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New approaches to Prunus transcriptome analysis

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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.

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Acknowledgments

This study has been supported by the projects “Importance, transmission and resistance sources in the main viruses affecting stone fruits in the Region of Murcia” (08672/PI/08) of the Seneca Foundation of the Region of Murcia and “Gene expression analysis of the resistance to Plum pox virus, PPV (Sharka) in apricot by transcriptome deep-sequencing (RNA-Seq)” of the Spanish Ministry of Science and Innovation (Project reference AGL2010-16335).

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  1. Department of Plant Breeding, CEBAS-CSIC, PO Box 164, 30100, Espinardo, Murcia, Spain

    Pedro Martínez-Gómez & Manuel Rubio

  2. Department of Plant Science, University of California-Davis, Davis, CA, 95616, USA

    Carlos H. Crisosto

  3. Department of Environm Agron and Crop Science, University of Padua, 35020, Padua, Italy

    Claudio Bonghi

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  1. Pedro Martínez-Gómez
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Correspondence to Pedro Martínez-Gómez.

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Martínez-Gómez, P., Crisosto, C.H., Bonghi, C. et al. New approaches to Prunus transcriptome analysis. Genetica 139, 755–769 (2011). https://doi.org/10.1007/s10709-011-9580-2

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