New methods of sequencing and new bioinformatics studies in Yaghooti grape transcriptome

Equally revolutionary technologies are currently emerging in the form of new methods of sequencing, termed massively parallel sequencing. New sequencing methods are widely used to sequence unknown genomes and investigate the location of protein and DNA interactions and other applications. More recently, an increasing number of studies have demonstrated the potential for the sequencing of total cDNA in order to observe the complete transcriptome. In a single RNA-Seq experiment, one can derive not only an accurate, quantitative measure of individual gene expression, but also discover novel transcribed regions in an unbiased manner. In addition, this methodology enables a global survey of the usage of the alternative splice sites. This article gives an overview of transcriptome analysis methods, and reviews the benefits of new techniques of sequencing to past methods. It also gives an overview of the usage of the new sequencing method in the grape transcriptome studies. Finally, it describes an experimental case using the RNA-Seq method for evaluating Yaghooti grape transcriptome in order to identify the mechanism involved in the grape cluster compactness. The study of Yaghooti grape transcriptome using RNA-Seq method resulted in identification the gene which controls the cluster compactness.

Keywords:

Yaghooti grape , NGS , Massively parallel sequencing , Transcriptome