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

New sequencing technologies, such as RNA-Seq, have provided powerful, efficient, and cost effective methods to rapidly generate comprehensive transcriptome sequence resources. RNA-Seq analysis has several advantages over classical transcriptome analysis methods including high throughput, high accuracy, and high speed. RNA-Seq methods are now being used widely to explore highly complex transcriptomes of reference and non-reference plant genomes. To improve our understanding of transcriptome analysis, multiple approaches and associated challenges for large-scale data analysis will be addressed including transcriptome assembly, differential gene expression analysis, and transcriptome annotation in reference, non-reference, and polyploidy plant genomes. In addition, specific example transcriptomes from Arabidopsis, Mesembryanthemum, and Opuntia will be discussed in order to represent the essential principles of specific computational methods.