A comprehensive analysis of the phylogeny, genomic organization and expression of immunoglobulin light chain genes in alligator sinensis, an endangered reptile species

Abstract

Crocodilians are evolutionary distinct reptiles that are distantly related to lizards and are thought to be the closest relatives of birds. Compared with birds and mammals, few studies have investigated the Ig light chain of crocodilians. Here, employing an Alligator sinensis genomic bacterial artificial chromosome (BAC) library and available genome data, we characterized the genomic organization of the Alligator sinensis IgLgene loci. The Alligator sinensis has two IgL isotypes, λ and K, the same as Anolis carolinensis. The IgA locus contains 6 Cλ genes, each preceded by a Jλ gene, and 86 potentially functional Vλ genes upstream of (Jλ-Cλ)n. The IgK locus contains a single CK gene, 6 JKs and 62 functional VKs. All VL genes are classified into a total of 31 families: 19 Vλ families and 12 VK families. Based on an analysis of the chromosomal location of the light chain genes among mammals, birds, lizards and frogs, the data further confirm that there are two IgL isotypes in the Alligator sinensis: Igλ and IgK. By analyzing the cloned Igλ/KcDNA, we identified a biased usage pattern of V families in the expressed Vλ and VK. An analysis of the junctions of the recombined VJ revealed the presence of N and P nucleotides in both expressed λ and K sequences. Phylogenetic analysis of the V genes revealed V families shared by mammals, birds, reptiles and Xenopus, suggesting that these conserved V families are orthologous and have been retained during the evolution of IgL. Our data suggest that the Alligator sinensis IgL gene repertoire is highly diverse and complex and provide insight into immunoglobulin gene evolution in vertebrates.