A comprehensive analysis of the germline and expressed TCR repertoire in White Peking duck

Recently, many immune-related genes have been extensively studied in ducks, but relatively little is known about their TCR genes. Here, we determined the germline and expressed repertoire of TCR genes in White Peking duck. The genomic organization of the duck TCR alpha/delta, TCR gamma and unconventional TCR delta 2 loci are highly conserved with their counterparts in mammals or chickens. By contrast, the duck TCR beta locus is organized in an unusual pattern, (V beta)(n)-D beta-(J beta)(2)-C beta 1-(J beta)(4)-C beta 2, which differs from the tandem-aligned clusters in mammals or the translocon organization in some teleosts. Excluding the first exon encoding the immunoglobulin domain, the subsequent exons of the two C beta show significant diversity in nucleotide sequence and exon structure. Based on the nucleotide sequence identity, 49V alpha, 30V delta, 13V beta and 15V gamma unique gene segments are classified into 3V alpha, 5V delta, 4V beta and 6V gamma subgroups, respectively. Phylogenetic analyses revealed that most duck V subgroups, excluding V beta 1, V gamma 5 and V gamma 6, have closely related orthologues in chicken. The coding joints of all cDNA clones demonstrate conserved mechanisms that are used to increase junctional diversity. Collectively, these data provide insight into the evolution of TCRs in vertebrates and improve our understanding of the avian immune system.