2.18 Opsin gene expression
Retina-specific transcriptomes were analyzed for C. undulatus to determine the expression of opsin genes. The filtered reads of transcriptomes from retina tissue, together with the reads of brain, muscle, liver, spleen, olfactory organs, and gonad tissues collected from the same individual were mapped against the coding sequences of opsin genes identified above in C. undulatus using Blast, and the mapping reads were input into Cufflinks (Trapnell et al. 2012) for the estimation of opsin gene expression. The confidence intervals for the estimation of fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using a Bayesian inference method (Trapnell et al. 2012). The criterion of expressed abundance was a statistic FPKM value of 0.1-3.75 for lower expression, 3.75-15 for model expression, and more than 15 for high expression (Pertea et al. 2015). Meanwhile, the difference in gene expression was identified by DESeq2 (Love et al. 2014), using the false discovery rate (FDR) to calculate the P value at a significant level.
3 Results and Discussion