This Is AuburnElectronic Theses and Dissertations

Immune and gustatory roles of the channel catfish skin as revealed by comparative transcriptomic analyses




Gao, Sen

Type of Degree

PhD Dissertation


Fisheries and Allied Aquacultures

Restriction Status


Restriction Type


Date Available



Fish scales are physical barriers protecting them from various external stresses, in particular, from pathogen infections. However, vast majority of catfishes are evolutionarily scaleless. How scaleless fish respond to external environment, particularly against pathogen infections, is of great interest to biologists. Besides, much effort has been put on the expression patterns of potential immune-related genes post bacterial challenges for the catfish skin. A number of genes have been identified as differentially expressed genes, which are expressed significantly higher at certain time points post bacterial challenges, suggesting their significant roles involved in the catfish skin immunity. However, the expression patterns of these genes in the catfish skin under normal status remains largely unknown. Recently, RNA-Sequencing of several channel catfish tissues and organs allows us to conduct intra-species transcriptomic comparison to learn about specific transcripts in the channel catfish skin involved in the immunity. Furthermore, the complete RNA-Sequencing of several armored fish species, along with the RNA-Seq datasets of the channel catfish skin, makes the skin transcriptomic comparison between scaleless fish and scaled fish feasible. Such comparisons should provide us insights into the special roles of the channel catfish skin against the pathogen invasion. In the present study, these objectives were achieved through extensively analysis of RNA-Seq datasets originated from Illumina sequencing platforms. The catfish skin transcriptome was compared to that from four catfish tissues, barbel, gill, liver, intestine to determine skin-specific transcripts, especially those involved in immune responses. Also, the catfish skin transcriptome was compared to that of four other fish species, zebrafish, rhodeus, notothenia and stickleback, to determine the skin specific transcripts, especially those involved in immune functions in the scaleless skin of catfish. My results indicated that the channel catfish skin is more involved in the host immunity than previously known. Inter-species transcriptomic comparison suggests that not only the percentage of catfish-specific genes involved in the immunity is the highest among all fish species used in our study, but also the percentage of catfish-specific GO term directly involved in the immunity is the highest, too. This might be related to the scaleless characteristic of the channel catfish skin. Taste sensation plays pivotal roles for nutrient identification and acquisition. Channel catfish lives in turbid waters with limited vision, and taste sensation can be even more important for food seeking and survival. This biological process are mainly mediated by taste receptors expressed in taste buds distributed in several organs and tissues, including the barbel and skin. It has been known for a long time, that taste receptors as well as gustatory associated G proteins are involved in the gustation. Although many studies were previously conducted on mammalian taste receptor genes and gustatory associated G protein genes, studies of these genes in fish species, especially in the channel catfish, is lacking. Considering the importance of the gustation for fish feeding, along with significant roles of these genes involved in gustation, comprehensive studies for these genes in fish species are needed. Thus, upon the completion of the reference genome assembly and the availability of RNA-Sequencing datasets from various tissues and organs, the author identified these genes in the catfish genome first, and then characterized their expression patterns in various tissues and organs, providing a general understanding of these genes in both genomic and transcriptomic levels in the channel catfish. In the present study, I identified a complete repertoire of taste receptor and gustatory associated G proteingenes in the catfish genome. A total of eight taste receptor genes were identified, including five type I taste receptor genes and three type II genes. Addition four genes for gustatory associate G protein genes were also identified. Their genomic location, copy numbers, phylogenetic relations, orthologies, and expression were determined. Phylogenetic and syntenic analysis allowed determination of their evolution dynamics of these gene families. Furthermore, motif and dN/dS analyses allowed the inference of selection pressure imposed on these receptors. Expression patterns of catfish taste receptors and gustatory associated G proteins across organs are similar to the distribution of taste buds across organs. Expression comparison between catfish and zebrafish skin transcriptome provided evidence for potential roles of catfish skin in taste sensation.