Transcriptome analysis of transgenic switchgrass plants
The control and transgenic switchgrass plants at the E2 stage were treated for 2 days with 20 mg·L-1 2,4-DNT. Subsequently, the root tissues were collected for transcriptome analysis by RNA sequencing (RNA-seq). Transcriptome de novo assembly of switchgrass was performed directly on the set of sequenced reads using the Trinity 2.4.0 (Broad Institute, Boston, USA). Raw Illumina pair-end reads were trimmed using FastQC including the Q20, Q30, and GC-content of the clean data to obtain high quality reads. All assembled unigenes were aligned against the non-redundant (Nr) database, GO, SwissProt, KEGG, and eggnog databases using DIAMOND (Crystal Impact GbR, Bonn, Germany) with a threshold of E-value < 0.00001. The differentially expressed unigenes were selected with log2 (fold change) ≥1 and with statistical significance (p ≤ 0.05) by R package edgeR. Furthermore, GO and KEGG enrichment analysis were used for data mining.