Characterization of gill transcriptome, SSR/SNP markers and expression analysis of lysozyme LysC gene from Carassius auratus upon Aeromonas hydrophila infection

The gills are large mucosal surfaces and play primary roles in respiration and immune defences. However, the molecular mechanism for gills of fish needs still to be explored. In the present study, transcriptomic analysis and identification of SSR and SNP markers were performed in the gills of crucian carp Carassius auratus. The results showed a total of 84,259 unigenes were annotated to NCBI NR, KEGG and GO databases for 55,283, 39,303, 33,388, respectively. Enriched KEGG pathway analyses for the identified genes showed the mainly functional modules such as metabolism, cellular processes, environmental adaptation, genetic processing, organismal and immune systems. Moreover, 22,102 SSRs (simple sequence repeats) were potentially identified and 9776 (44.2%) were accounted for the most dinucleotides. Transition and transversion sites of SNPs (single nucleotide polymorphisms) were also observed. Tissue distribution showed that the expression level of lysozyme LysC gene was relatively high in intestine, liver, spleen and kidney tissues and up-regulated in gills, skin and brain after the A. hydrophila infection. We discovered the immune-related pathways through the transcriptome analysis in the gills of crucian carp, some potential SSR/SNP markers were identified, and lysozyme gene predominantly expressed in mucosal immune organs (eg., gills, skin, intestine) responded to A. hydrophila infection. To the best of our knowledge, this was the detailed report on the molecular characteristics in crucian carp gills with transcriptome analysis, which will not only provide a scientific reference for further understanding the local defense mechanism, but also lay a foundation for molecular marker-assisted breeding in fish.