title: Casuarina equisetifolia repeat A3
design: Total RNA was extracted from root samples using TRIzol eagent according to the manufacturers instructions (Invitrogen, Waltham, MA). A paired-end RNA sequencing library was constructed and sequenced with the Illumina HiSeq xten/NovaSeq 6000 sequencer (2  150 bp read length) (Majorbio, Beijing, China). All clean reads were mapped to the reference genome (GenBank accession number: RDRV00000000.1) using HISAT2 (http://ccb.jhu.edu/software/hisat2). The mapped reads of each sample were assembled by StringTie (https://ccb.jhu.edu/software/stringtie). The expression level of each transcript was calculated according to the transcripts per million reads method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify the gene abundances. Differential expression analysis was performed using DESeq2 with q 0.05. The KEGG pathway analysis was performed by Python scipy software (https://scipy.org/install/) at Bonferroni-corrected p  0.05 compared with the whole-transcriptome background.