Abstract
In this study, we analyzed the loci structure of raccoon dog genes using a comparative genomics approach. We investigated the mechanism of expression diversity and its preference using the Next-generation sequencing. The results indicated that the raccoon dog gene loci structure were similar to that of most mammals, with a relative abundance of V(D)J genes, which ensures its expression diversity. We identified the following potentially functional genes: 7 VH genes, 6 Vκ genes, 23 Vλ genes, 24 DH genes, 5 JH genes, 4 Jκ genes, and 6 Jλ genes, arranged in a manner similar to that of other mammals. Analysis of the raccoon dog expression diversity mechanism showed that raccoon dog have a strong preference for the use of V genes, and the same was true for DH genes. The main modes of expression diversity in raccoon dog were V(D)J recombination and somatic hypermutation, in which the high mutation region of somatic hypermutation was not only concentrated in the CDR region, but also has a high mutation in the FR region, and the main types of somatic hypermutation were G > A, C > T, T > C, and A > G. Interestingly, we compared the expression differences between normal and diseased raccoon dogs, and the results showed that there were significant differences in the expression of the same gene (P < 0.05), whereas there were no significant differences in the types of gene expression, gene utilization preference, V(D)J recombination, and somatic hypermutation mutation types. In summary, we have described the IgH and IgL gene loci structure of raccoon dog, mapped the gene loci, and analyzed the mechanism of expression diversity and its preference using PE300 Next-generation sequencing. The results of this study could provide a theoretical basis for an in-depth understanding of raccoon dog immunoglobulins, and provide theoretical references for raccoon dog disease-resistant breeding.