A Comprehensive Analysis Of The Phylogeny, Genomic Organization And Expression Of Immunoglobulin Light Chain Genes In Alligator Sinensis, An Endangered Reptile Species

Crocodilians are evolutionarily 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 IgL gene loci. The Alligator sinensis has two IgL isotypes, lambda and kappa, the same as Anolis carolinensis. The Ig(lambda) locus contains 6 C-lambda genes, each preceded by a J(lambda) gene, and 86 potentially functional V-lambda genes upstream of (J(lambda)-C-lambda)(n). The Ig kappa locus contains a single C-kappa gene, 6 J(kappa)s and 62 functional V(kappa)s. All V-L genes are classified into a total of 31 families: 19 V-lambda families and 12 V-kappa 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: Ig lambda and Ig kappa. By analyzing the cloned Ig lambda/kappa cDNA, we identified a biased usage pattern of V families in the expressed V-lambda and V-kappa. An analysis of the junctions of the recombined VJ revealed the presence of N and P nucleotides in both expressed. and. 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.