Tag-based approaches for deep transcriptome analysis in plants

Serial analysis of gene expression (SAGE) has pioneered the use of short-tag sequences derived from the 3′-ends of cDNAs for transcriptome research. Many new tag-based technologies, capitalizing on the success of SAGE, have been developed in the last decade greatly improving the tag length, cloning efficacy and the depth of transcriptome analysis in targeted genomes. Moreover, the recent introduction of novel 5′ mRNA-end isolation methods has allowed for transcription start site determination and promoter region analyses and thus has facilitated accurate annotation of sequenced genomes. Another deep transcriptome analysis method called massively parallel signature sequencing (MPSS) has recently been applied to the annotation of both Arabidopsis and rice genomes, not only unraveling the complexities of transcribed regions in plants, but also leading to the identification of novel small RNA species. As new robust sequencing technologies are being developed, tag-based transcriptome analysis will become more affordable and popular in the plant research community. The present review discusses the current status and future challenges of tag-based technologies for the in-depth analysis of plant transcriptomes.