Alternative transcriptome analysis to build the genome-phenome bridges in animals

Understanding the genetic links between an animal’s genome and phenome is one of the most challenging tasks in the postgenome sequencing era. These links may be provided through the usage of alternative transcription start, termination and splicing sites in RNA, which promote the synthesis of multiple proteins from a single gene and enable a finite genome to build an infinite phenome during an animal’s lifespan. Therefore, alternative transcripts, rather than individual genes, are the minimal functional units in a genome. This chapter focuses on alternative transcriptome analysis, including platforms, strategies, methods, and applications. We will also demonstrate how these data can help us understand the genetic information flows from genome to phenome that are relevant to physical, physiological, pathological, and psychological processes.