Comparison of gene expression profiles in nonmodel eukaryotic organisms with RNA-seq

With recent advances of next-generation sequencing technology, RNA-Sequencing (RNA-Seq) has emerged as a powerful approach for the transcriptomic profiling. RNA-Seq has been used in almost every field of biological studies, and has greatly extended our view of transcriptomic complexity in different species. In particular, for nonmodel organisms which are usually without high-quality reference genomes, the de novo transcriptome assembly from RNA-Seq data provides a solution for their comparative transcriptomic study. In this chapter, we focus on the comparative transcriptomic analysis of nonmodel organisms. Two analysis strategies (without or with reference genome) are described step-by-step, with the differentially expressed genes explored.