Transcriptome Analysis of a Warm-Season Grass, Spartina pectinata, in Response to Freezing Stress

Prairie cordgrass (Spartina pectinata Link) is a perennial C₄ grass native to the North American Prairie. Prairie cordgrass has several distinctive characteristics that make it a potential candidate as a model crop tolerating stressful environments. However, little is known about the transcriptome dynamics of prairie cordgrass despite its unique freezing stress tolerance. The purpose of this experiment was to understand the transcriptome dynamics of prairie cordgrass in response to freezing stress at -5^oC for 5-min and 30-min. Prairie cordgrass RNA was extracted and sequenced using an Illumina HiSeq 2500. Over 385 million high quality paired-end reads was generated and assembled into 44,465 contigs. Our transcriptome analysis identified 942 differentially expressed genes (DEGs) and among those, 342 DEGs showed the fold changes of  > 1 or <-1 in response to freezing stress. Those 342 genes were categorized into three main groups and six sub-groups based on expression patterns; more than 14% were immediately up-regulated at 5-min and maintained until 30-min, 12% were immediately down-regulated at 5-min and up-regulated through 5-min to 30-min, and 13% were immediately up-regulated at 5-min and down-regulated through 5-min to 30-min. To validate the expression profiles of the gene in our Illumina sequencing data, 12 DEGs, including six transcriptomes factor, was selected, and there was the significant correlation between qRT-PCR analysis and RNA sequencing data.  Interestingly, we found transcriptional, post-translational and epigenetic components in DEGs, suggesting dynamic change in multiple cellular mechanisms during early response to freezing exposure.