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Home / Equine Research Bank / Sci Rep / Genomic structure of the horse major histocompatibility comp...
Scientific reports2017; 7; 45518; doi: 10.1038/srep45518

Genomic structure of the horse major histocompatibility complex class II region resolved using PacBio long-read sequencing technology.

Abstract: The mammalian Major Histocompatibility Complex (MHC) region contains several gene families characterized by highly polymorphic loci with extensive nucleotide diversity, copy number variation of paralogous genes, and long repetitive sequences. This structural complexity has made it difficult to construct a reliable reference sequence of the horse MHC region. In this study, we used long-read single molecule, real-time (SMRT) sequencing technology from Pacific Biosciences (PacBio) to sequence eight Bacterial Artificial Chromosome (BAC) clones spanning the horse MHC class II region. The final assembly resulted in a 1,165,328 bp continuous gap free sequence with 35 manually curated genomic loci of which 23 were considered to be functional and 12 to be pseudogenes. In comparison to the MHC class II region in other mammals, the corresponding region in horse shows extraordinary copy number variation and different relative location and directionality of the Eqca-DRB, -DQA, -DQB and -DOB loci. This is the first long-read sequence assembly of the horse MHC class II region with rigorous manual gene annotation, and it will serve as an important resource for association studies of immune-mediated equine diseases and for evolutionary analysis of genetic diversity in this region.
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Publication Date: 2017-03-31 PubMed ID: 28361880PubMed Central: PMC5374520DOI: 10.1038/srep45518Google Scholar: Lookup
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  • Journal Article
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  • Non-U.S. Gov't

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research, using advanced sequencing technology, successfully detailed the structure of a complex horse gene region, known as the Major Histocompatibility Complex class II, which was previously challenging due to its variability and complexity. The findings of this study will be beneficial for further studies related to immune-mediated horse diseases and genetic diversity.

Objective of the Study

  • The research aimed to construct a reliable genomic reference sequence for the complicated Major Histocompatibility Complex (MHC) class II region in the horse genome – a task that had remained primarily unaccomplished due to the region’s high polymorphism, variations in the number of similar genes, and long repetitive sequences.

Methodology

  • The scientists employed long-read single molecule, real-time (SMRT) sequencing technology from Pacific Biosciences (PacBio), known for efficiently sequencing large and complex gene regions.
  • They sequenced eight Bacterial Artificial Chromosome (BAC) clones spanning the horse MHC class II region, allowing them to cover the full stretch of this difficult genomic region.

Results

  • The final assembled sequence was a continuous, gap-free span of 1,165,328 base pairs, which included 35 genomic loci (locations of genes).
  • These included 23 functional genomic loci and 12 pseudogenes (genes that no longer function due to mutations).
  • Compared to the MHC class II region in other mammals, the horse’s region presented unique attributes such as extraordinary copy number variation and different locations and directionality of specific loci (Eqca-DRB, -DQA, -DQB, and -DOB).

Significance of the Study

  • This research produced the first long-read sequence assembly of the horse MHC class II region with meticulous manual gene annotation.
  • The findings provide an essential resource for future studies focusing on immune-mediated diseases in horses and for exploring genetic diversity within this specific region.

Cite This Article

APA
Viļuma A, Mikko S, Hahn D, Skow L, Andersson G, Bergström TF. (2017). Genomic structure of the horse major histocompatibility complex class II region resolved using PacBio long-read sequencing technology. Sci Rep, 7, 45518. https://doi.org/10.1038/srep45518

Publication

Scientific reports
ISSN: 2045-2322
NlmUniqueID: 101563288
Country: England
Language: English
Volume: 7
Pages: 45518
PII: 45518

Researcher Affiliations

Viļuma, Agnese
  • Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences (SLU), Box 7023, 750 07 Uppsala, Sweden.
Mikko, Sofia
  • Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences (SLU), Box 7023, 750 07 Uppsala, Sweden.
Hahn, Daniela
  • Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences (SLU), Box 7023, 750 07 Uppsala, Sweden.
Skow, Loren
  • Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843, USA.
Andersson, Göran
  • Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences (SLU), Box 7023, 750 07 Uppsala, Sweden.
Bergström, Tomas F
  • Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences (SLU), Box 7023, 750 07 Uppsala, Sweden.

MeSH Terms

  • Animals
  • Chromosomes, Artificial, Bacterial
  • Cloning, Molecular
  • Gene Dosage
  • Gene Order
  • Genetic Variation
  • Histocompatibility Antigens Class II / genetics
  • Horses
  • Sequence Analysis, DNA / methods

Conflict of Interest Statement

The authors declare no competing financial interests.

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