A high-density BAC physical map covering the entire MHC region of addax antelope genome
Abstract Background The 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. Results The...
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| Format: | Article |
| Language: | English |
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BMC
2019-06-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-019-5790-2 |
| _version_ | 1818307270937673728 |
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| author | Chaokun Li Longxin Chen Xuefeng Liu Xiaoqian Shi Yu Guo Rui Huang Fangyuan Nie Changming Zheng Chenglin Zhang Runlin Z. Ma |
| author_facet | Chaokun Li Longxin Chen Xuefeng Liu Xiaoqian Shi Yu Guo Rui Huang Fangyuan Nie Changming Zheng Chenglin Zhang Runlin Z. Ma |
| author_sort | Chaokun Li |
| collection | DOAJ |
| description | Abstract Background The 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. Results The 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. Conclusions We 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. |
| first_indexed | 2024-12-13T06:55:43Z |
| format | Article |
| id | doaj.art-1c9ddc5d48c841bba69de1ae5e03325a |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-13T06:55:43Z |
| publishDate | 2019-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-1c9ddc5d48c841bba69de1ae5e03325a2022-12-21T23:56:02ZengBMCBMC Genomics1471-21642019-06-0120111210.1186/s12864-019-5790-2A high-density BAC physical map covering the entire MHC region of addax antelope genomeChaokun Li0Longxin Chen1Xuefeng Liu2Xiaoqian Shi3Yu Guo4Rui Huang5Fangyuan Nie6Changming Zheng7Chenglin Zhang8Runlin Z. Ma9State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesZhengzhou Key Laboratory of Molecular Biology, Zhengzhou Normal UniversityBeijing Key Laboratory of Captive Wildlife Technologies, Beijing ZooState Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesState Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesState Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesState Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing Key Laboratory of Captive Wildlife Technologies, Beijing ZooBeijing Key Laboratory of Captive Wildlife Technologies, Beijing ZooState Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesAbstract Background The 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. Results The 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. Conclusions We 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.http://link.springer.com/article/10.1186/s12864-019-5790-2MHCAddax nasomaculatusBACPhysical map |
| spellingShingle | Chaokun Li Longxin Chen Xuefeng Liu Xiaoqian Shi Yu Guo Rui Huang Fangyuan Nie Changming Zheng Chenglin Zhang Runlin Z. Ma A high-density BAC physical map covering the entire MHC region of addax antelope genome BMC Genomics MHC Addax nasomaculatus BAC Physical map |
| title | A high-density BAC physical map covering the entire MHC region of addax antelope genome |
| title_full | A high-density BAC physical map covering the entire MHC region of addax antelope genome |
| title_fullStr | A high-density BAC physical map covering the entire MHC region of addax antelope genome |
| title_full_unstemmed | A high-density BAC physical map covering the entire MHC region of addax antelope genome |
| title_short | A high-density BAC physical map covering the entire MHC region of addax antelope genome |
| title_sort | high density bac physical map covering the entire mhc region of addax antelope genome |
| topic | MHC Addax nasomaculatus BAC Physical map |
| url | http://link.springer.com/article/10.1186/s12864-019-5790-2 |
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