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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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Related in: MedlinePlus

A 14 Mb BAC clone physical map covering the entire region between ovine MHC Class IIa and IIb. The order and orientation of BAC clones (overlapping horizontal bars with clone ID name listed above) were determined by combinations of DNA fingerprinting, BAC-end sequencing, and sequence-specific-PCR. Target gene identified by BAC-end sequencing is marked with a vertical bar along the horizontal line, with locus name listed above. The continuous BAC map is represented by three panels with the overlapping regions marked with the same colored shadows at the both ends.
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Figure 4: A 14 Mb BAC clone physical map covering the entire region between ovine MHC Class IIa and IIb. The order and orientation of BAC clones (overlapping horizontal bars with clone ID name listed above) were determined by combinations of DNA fingerprinting, BAC-end sequencing, and sequence-specific-PCR. Target gene identified by BAC-end sequencing is marked with a vertical bar along the horizontal line, with locus name listed above. The continuous BAC map is represented by three panels with the overlapping regions marked with the same colored shadows at the both ends.

Mentions: A complete physical map of a BAC clone contig for the ovine MHC region between class IIa and IIb was successfully assembled (Figure4), based on the integrated results of DNA fingerprinting, BAC-end sequencing, and confirmation PCR of the BAC ends. The fully assembled physical map was composed of 108 effective ovine BAC clones organized into a continuous contig that covered the entire region between ovine MHC class IIa and IIb (Figure4). Based on the results of DNA fingerprinting, no gaps exist in the constructed BAC clone physical map which spans approximately 14 Mb genome region of ovine chromosome 20, indicating the even distribution of BAC clones in the library we previously constructed.


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)

A 14 Mb BAC clone physical map covering the entire region between ovine MHC Class IIa and IIb. The order and orientation of BAC clones (overlapping horizontal bars with clone ID name listed above) were determined by combinations of DNA fingerprinting, BAC-end sequencing, and sequence-specific-PCR. Target gene identified by BAC-end sequencing is marked with a vertical bar along the horizontal line, with locus name listed above. The continuous BAC map is represented by three panels with the overlapping regions marked with the same colored shadows at the both ends.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: A 14 Mb BAC clone physical map covering the entire region between ovine MHC Class IIa and IIb. The order and orientation of BAC clones (overlapping horizontal bars with clone ID name listed above) were determined by combinations of DNA fingerprinting, BAC-end sequencing, and sequence-specific-PCR. Target gene identified by BAC-end sequencing is marked with a vertical bar along the horizontal line, with locus name listed above. The continuous BAC map is represented by three panels with the overlapping regions marked with the same colored shadows at the both ends.
Mentions: A complete physical map of a BAC clone contig for the ovine MHC region between class IIa and IIb was successfully assembled (Figure4), based on the integrated results of DNA fingerprinting, BAC-end sequencing, and confirmation PCR of the BAC ends. The fully assembled physical map was composed of 108 effective ovine BAC clones organized into a continuous contig that covered the entire region between ovine MHC class IIa and IIb (Figure4). Based on the results of DNA fingerprinting, no gaps exist in the constructed BAC clone physical map which spans approximately 14 Mb genome region of ovine chromosome 20, indicating the even distribution of BAC clones in the library we previously constructed.

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