Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development

Fiammetta Alagna,Laura Torchia,Marco Pietrella,Maurizio Servili,Luciana Baldoni,Gaetano Perrotta,Giovanni Giuliano,Maria Luisa Chiusano,Nunzio D'Agostino,Rosa Rao

doi:10.1186/1471-2164-10-399

Abstract

BackgroundDespite its primary economic importance, genomic information on olive tree is still lacking. 454 pyrosequencing was used to enrich the very few sequence data currently available for the Olea europaea species and to identify genes involved in expression of fruit quality traits.ResultsFruits of Coratina, a widely cultivated variety characterized by a very high phenolic content, and Tendellone, an oleuropein-lacking natural variant, were used as starting material for monitoring the transcriptome. Four different cDNA libraries were sequenced, respectively at the beginning and at the end of drupe development. A total of 261,485 reads were obtained, for an output of about 58 Mb. Raw sequence data were processed using a four step pipeline procedure and data were stored in a relational database with a web interface.ConclusionMassively parallel sequencing of different fruit cDNA collections has provided large scale information about the structure and putative function of gene transcripts accumulated during fruit development. Comparative transcript profiling allowed the identification of differentially expressed genes with potential relevance in regulating the fruit metabolism and phenolic content during ripening.

Highlights

Despite its primary economic importance, genomic information on olive tree is still lacking. 454 pyrosequencing was used to enrich the very few sequence data currently available for the Olea europaea species and to identify genes involved in expression of fruit quality traits
Despite the fact that cDNA samples were prepared without any normalization process, we only found a moderate degree of redundancy
Analysis of differentially expressed gene transcripts evidenced large differences in key genes involved in a number of metabolic pathways that can potentially alter most quality traits in olive fruits

Summary

Introduction

Despite its primary economic importance, genomic information on olive tree is still lacking. 454 pyrosequencing was used to enrich the very few sequence data currently available for the Olea europaea species and to identify genes involved in expression of fruit quality traits. The ability to monitor simultaneously the expression of a large set of genes is one of the most important objectives of genome sequencing efforts In this respect, the 454 pyrosequencing technology [1] is a rather novel method for high-throughput DNA sequencing, allowing gene discovery and parallel efficient and quantitative analysis of expression patterns in cells, tissues and organs. In the past few years, several studies based on comparative high throughput sequencing of plant transcriptomes have, allowed the identification of new gene functions, contaminant sequences from other organisms, alterations of gene expression in response to genotype, tissue or physiological changes, as well as large scale discovery of SNPs (Single Nucleotide Polymorphisms) in a number of model and non model species, such us maize, grapevine and eucalyptus [2,3,4,5].

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