Genomic architecture and repertoire of the rainbow trout immunoglobulin light chain genes

The genomic loci encoding the four immunoglobulin light chains (IgL1, IgL2, IgL3, and IgL4) in the Swanson trout genome assembly were annotated in order to provide a measurement of the potential IgL repertoire. IgL1 and IgL3 gene segments are co-localized on chromosomes 21, 18, 15, and 7 while IgL2 and IgL4 were found on chromosomes 13 and 17, respectively. In total, 48 constant (CL), 87 variable (VL), and 59 joining (JL) productive genes are described. Pairwise alignment of the VL segments revealed that they belong to nine different families, three of which (kappa IV, V, and VI) are described for the first time in this study. VL and CL sequences on chromosome 15 and 21 and those on chromosomes 7 and 18 clustered together in phylogenetic analysis. PCR was used to examine IgL CL and VL genes in 9 lines of rainbow trout. IgL4 in the Hot Creek and Golden trout lines was missing 42 nucleotides resulting in a loss of 14 amino acids. The sigma IV variable family was completely absent from the Swanson, Arlee, Hot Creek, and wild type lines and silenced in the Skamania line with the addition of 176 bp mini-satellite insert. Similarly, the Whale Rock, Arlee, and wild type lines were all found to encode two sigma II products, a functional 252 bp product and a larger 425 bp product that contained a 172 bp insert. Results from this study indicate that there are genomic differences in IgL repertoire between different lines of trout that could affect humoral immune responses post vaccination and during disease. •IgL1 and IgL3 genomic segments are co-localized on chromosomes 21, 18, 15, and 7.•Trout variable region gene segments can be divided into nine different variable families.•Gene segments on chromosomes 15 and 21 and on chromosomes 7 and 18 cluster together.•There are genomic differences in IgL isotypes and variable families between trout lines.