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PLoS One. 2016 Dec 20;11(12):e0168744. doi: 10.1371/journal.pone.0168744. eCollection 2016.

Signatures of Crested Ibis MHC Revealed by Recombination Screening and Short-Reads Assembly Strategy.

Chang L1,2, He S2, Mao D2, Liu Y2, Xiong Z1,2, Fu D1, Li B2, Wei S1, Xu X2, Li S1,2, Yuan H2,3.

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College of Medicine and Forensics, Xi'an Jiaotong University, Xi'an, Shaanxi, China.
BGI-Shenzhen, Shenzhen, Guangdong, China.
College of Animal Science and Technology, Northeast Agricultural University, Harbin, Heilongjiang, China.


Whole-genome shotgun (WGS) sequencing has become a routine method in genome research over the past decade. However, the assembly of highly polymorphic regions in WGS projects remains a challenge, especially for large genomes. Employing BAC library constructing, PCR screening and Sanger sequencing, traditional strategy is laborious and expensive, which hampers research on polymorphic genomic regions. As one of the most highly polymorphic regions, the major histocompatibility complex (MHC) plays a central role in the adaptive immunity of all jawed vertebrates. In this study, we introduced an efficient procedure based on recombination screening and short-reads assembly. With this procedure, we constructed a high quality 488-kb region of crested ibis MHC that consists of 3 superscaffolds and contains 50 genes. Our sequence showed comparable quality (97.29% identity) to traditional Sanger assembly, while the workload was reduced almost 7 times. Comparative study revealed distinctive features of crested ibis by exhibiting the COL11A2-BLA-BLB-BRD2 cluster and presenting both ADPRH and odorant receptor (OR) gene in the MHC region. Furthermore, the conservation of the BF-TAP1-TAP2 structure in crested ibis and other vertebrate lineages is interesting in light of the hypothesis that coevolution of functionally related genes in the primordial MHC is responsible for the appearance of the antigen presentation pathways at the birth of the adaptive immune system.

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