Transcriptome Analysis & Beyond: Advanced Approaches for Transcriptome Analysis in Diploid and Polyploid Plant Species

New sequencing technology is a powerful and cost efficient method to get comprehensive and integrated transcriptome sequence resource such as RNA-Seq. The RNA-Seq analysis has several advance over classical transcriptome analysis method in high-throughput, high-sensitivity, and high-speed. Application of RNA-Seq is now being used widely for uncovering complex transcrtiptome abundance to facilitate the biological understanding in reference and non-reference genome plant. To improve our understanding of transcrtiptome analysis, we present multiple approach of the large scale data analyses associated the RNA-Seq technology and the challenges that need to be addressed, including transcriptome assembly, differential gene expression and transcriptome annotation in reference, non-reference and polyploidy genome plant. In addition, we discuss the examples that represent essential principles of computational methods of the Arabidopsis, Ice plant and Opuntia.