Designing a transcriptome next‐generation sequencing project for a nonmodel plant species1

The application of next‐generation sequencing (NGS) to transcriptomics, commonly called RNA‐seq, allows the nearly complete characterization of transcriptomic events occurring in a specific tissue. It has proven particularly useful in nonmodel species, which often lack the resources available for sequenced organisms. Mainly, RNA‐seq does not require a reference genome to gain useful transcriptomic information. In this review, the application of RNA‐seq to nonmodel plant species will be addressed. Important experimental considerations from presequencing issues to postsequencing analysis, including sample and platform selection, and useful bioinformatics tools for assembly and data analysis, are covered. Methods of assembling RNA‐seq data and analyses commonly performed with RNA‐seq data, including single nucleotide polymorphism detection and analysis of differential expression, are explored. In addition, studies that have used RNA‐seq to elucidate nonmodel plant transcriptomics are highlighted.