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New approaches to fruit tree transcriptome analysis

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The transcriptome can be described in plants, including in fruit tree species, as the complete list of all types of RNA molecules expressed in a cell, tissue or whole organism. The transcriptome comprises the protein-coding RNA (messenger RNA, mRNA) and the noncoding RNA, including the noncoding, ...

The transcriptome can be described in plants, including in fruit tree species, as the complete list of all types of RNA molecules expressed in a cell, tissue or whole organism. The transcriptome comprises the protein-coding RNA (messenger RNA, mRNA) and the noncoding RNA, including the noncoding, non-regulatory RNA [ribosomal RNA (rRNA) and transfer RNA (tRNA)] and the noncoding regulatory RNA [small interfering RNA (siRNA); micro RNA (miRNA); small nucleolar RNA (snoRNA); piwi-interacting RNA (piRNA); long noncoding RNA (lncRNA), etc.]. First works on transcriptome analysis in fruit tree species started at the mRNA level in the early 2000s with cDNA-AFLP (cDNA Amplified Fragment Length Polymorphism) analysis, the development of ESTs (expressed sequence tags) and the analysis of several candidate genes. More recently, 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 labeled with fluorescence. Microarray analysis continues to be one of the most important approaches for transcriptome analysis in fruit trees. However, the recent sequencing of the complete genome of different tree fruit species including apple, peach or Japanese apricot, together with the availability of new high-throughput sequencing ("deep-sequencing") technologies, is offering new possibilities for fruit tree transcriptome analysis. High-throughput sequencing of RNA (RNA-Seq), based on lowering the costs of DNA sequencing (in this case complementary, cDNA), makes it possible to obtain nearly the complete characterization of transcriptomic events occurring in a specific tissue or plant and represents the latest and most powerful tool for characterizing transcriptomes. RNA-Seq experiments have been primarily oriented in fruit trees to the high-throughput sequencing of the messenger RNA. In addition, high-throughput micro RNA sequencing is another part of the global RNA-Seq application and is being applied to a great range of fruit species. These noncoding regulatory RNAs (including miRNA and lncRNA) are beginning to be studied in fruit trees and offer great potential in terms of clarifying the gene expression process.


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