Genetic diversity, evolution and selection in the major histocompatibility complex DRB and DQB loci in the family Equidae
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Genetic diversity, evolution and selection in the major histocompatibility complex DRB and DQB loci in the family Equidae. / Klumplerova, Marie; Splichalova, Petra; Oppelt, Jan; Futas, Jan; Kohutova, Aneta; Musilova, Petra; Kubickova, Svatava; Vodicka, Roman; Orlando, Ludovic; Horin, Petr.
In: BMC Genomics, Vol. 21, 677, 2020.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Genetic diversity, evolution and selection in the major histocompatibility complex DRB and DQB loci in the family Equidae
AU - Klumplerova, Marie
AU - Splichalova, Petra
AU - Oppelt, Jan
AU - Futas, Jan
AU - Kohutova, Aneta
AU - Musilova, Petra
AU - Kubickova, Svatava
AU - Vodicka, Roman
AU - Orlando, Ludovic
AU - Horin, Petr
PY - 2020
Y1 - 2020
N2 - Background: The mammalian Major Histocompatibility Complex (MHC) is a genetic region containing highly polymorphic genes with immunological functions. MHC class I and class II genes encode antigen-presenting molecules expressed on the cell surface. The MHC class II sub-region contains genes expressed in antigen presenting cells. The antigen binding site is encoded by the second exon of genes encoding antigen presenting molecules. The exon 2 sequences of these MHC genes have evolved under the selective pressure of pathogens. Interspecific differences can be observed in the class II sub-region. The family Equidae includes a variety of domesticated, and free-ranging species inhabiting a range of habitats exposed to different pathogens and represents a model for studying this important part of the immunogenome. While equine MHC class II DRA and DQA loci have received attention, the genetic diversity and effects of selection on DRB and DQB loci have been largely overlooked. This study aimed to provide the first in-depth analysis of the MHC class II DRB and DQB loci in the Equidae family. Results: Three DRB and two DQB genes were identified in the genomes of all equids. The genes DRB2, DRB3 and DQB3 showed high sequence conservation, while polymorphisms were more frequent at DRB1 and DQB1 across all species analyzed. DQB2 was not found in the genome of the Asiatic asses Equus hemionus kulan and E. h. onager. The bioinformatic analysis of non-zero-coverage-bases of DRB and DQB genes in 14 equine individual genomes revealed differences among individual genes. Evidence for recombination was found for DRB1, DRB2, DQB1 and DQB2 genes. Trans-species allele sharing was identified in all genes except DRB1. Site-specific selection analysis predicted genes evolving under positive selection both at DRB and DQB loci. No selected amino acid sites were identified in DQB3. Conclusions: The organization of the MHC class II sub-region of equids is similar across all species of the family. Genomic sequences, along with phylogenetic trees suggesting effects of selection as well as trans-species polymorphism support the contention that pathogen-driven positive selection has shaped the MHC class II DRB/DQB sub-regions in the Equidae.
AB - Background: The mammalian Major Histocompatibility Complex (MHC) is a genetic region containing highly polymorphic genes with immunological functions. MHC class I and class II genes encode antigen-presenting molecules expressed on the cell surface. The MHC class II sub-region contains genes expressed in antigen presenting cells. The antigen binding site is encoded by the second exon of genes encoding antigen presenting molecules. The exon 2 sequences of these MHC genes have evolved under the selective pressure of pathogens. Interspecific differences can be observed in the class II sub-region. The family Equidae includes a variety of domesticated, and free-ranging species inhabiting a range of habitats exposed to different pathogens and represents a model for studying this important part of the immunogenome. While equine MHC class II DRA and DQA loci have received attention, the genetic diversity and effects of selection on DRB and DQB loci have been largely overlooked. This study aimed to provide the first in-depth analysis of the MHC class II DRB and DQB loci in the Equidae family. Results: Three DRB and two DQB genes were identified in the genomes of all equids. The genes DRB2, DRB3 and DQB3 showed high sequence conservation, while polymorphisms were more frequent at DRB1 and DQB1 across all species analyzed. DQB2 was not found in the genome of the Asiatic asses Equus hemionus kulan and E. h. onager. The bioinformatic analysis of non-zero-coverage-bases of DRB and DQB genes in 14 equine individual genomes revealed differences among individual genes. Evidence for recombination was found for DRB1, DRB2, DQB1 and DQB2 genes. Trans-species allele sharing was identified in all genes except DRB1. Site-specific selection analysis predicted genes evolving under positive selection both at DRB and DQB loci. No selected amino acid sites were identified in DQB3. Conclusions: The organization of the MHC class II sub-region of equids is similar across all species of the family. Genomic sequences, along with phylogenetic trees suggesting effects of selection as well as trans-species polymorphism support the contention that pathogen-driven positive selection has shaped the MHC class II DRB/DQB sub-regions in the Equidae.
KW - Family Equidae
KW - Major histocompatibility complex
KW - MHC class II loci
KW - MHC exon 2
KW - Positive selection
KW - Selected amino acid sites
KW - Trans-species polymorphism
U2 - 10.1186/s12864-020-07089-6
DO - 10.1186/s12864-020-07089-6
M3 - Journal article
C2 - 32998693
AN - SCOPUS:85092323411
VL - 21
JO - BMC Genomics
JF - BMC Genomics
SN - 1471-2164
M1 - 677
ER -
ID: 274175842