Obtaining sequence information for a plant species of interest greatly facilitates functional genomic research. However, many plant species have not been sequenced due to the complexities of their genomes and the high cost of sequencing. Therefore, the transcriptomes of several plants were sequenced using next-generation sequencing technology. RNA-seq technology is an important high-throughput tool for both gene mapping and the transcriptome analysis of non-model organisms lacking genome information (Schuster, 2008; Wang et al., 2009; Klie et al., 2012; Drogue et al., 2014; Druege et al., 2014). Additionally, RNA-seq data can help connect the genome to gene function (Adams, 2008) and have tremendously expanded the volume of transcriptome information available for non-model plants. The uniformly processed and matched nature of the transcriptome data also facilitates their integration with upstream factor-binding and chromatin-modification signals (Gerstein et al., 2014).