New approaches to Prunus transcriptome analysis

Abstract

The recent sequencing of the complete genome of the peach offers new opportunities for further transcriptomic studies in Prunus species in the called post-genomics era. First works on transcriptome analysis in Prunus species started in the early 2000s with the development of ESTs (expressed sequence tags) and the analysis of several candidate genes. Later, new strategies of massive analysis (high throughput) of transcriptomes have been applied, producing larger amounts of data in terms of expression of a large number of genes in a single experiment. One of these systems is massive transcriptome analysis using cDNA biochips (microarrays) to analyze thousands of genes by hybridization of mRNA labelled with fluorescence. However, the recent emergence of a massive sequencing methodology ("deep-sequencing") of the transcriptome (RNA-Seq), based on lowering the costs of DNA (in this cases complementary, cDNA) sequencing, could be more suitable than the application of microarrays. Recent papers have described the tremendous power of this technology, both in terms of profiling coverage and quantitative accuracy in transcriptomic studies. Now this technology is being applied to plant species, including Prunus. In this work, we analyze the potential in using this RNA-Seq technology in the study of Prunus transcriptomes and the development of genomic tools. In addition, the strengths and limitations of RNA-Seq relative to microarray profiling have been discussed.

Transcriptomic analysis of developing embryos of apricot (Prunus armeniaca L.)

“…Separate microarray analyses of peach and apricot fruits used to profile transcriptome changes during fruit development revealed that 70% of genes had the same expression pattern in both species, but also demonstrated the presence of species-specific transcript changes (Manganaris et al, 2011). Because a high degree of sequence conservation exists within Prunus, the availability of the complete peach genome facilitates the investigation of other members of the genus (Martínez-Gómez et al, 2011). Synteny analysis across species provides insights into the evolutionary interrelationships of different lineages and the opportunity to study the relationship between genome structure and function of organisms (Jung et al, 2009).…”

“…Apricot and peach are diploid species, with apricot possessing a genome slightly larger than that of peach (Geuna et al, 2005). The construction of two apricot linkage maps using simple sequence repeat (SSR) markers has revealed that peach and apricot genomes exhibit complete co-linearity, while sequencing of the complete peach genome has provided opportunities for further studies of other Prunus species (Martínez-Gómez et al, 2011;Verde et al, 2013). The origin of the apricot is disputed.…”

Identification of volatile and softening-related genes using digital gene expression profiles in melting peach

“…The DGE profiles produced a large dataset, much greater than with an EST library or microarray Martinez-Gomez et al 2011). By mapping to the peach reference genome v1, a large number of genes were annotated with GO terms and the KEGG pathway.…”

Clarifying Omics Concepts, Challenges, and Opportunities forPrunusBreeding in the Postgenomic Era

“…A major drawback of the cDNA microarray approach for the study of this Gordian knot is that transcriptome profiling coverage is strictly limited to the probe sets available for specific hybridization in each species as we have described before. This classical microarray usually contained EST (cDNA from mRNA) previously developed by Sanger DNA sequencing technology (Aharoni and Vost, 2001;Martínez-Gó mez et al, 2011;Wullscheleger and Difacio, 2003). For this reason, and thanks to the availability of a full genome sequence for some species, new tilling microarray platforms have been developed using different spaced oligonucleotides that span the entire genome of an organism (Comai et al, 2004;Yazaki et al 2007).…”