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A physical map of a BAC clone contig covering the entire autosome insertion between ovine MHC Class IIa and IIb.

Li G, Liu K, Jiao S, Liu H, Blair HT, Zhang P, Cui X, Tan P, Gao J, Ma RZ - BMC Genomics (2012)

Bottom Line: A total of 368 positive BAC clones were identified and 108 of the effective clones were ordered into an overlapping BAC contig to cover the consensus region between ovine MHC class IIa and IIb.The map confirmed the bovine sequence assembly for the same homologous region.The entire ovine MHC region is now fully covered by a continuous BAC clone contig.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Life Sciences, Shihezi University, Xinjiang 832003, China.

ABSTRACT

Background: The ovine Major Histocompatibility Complex (MHC) harbors genes involved in overall resistance/susceptibility of the host to infectious diseases. Compared to human and mouse, the ovine MHC is interrupted by a large piece of autosome insertion via a hypothetical chromosome inversion that constitutes ~25% of ovine chromosome 20. The evolutionary consequence of such an inversion and an insertion (inversion/insertion) in relation to MHC function remains unknown. We previously constructed a BAC clone physical map for the ovine MHC exclusive of the insertion region. Here we report the construction of a high-density physical map covering the autosome insertion in order to address the question of what the inversion/insertion had to do with ruminants during the MHC evolution.

Results: A total of 119 pairs of comparative bovine oligo primers were utilized to screen an ovine BAC library for positive clones and the orders and overlapping relationships of the identified clones were determined by DNA fingerprinting, BAC-end sequencing, and sequence-specific PCR. A total of 368 positive BAC clones were identified and 108 of the effective clones were ordered into an overlapping BAC contig to cover the consensus region between ovine MHC class IIa and IIb. Therefore, a continuous physical map covering the entire ovine autosome inversion/insertion region was successfully constructed. The map confirmed the bovine sequence assembly for the same homologous region. The DNA sequences of 185 BAC-ends have been deposited into NCBI database with the access numbers HR309252 through HR309068, corresponding to dbGSS ID 30164010 through 30163826.

Conclusions: We have constructed a high-density BAC clone physical map for the ovine autosome inversion/insertion between the MHC class IIa and IIb. The entire ovine MHC region is now fully covered by a continuous BAC clone contig. The physical map we generated will facilitate MHC functional studies in the ovine, as well as the comparative MHC evolution in ruminants.

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Schematic presentation of MHC structures among representative mammal species. Bovine and ovine MHC is interrupted by a long piece of non-MHC insertion that divided class II into IIa and IIb subregions. The red, blue, and green color stands for MHC Class I, Class III, and Class II, respectively. The grey color gradient represents the extended Class II region. The order of loci in the extended Class II region of bovine and ovine is in an opposite orientation compared to that of human, chimpanzees, and mouse. Dash line marks the break point of a hypothetical chromosome inversion. Dashed circles indicate the hypothetical chromosome looping and the subsequent crossover occurred during the evolution of ruminants. The drawing is not to the scale.
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Figure 5: Schematic presentation of MHC structures among representative mammal species. Bovine and ovine MHC is interrupted by a long piece of non-MHC insertion that divided class II into IIa and IIb subregions. The red, blue, and green color stands for MHC Class I, Class III, and Class II, respectively. The grey color gradient represents the extended Class II region. The order of loci in the extended Class II region of bovine and ovine is in an opposite orientation compared to that of human, chimpanzees, and mouse. Dash line marks the break point of a hypothetical chromosome inversion. Dashed circles indicate the hypothetical chromosome looping and the subsequent crossover occurred during the evolution of ruminants. The drawing is not to the scale.

Mentions: Using the comparative approaches, we successfully constructed a 14 Mb BAC clone contig map for a region in ovine chromosome 20 that harbors the MHC. Comparison between the identified ovine BAC contig and the orthologous bovine genomic region showed that the two species share essentially the same genomic structure and organization for the entire inversion/insertion between MHC class IIa and IIb (Figure5). For the available genetic loci generated via the SP-PCR and BAC-end sequencing, our results essentially confirmed the sheep genome sequence assembly presented by ISGC in the MHC region [33].


A physical map of a BAC clone contig covering the entire autosome insertion between ovine MHC Class IIa and IIb.

Li G, Liu K, Jiao S, Liu H, Blair HT, Zhang P, Cui X, Tan P, Gao J, Ma RZ - BMC Genomics (2012)

Schematic presentation of MHC structures among representative mammal species. Bovine and ovine MHC is interrupted by a long piece of non-MHC insertion that divided class II into IIa and IIb subregions. The red, blue, and green color stands for MHC Class I, Class III, and Class II, respectively. The grey color gradient represents the extended Class II region. The order of loci in the extended Class II region of bovine and ovine is in an opposite orientation compared to that of human, chimpanzees, and mouse. Dash line marks the break point of a hypothetical chromosome inversion. Dashed circles indicate the hypothetical chromosome looping and the subsequent crossover occurred during the evolution of ruminants. The drawing is not to the scale.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3475007&req=5

Figure 5: Schematic presentation of MHC structures among representative mammal species. Bovine and ovine MHC is interrupted by a long piece of non-MHC insertion that divided class II into IIa and IIb subregions. The red, blue, and green color stands for MHC Class I, Class III, and Class II, respectively. The grey color gradient represents the extended Class II region. The order of loci in the extended Class II region of bovine and ovine is in an opposite orientation compared to that of human, chimpanzees, and mouse. Dash line marks the break point of a hypothetical chromosome inversion. Dashed circles indicate the hypothetical chromosome looping and the subsequent crossover occurred during the evolution of ruminants. The drawing is not to the scale.
Mentions: Using the comparative approaches, we successfully constructed a 14 Mb BAC clone contig map for a region in ovine chromosome 20 that harbors the MHC. Comparison between the identified ovine BAC contig and the orthologous bovine genomic region showed that the two species share essentially the same genomic structure and organization for the entire inversion/insertion between MHC class IIa and IIb (Figure5). For the available genetic loci generated via the SP-PCR and BAC-end sequencing, our results essentially confirmed the sheep genome sequence assembly presented by ISGC in the MHC region [33].

Bottom Line: A total of 368 positive BAC clones were identified and 108 of the effective clones were ordered into an overlapping BAC contig to cover the consensus region between ovine MHC class IIa and IIb.The map confirmed the bovine sequence assembly for the same homologous region.The entire ovine MHC region is now fully covered by a continuous BAC clone contig.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Life Sciences, Shihezi University, Xinjiang 832003, China.

ABSTRACT

Background: The ovine Major Histocompatibility Complex (MHC) harbors genes involved in overall resistance/susceptibility of the host to infectious diseases. Compared to human and mouse, the ovine MHC is interrupted by a large piece of autosome insertion via a hypothetical chromosome inversion that constitutes ~25% of ovine chromosome 20. The evolutionary consequence of such an inversion and an insertion (inversion/insertion) in relation to MHC function remains unknown. We previously constructed a BAC clone physical map for the ovine MHC exclusive of the insertion region. Here we report the construction of a high-density physical map covering the autosome insertion in order to address the question of what the inversion/insertion had to do with ruminants during the MHC evolution.

Results: A total of 119 pairs of comparative bovine oligo primers were utilized to screen an ovine BAC library for positive clones and the orders and overlapping relationships of the identified clones were determined by DNA fingerprinting, BAC-end sequencing, and sequence-specific PCR. A total of 368 positive BAC clones were identified and 108 of the effective clones were ordered into an overlapping BAC contig to cover the consensus region between ovine MHC class IIa and IIb. Therefore, a continuous physical map covering the entire ovine autosome inversion/insertion region was successfully constructed. The map confirmed the bovine sequence assembly for the same homologous region. The DNA sequences of 185 BAC-ends have been deposited into NCBI database with the access numbers HR309252 through HR309068, corresponding to dbGSS ID 30164010 through 30163826.

Conclusions: We have constructed a high-density BAC clone physical map for the ovine autosome inversion/insertion between the MHC class IIa and IIb. The entire ovine MHC region is now fully covered by a continuous BAC clone contig. The physical map we generated will facilitate MHC functional studies in the ovine, as well as the comparative MHC evolution in ruminants.

Show MeSH
Related in: MedlinePlus