Skin transcriptome analysis of the genes involved in mucous immunity and discovery of SSRs and SNPs in Crucian carp Carassius auratus

Abstract

Fish skin is first line of defence against attachment and penetration of pathogens. Crucian carp (Carassius auratus) is one of the major freshwater species and important food fish in China, yet its molecular mechanism of skin immune response remains unclear. In this study, a de novo transcriptome assembly of crucian carp skin was performed by using Illumina Hiseq 2000 platform. A total of 49,154,776 unigenes were assembled, among which 60,824 (25.16%) unigenes were annotated against the NCBI database. Gene ontology and KEGG mapping assigned the terms to 37,103 (39.15%), 9,337 (23.23%) unigenes, repectively. The best represented KEGG categories were immune system (8,871, 20.50%) and signal transduction (7,805, 18.04%), and several mucin proteins (MUC1, MUC2, MUC5B, MUC5AC, MUC18, etc.) as the main membrane-bound and secreted components of the mucosal layer, implying the differentiation of immune responses in the crucian carp skin. Moreover, the results revealed that potential 28,928 SSRs and 249,964 SNPs were detected in crucian carp. This is the first report on transcriptome analysis in the skin of C. auratus, which contribute to understanding the molecular mechanisms of mucous immunogenectics response and epidermal mucus secretion of the skin in fish.