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The major histocompatibility complex (MHC) is highly polymorphic and plays a central role in the vertebrate immune system. Despite its functional consistency, the MHC genomic structure differs substantially among organisms. In birds, the MHCs of Galliformes and the Japanese crested ibis (Pelecaniformes) are well-characterized, but information about other avian MHCs remains scarce. The Oriental stork ( Ciconia boyciana , order Ciconiiformes) is a large endangered migrant. The current Japanese population of this bird originates from a few founders; thus, understanding the genetic diversity among them is critical for effective population management. We report the structure and polymorphisms in  C. boyciana  MHC. One contig (approximately 128 kb) was assembled by screening of lambda phage genomic library and its complete sequence was determined, revealing a gene order of  COL11A2 , two copies of MHC-IIA/IIB pairs,  BRD2, DMA/B1/B2 , MHC-I,  TAP1/2 , and two copies each of pseudo MHC-I and  TNXB . This structure was highly similar to that of the Japanese crested ibis, but largely different from that of Galliformes, at both the terminal regions. Genotyping of the MHC-II region detected 10 haplotypes among the six founders. These results provide valuable insights for future studies on the evolution of the avian MHCs and for conservation of  C. boyciana .

Structure and polymorphisms of the major histocompatibility complex in the Oriental stork, Ciconia boyciana