RNA-Seq application in Prunus species

contributed by an RNA-Seq Blog reader…

prunusThe genus Prunus, family Rosaceae subfamily Amygyloidea, is an important genus originated from Central Asia and widely spread around the world which includes several species [peaches and nectarines [P. persica (L.) Batsch]; prunes (P. domestica L.), plums (P. salicina Lindl), sloes (P. spinosa L.), and cherry plums (P. cerasifera Ehrh.); apricots (P. armeniaca L.); almonds (P. amygdalus Batsch syn. P. dulcis (Miller) D.A. Webb); and sweet (P. avium L.) and sour cherries (P. cerasus L.)] producing edible drupes with economic importance for fresh fruit, dry fruit and nut consumption. We present the first application of the deep sequencing of the transcriptome (RNA-seq) in a Prunus specie, concretely apricot.

First results apricot RNA-seq performed in collaboration with the Ultrasequencing Unit of the Centre for Genomic Regulation of Barcelona (Spain) (http://www.crg.es) showed the high number of reads of 32 nucleotides (more than 20 million) obtained per line of a flow cell from Illumina Genome Analyzer IIx, and their good quality (only 2% of the reads have been discarded). In addition, 72% of these reads have been aligned to a single location to the reference peach genome (v1.0) (http://www.rosaceae.org/peach/genome) with 0, 1 or 2 mismatches. These alignement results confirmed the high levels of synteny between Prunus transcriptomes, also evidenced for Prunus genomes, and the utility of the peach genome as reference in first RNA-Seq studies in other Prunus species. Differential analysis of this RNA-Seq data is being performed with a great potential application in the identification of differentially expressed genes that may be correlated with the differential response of apricot against Plum pox virus (PPV).

Martínez-Gómez P, Crisosoto C, Bonghi C, Rubio M (2011) New approaches to Prunus transcriptome analysis. Genetica 139 (6): 755-769