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.