A high-density BAC physical map covering the entire MHC region of addax antelope genome

Chaokun Li,Fangyuan Nie,Xiaoqian Shi,Runlin Z Ma,Yu Guo,Chenglin Zhang,Rui Huang,Changming Zheng,Xuefeng Liu,Longxin Chen

doi:10.1186/s12864-019-5790-2

Abstract

BackgroundThe mammalian major histocompatibility complex (MHC) harbours clusters of genes associated with the immunological defence of animals against infectious pathogens. At present, no complete MHC physical map is available for any of the wild ruminant species in the world.ResultsThe high-density physical map is composed of two contigs of 47 overlapping bacterial artificial chromosome (BAC) clones, with an average of 115 Kb for each BAC, covering the entire addax MHC genome. The first contig has 40 overlapping BAC clones covering an approximately 2.9 Mb region of MHC class I, class III, and class IIa, and the second contig has 7 BAC clones covering an approximately 500 Kb genomic region that harbours MHC class IIb. The relative position of each BAC corresponding to the MHC sequence was determined by comparative mapping using PCR screening of the BAC library of 192,000 clones, and the order of BACs was determined by DNA fingerprinting. The overlaps of neighboring BACs were cross-verified by both BAC-end sequencing and co-amplification of identical PCR fragments within the overlapped region, with their identities further confirmed by DNA sequencing.ConclusionsWe report here the successful construction of a high-quality physical map for the addax MHC region using BACs and comparative mapping. The addax MHC physical map we constructed showed one gap of approximately 18 Mb formed by an ancient autosomal inversion that divided the MHC class II into IIa and IIb. The autosomal inversion provides compelling evidence that the MHC organizations in all of the ruminant species are relatively conserved.

Highlights

The mammalian major histocompatibility complex (MHC) harbours clusters of genes associated with the immunological defence of animals against infectious pathogens
We noticed that DY is a newly evolved gene at the boundary of the autosomal inversion [20]; this gene is highly expressed in dendritic cells which are involved in the induction and function of regulatory T cells in the context of microbial exposure [21, 22]
According to the Animal Genome Size Database, the C value of the addax is 3.98, as estimated by flow cytometry [43]. This library should contain 5.4-fold genomic equivalents. This library could serve as a genetic resource in zoo-fluorescence in situ hybridization (Zoo-FISH) for MHC comparative genomic research and provide genomic content information for other chromosome regions

Summary

Introduction

The mammalian major histocompatibility complex (MHC) harbours clusters of genes associated with the immunological defence of animals against infectious pathogens. Mammalian major histocompatibility complex (MHC) plays an indispensable role in host defence against infection by various pathogens [1]. MHC is encoded by a highly polymorphic region organized into three clusters (classes I, II and III) [2]. MHC class I and class II encode molecules on the cell surface that present exogenous and endogenous antigens to T lymphocytes [3]. In contrast to MHCs of humans and mice, ruminant MHC was divided in the class II region by a substantial autosomal inversion that divided class II into. The evolutionary significance of the autosomal inversion still remains largely unclear

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Conclusion