2.12 Identification of differentially expressed genes
To identify the differentially expressed genes in the genome of C.
sonnerati , 11 tissues (liver, gill, intestines, kidney, head kidney,
brain, pituitary, gonad, heart, skin, and muscle) were used to conduct
the transcriptome sequencing. For each of the samples, the trimmed short
reads were mapped to the genome sequence using Tophat (v2.1.1; https
://ccb.jhu.edu/software/tophat). RSEM (v1.3.0; https://deweylab. github.
io/RSEM) was used to calculate isoform level expression in terms of FPKM
and TPM (transcripts per million). Differentially expressed genes (DEGs)
between sample groups were evaluated by DESeq2 (Love, Huber, & Anders,
2014). The corrected read count data of genes were imported into the R
package EdgeR to identify DEGs with the criteria of a fold change of ≥
2.0, a false discovery rate [FDR] and adjusted p value of
< 0.05, and expression (FPKM ≥ 1) in at least one sample for
each comparison.