2.8 Differentially expression analysis and functional enrichment
The clean reads of each sample were assembled by using StringTie software. FPKM (fragments per kilobase of transcript per million mapped reads) value of every transcript was analyzed and calculated by using StringTie software. Additionally, the DGEs (differentially expressed genes) were recognized by using the technique DESeq software in bothT. laevis and T. controversa infected and control samples. The genes/transcripts with the parameter of false discovery rate (FDR) ˂ 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes/transcripts (Samac et al., 2011). In addition, functional-enrichment analysis including GO and KEGG were performed to identify which DEGs by using R based on the hypergeometric distribution test with the FDR ˂ 0.05 represents the significantly expressed transcripts (Kanehisa et al., 2008).