All SRA format data were converted into FASTQ using the SRA toolkit. All raw reads were first filtered with NGS QC Toolkit (v2.3.3) to remove adapter sequences, reads containing poly-N, and low-quality sequences (Q < 20). An index of the lotus genome was built using Bowtie 2 and paired-end or single-end clean reads were aligned to the reference genome using TopHat. The expression levels (fragments per kb per million mapped read, FPKM) from the representative transcript were determined using cufflinks program (cufflinks v2.2.142) with default settings. We used a threshold of FPKM ≥ 1 to define a gene as “expressed.”