Copy number variation and population-specific immune genes in the model vertebrate zebrafish

Abstract

Many species have hundreds of immune genes from the NLR family (Nucleotide-binding domain Leucine-rich Repeat containing). In plants they have a considerable amount of within-species variation, but not much is known about their variability in fishes. Here we captured and analysed the diversity of NLRs in zebrafish (Danio rerio) by sequencing 93 individuals from four wild and two laboratory strains. We found 1,560 unique NLR genes, and theoretical modelling revealed each wild population to have around 2,000. Only 100-550 were detected in each individual fish, and the observed variance of copy numbers differed among populations. Laboratory strains were found to have three times less NLRs than wild populations, and their genetic diversity was lower in general. Many NLRs showed no single nucleotide variation, but those that did showed evidence of purifying selection. Our study lays the groundwork for unraveling mechanisms driving the evolution of this large gene family in vertebrates. Significance statementWe show here that the gene repertoires of vertebrates can be extremely variable, with different individuals having different genes. By sequencing one large family of immune receptors from 93 wild and laboratory zebrafish we found hundreds of novel gene copies, each only present in specific strains or specific individuals. Our observations can be explained by a combination of complex patterns of inheritance and a high rate of gene birth and death.