Integrative and Comparative Analysis of Skin Transcriptome of Various Fish Species

Fish scales are physical barriers protecting them from various external stresses including infections. However, vast majority of catfishes are evolutionarily scaleless. How scaleless fish respond to external environment, particularly against infections, is of great interest to biologists. In this study, our objectives were to conduct comparative transcriptome studies using available RNA-Seq datasets from scaled and scaleless fish. We generated the RNA-Seq dataset of the channel catfish (scaleless) skin using the Illumina sequencing platform, and used skin RNA-Seq datasets of zebrafish (scaled), rhodeus (scaled), notothenia (scaled) and stickleback (barely scaled) from publicly available databases. The skin transcriptomes of the five species were first assembled de novo using Trinity. The transcriptomes were annotated by BLASTP analysis against the zebrafish reference protein database. Comparative analysis was conducted to identify genes specifically expressed in the skin of each species.  A total of 11,843 orthologous gene sets were established that are common to all five species. Species-specific transcripts were identified for each of the five species, with 1,536 genes as catfish-specific. Of the catfish-specific genes, 33 genes were involved in immune-related functions, suggesting that a significant fraction of catfish-specific skin genes are involved in both innate and adaptive immunity.  A total of 165 genes were identified as genes preferentially expressed in the skin (at least 16 X more than expression in any of the four tissues used in the analysis: liver, gill, barbel, intestine; FDR < 0.01).