Genetic diversity, evolution and selection in the major
histocompatibility complex DRB and DQB loci in the family
Equidae

J 2020

Genetic diversity, evolution and selection in the major histocompatibility complex DRB and DQB loci in the family Equidae

KLUMPLEROVA, Marie, Petra SPLICHALOVA, Jan OPPELT, Jan FUTAS, Aneta KOHUTOVÁ et. al.

Základní údaje

Originální název

Genetic diversity, evolution and selection in the major histocompatibility complex DRB and DQB loci in the family Equidae

Autoři

KLUMPLEROVA, Marie (203 Česká republika), Petra SPLICHALOVA (203 Česká republika), Jan OPPELT (203 Česká republika, domácí), Jan FUTAS (203 Česká republika), Aneta KOHUTOVÁ (703 Slovensko, domácí), Petra MUSILOVA (203 Česká republika), Svatava KUBICKOVA (203 Česká republika), Roman VODICKA (203 Česká republika), Ludovic ORLANDO a Petr HORIN (203 Česká republika)

Vydání

BMC Genomics, LONDON, BioMed Central, 2020, 1471-2164

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10603 Genetics and heredity

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 3.969

Kód RIV

RIV/00216224:14110/20:00118279

Organizační jednotka

Lékařská fakulta

DOI

http://dx.doi.org/10.1186/s12864-020-07089-6

UT WoS

000576982800002

Klíčová slova anglicky

Major histocompatibility complex; Family Equidae; MHC exon 2; MHC class II loci; Positive selection; Trans-species polymorphism; Selected amino acid sites

Štítky

14110513, podil, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 17. 3. 2021 14:05, Mgr. Tereza Miškechová

Anotace

V originále

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 ORB1 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 ORB1. 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.

Návaznosti

ED1.1.00/02.0068, projekt VaV

Název: CEITEC - central european institute of technology

LQ1601, projekt VaV

Název: CEITEC 2020 (Akronym: CEITEC2020)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CEITEC 2020

Citovat

KLUMPLEROVA, Marie, Petra SPLICHALOVA, Jan OPPELT, Jan FUTAS, Aneta KOHUTOVÁ, Petra MUSILOVA, Svatava KUBICKOVA, Roman VODICKA, Ludovic ORLANDO a Petr HORIN. Genetic diversity, evolution and selection in the major histocompatibility complex DRB and DQB loci in the family Equidae. BMC Genomics. LONDON: BioMed Central, 2020, roč. 21, č. 1, s. 1-15. ISSN 1471-2164. Dostupné z: https://dx.doi.org/10.1186/s12864-020-07089-6.

@article{1746833,
   author = {Klumplerova, Marie and Splichalova, Petra and Oppelt, Jan and Futas, Jan and Kohutová, Aneta and Musilova, Petra and Kubickova, Svatava and Vodicka, Roman and Orlando, Ludovic and Horin, Petr},
   article_location = {LONDON},
   article_number = {1},
   doi = {http://dx.doi.org/10.1186/s12864-020-07089-6},
   keywords = {Major histocompatibility complex; Family Equidae; MHC exon 2; MHC class II loci; Positive selection; Trans-species polymorphism; Selected amino acid sites},
   language = {eng},
   issn = {1471-2164},
   journal = {BMC Genomics},
   title = {Genetic diversity, evolution and selection in the major histocompatibility complex DRB and DQB loci in the family Equidae},
   url = {https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/s12864-020-07089-6.pdf},
   volume = {21},
   year = {2020}
}

TY  - JOUR
ID  - 1746833
AU  - Klumplerova, Marie - Splichalova, Petra - Oppelt, Jan - Futas, Jan - Kohutová, Aneta - Musilova, Petra - Kubickova, Svatava - Vodicka, Roman - Orlando, Ludovic - Horin, Petr
PY  - 2020
TI  - Genetic diversity, evolution and selection in the major histocompatibility complex DRB and DQB loci in the family Equidae
JF  - BMC Genomics
VL  - 21
IS  - 1
SP  - 1-15
EP  - 1-15
PB  - BioMed Central
SN  - 14712164
KW  - Major histocompatibility complex
KW  - Family Equidae
KW  - MHC exon 2
KW  - MHC class II loci
KW  - Positive selection
KW  - Trans-species polymorphism
KW  - Selected amino acid sites
UR  - https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/s12864-020-07089-6.pdf
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 ORB1 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 ORB1. 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.
ER  -

KLUMPLEROVA, Marie, Petra SPLICHALOVA, Jan OPPELT, Jan FUTAS, Aneta KOHUTOVÁ, Petra MUSILOVA, Svatava KUBICKOVA, Roman VODICKA, Ludovic ORLANDO a Petr HORIN. Genetic diversity, evolution and selection in the major histocompatibility complex DRB and DQB loci in the family Equidae. \textit{BMC Genomics}. LONDON: BioMed Central, 2020, roč.~21, č.~1, s.~1-15. ISSN~1471-2164. Dostupné z: https://dx.doi.org/10.1186/s12864-020-07089-6.

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