Transcriptional responses of P-stressed switchgrass
Several studies have used RNA-sequencing to explore responses to P limitation in different plant species (Oono et al., 2011, 2013; O’Rourke et al., 2013; Secco et al., 2013, 2014; Zeng et al., 2018; Wang et al., 2019). This study represents the first analysis of transcriptome responses of switchgrass to P limitation, and uncovered a total of 8302 P-responsive transcripts involved in diverse biological processes (Table S2 ). Many of the previously reported transcriptional P-stress responses were tracked in switchgrass (Table S3 ). However, less known or unknown responses were also present, and many more DEGs without clear or any homology point towards further unknown transcriptional P-stress responses. The massive, genome-wide changes in gene expression in response to P-limitation were accompanied, and presumably orchestrated, by changes in the expression of hundreds of transcription factor (TF) genes, especially induction of members from the MYB, AP2, WRKY, bZIP and B3 families (Figure S4 ), indicating complex regulation of diverse plant responses. Interestingly, we could not identify clear homologs of TFs previously involved in P-regulation processes (Devaiah et al., 2007; Pant et al., 2015a; Pant et al., 2015b). Possible explanations may include: (i) that other studies have focused on initial stages of the P-response while our transcriptome analysis was performed after 3 weeks of exposure to P-stress; (ii) key regulatory functions may be carried out by different TFs in different species; and (iii) TFs are not completely annotated in the switchgrass genome. In fact, detailed homology searches, including unannotated transcripts, among strongly induced or repressed (>5-fold) transcripts, identified new actors associated with P responses in switchgrass (Table S4 ). Therefore, careful re-annotation of the switchgrass genome, and of our transcriptome data (Table S2 ), will open new avenues to discoveries.