4.4.2. Mapping and DEG Analysis

After quality control to remove low-quality reads and adapter contaminants from the raw reads, the remaining clean reads were aligned to the *P. mume* reference genome [1] using HISAT2.0.4 software with default parameters [101]. Cufflinks v2.1.1 was then used to assemble and identify known and novel transcripts, and HTSeq v0.6.1 (-m union) was used to estimate gene expression levels based on fragments per kilobase of transcript sequence per millions of base pairs (FPKM) [102]. Differential expression analysis of WT and RT groups, with three biological replicates per group, was performed in DESeq v1.10.1, a program providing statistical routines for the determination of differential expression in digital gene expression data with a negative binomial distribution (Kij~NB(µij,σij2)) [103,104]. Significant DEGs were identified using an adjusted *p*-value cutoff of 0.05 and then subjected to GO [98] and KEGG [100] annotation.
