Differential expression analysis and Functional enrichment
To identify DEGs (differential expression genes) between two different samples, the expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) method. RSEM (http:// deweylab. biostat.wisc.edu/rsem/) (B. Li & Dewey, 2011) was used to quantify gene and isoform abundances. R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R,http://www.bioconductor.org/packages/2.12/bioc/html/edgeR.html) (Robinson, McCarthy, & Smyth, 2010) was utilized for differential expression analysis. In addition, functional-enrichment analysis include- ing GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni-corrected P-value ≤0.05 compared with the whole-transcriptome background. GO functional enrichment and KEGG pathway analysis were carried out by Goatools (https://github.com/tanghaibao/ Goatools) and KOBAS (http://kobas.cbi.pku.edu.cn/home.do) (Xie et al., 2011).