoroughly investigated. The present study examines the transcriptome of olive fruit and their AZ tissues at the last stage of ripening, monitored using mRNA-Seq.ResultsRoche-454 massive parallel pyrosequencing enabled us to generate 397,457 high-quality EST sequences, among which 199,075 were from ripe-fruit pericarp and 198,382 from AZ tissues. We assembled these sequences into 19,062 contigs, grouped as 17,048 isotigs. Using the read amounts for each annotated isotig (from a total of 15,671), we identified 7,756 transcripts. A comparative analysis of the transcription profiles conducted in ripe-fruit pericarp and AZ evidenced that 4,391 genes were differentially expressed genes (DEGs) in fruit and AZ. Functional categorization of the DEGs revealed that AZ tissue has an apparently higher response to external stimuli than does that of ripe fruit, revealing a higher expression of auxin-signaling genes, as well as lignin catabolic and biosynthetic pathway, aromatic amino acid biosynthetic pathway, isoprenoid biosynthetic pathway, protein amino acid dephosphorylation, amino acid transport, and photosynthesis. By contrast, fruit-enriched transcripts are involved in ATP synthesis coupled proton transport, glycolysis, and cell-wall organization. Furthermore, over 150 transcripts encoding putative transcription-factors (TFs) were identified (37 fruit TFs and 113 AZ TFs), of which we randomly selected eight genes and we confirmed their expression patterns using quantitative RT-PCR.ConclusionWe generated a set of EST sequences from olive fruit at full ripening, and DEGs between two different olive tissues, ripe fruit and their AZ, were also identified. Regarding the cross-talk between fruit and AZ, using qRT-PCR, we confirmed a set of TF genes that were differentially expressed, revealing profiles of expression that have not previously been reported, this offering a promising beginning for studies on the different transcription regulation in such tissues.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-14-866) contains supplementary material, which is available to authorized users.

Highlights

In fleshy fruit, abscission of fully ripe fruit is a process intimately linked to the ripening process
We reported the comparison of the Picual fruit AZ transcriptomes at two different stages using the RNA-Seq technique; 148 Mb of sequences (443,811 good-quality sequence reads) resulted and 4,728 differentially expressed genes were identified from these two samples [9]
454 sequencing of olive transcriptomes To characterize olive transcriptomes and generate expression profiles between fruit ripening and abscission, Roche/454 GS-FLX (Titanium) pyrosequencing technology was used to sequence two Complementary deoxyribonucleic acid (cDNA) samples from fruit pericarp and the AZ, which were collected from olive

Summary

Introduction

Abscission of fully ripe fruit is a process intimately linked to the ripening process. The present study examines the transcriptome of olive fruit and their AZ tissues at the last stage of ripening, monitored using mRNA-Seq. Olive (Olea europaea L.), of worldwide economic importance, has high intra-specific genetic variation with a genome size of about 1,800 Mb [1]. Olive (Olea europaea L.), of worldwide economic importance, has high intra-specific genetic variation with a genome size of about 1,800 Mb [1] This feature serves to analyze biological processes of biotechnological interest such as phenolic and lipid metabolism during fruit development [2,3,4] as well as terpenoids and sterols [5]. A number of large datasets of expressed sequence tag (EST) datasets have recently been reported for olive, generating 261,485 ESTs [2] and 443,811 ESTs [9] employing the 454 pyrosequencing technologies, an additional 1,132 ESTs with the use of suppression subtractive hybridization [3], as well as 2 million ESTs using Sanger and 454 pyrosequencing technologies [10], this being important for extending the catalog of olive transcripts in order to facilitate gene discovery, functional analysis, and molecular breeding

Methods

Results

Conclusion