Danio rerio SVCV infection

Zebrafish (Danio rerio) is a model fish species for genomic, developmental, biomedical and pharmacological studies, among other areas of inquiry. The existence of numerous zebrafish mutant lines is a wonderful tool to study diverse biological aspects in this teleost. This is the case of the zebrafish mutant line rag1. V(D)J recombination, carried out by the combined endonuclease activity of recombination activating gene 1 (RAG1) and RAG2, assembles the vast diversity of immunoglobulins and T cell receptor (TCR) genes. A point mutation of the rag1 gene in zebrafish causes a premature stop codon in the rag1 catalytic domain; therefore, this mutation presumably abolishes the adaptive immune system. The use of heterogygous rag1 zebrafish could help us to discover compensatory mechanisms in these animals, which are partially deficient in Rag1 protein, to effectively fisght an infection. We were interested in the long non-coding RNAs (lncRNAs) differentially modulated in both lines after infection with spring viraemia of carp virus (SVCV).For this, we conducted Illumina sequencing of wild-type (WT) and heterozygous rag1 mutant (rag1+/-) zebrafish at 24 h after the infection with SVCV. Kidney samples were taken from infected and uninfected fish for transcriptome sequencing. Transcriptome de novo aseembly generated 198,540 contigs among which 58,805 contigs represented coding sequences, and 12,165 were putative lncRNA sequences Differential expression analysis of lncRNAs modulated after SVCV in both zebrafish lines helped us to to identify lncRNAs involved in the adaptive immune response.