Positive selection in the SLC11A1 gene in the family Equidae

J 2016

Positive selection in the SLC11A1 gene in the family Equidae

BAYEROVÁ, Zuzana; Eva JÁNOVÁ; Ján MATIAŠOVIC; Ludovic ORLANDO; Petr HOŘÍN et al.

Základní údaje

Originální název

Positive selection in the SLC11A1 gene in the family Equidae

Autoři

BAYEROVÁ, Zuzana; Eva JÁNOVÁ; Ján MATIAŠOVIC; Ludovic ORLANDO a Petr HOŘÍN

Vydání

Immunogenetics, Springer, 2016, 0093-7711

Další údaje

Typ výsledku

Článek v odborném periodiku

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 2.092

Označené pro přenos do RIV

DOI

https://doi.org/10.1007/s00251-016-0905-2

Klíčová slova anglicky

SLC11A1 gene; NRAMP1 gene; Polymorphism; Equidae; horse; natural-resistance

Změněno: 31. 8. 2016 16:15, Mgr. Zuzana Strnadová

Anotace

V originále

Immunity-related genes are a suitable model for studying effects of selection at the genomic level. Some of them are highly conserved due to functional constraints and purifying selection, while others are variable and change quickly to cope with the variation of pathogens. The SLC11A1 gene encodes a transporter protein mediating antimicrobial activity of macrophages. Little is known about the patterns of selection shaping this gene during evolution. Although it is a typical evolutionarily conserved gene, functionally important polymorphisms associated with various diseases were identified in humans and other species. We analyzed the genomic organization, genetic variation, and evolution of the SLC11A1 gene in the family Equidae to identify patterns of selection within this important gene. Nucleotide SLC11A1 sequences were shown to be highly conserved in ten equid species, with more than 97 % sequence identity across the family. Single nucleotide polymorphisms (SNPs) were found in the coding and noncoding regions of the gene. Seven codon sites were identified to be under strong purifying selection. Codons located in three regions, including the glycosylated extracellular loop, were shown to be under diversifying selection. A 3-bp indel resulting in a deletion of the amino acid 321 in the predicted protein was observed in all horses, while it has been maintained in all other equid species. This codon comprised in an N-glycosylation site was found to be under positive selection. Interspecific variation in the presence of predicted N-glycosylation sites was observed.

Citovat

BAYEROVÁ, Zuzana; Eva JÁNOVÁ; Ján MATIAŠOVIC; Ludovic ORLANDO a Petr HOŘÍN. Positive selection in the SLC11A1 gene in the family Equidae. Immunogenetics. Springer, 2016, roč. 68, č. 5, s. 353–364, 11 s. ISSN 0093-7711. Dostupné z: https://doi.org/10.1007/s00251-016-0905-2.

@article{1352789,
   author = {Bayerová, Zuzana and Jánová, Eva and Matiašovic, Ján and Orlando, Ludovic and Hořín, Petr},
   article_number = {5},
   doi = {https://doi.org/10.1007/s00251-016-0905-2},
   keywords = {SLC11A1 gene; NRAMP1 gene; Polymorphism; Equidae; horse; natural-resistance},
   issn = {0093-7711},
   journal = {Immunogenetics},
   title = {Positive selection in the SLC11A1 gene in the family Equidae},
   url = {http://link.springer.com/article/10.1007%2Fs00251-016-0905-2},
   volume = {68},
   year = {2016}
}

TY  - JOUR
ID  - 1352789
AU  - Bayerová, Zuzana - Jánová, Eva - Matiašovic, Ján - Orlando, Ludovic - Hořín, Petr
PY  - 2016
TI  - Positive selection in the SLC11A1 gene in the family Equidae
JF  - Immunogenetics
VL  - 68
IS  - 5
SP  - 353–364
EP  - 353–364
PB  - Springer
SN  - 00937711
KW  - SLC11A1 gene
KW  - NRAMP1 gene
KW  - Polymorphism
KW  - Equidae
KW  - horse
KW  - natural-resistance
UR  - http://link.springer.com/article/10.1007%2Fs00251-016-0905-2
L2  - http://link.springer.com/article/10.1007%2Fs00251-016-0905-2
N2  - Immunity-related genes are a suitable model for studying effects of selection at the genomic level. Some of them are highly conserved due to functional constraints and purifying selection, while others are variable and change quickly to cope with the variation of pathogens. The SLC11A1 gene encodes a transporter protein mediating antimicrobial activity of macrophages. Little is known about the patterns of selection shaping this gene during evolution. Although it is a typical evolutionarily conserved gene, functionally important polymorphisms associated with various diseases were identified in humans and other species. We analyzed the genomic organization, genetic variation, and evolution of the SLC11A1 gene in the family Equidae to identify patterns of selection within this important gene. Nucleotide SLC11A1 sequences were shown to be highly conserved in ten equid species, with more than 97 % sequence identity across the family. Single nucleotide polymorphisms (SNPs) were found in the coding and noncoding regions of the gene. Seven codon sites were identified to be under strong purifying selection. Codons located in three regions, including the glycosylated extracellular loop, were shown to be under diversifying selection. A 3-bp indel resulting in a deletion of the amino acid 321 in the predicted protein was observed in all horses, while it has been maintained in all other equid species. This codon comprised in an N-glycosylation site was found to be under positive selection. Interspecific variation in the presence of predicted N-glycosylation sites was observed.
ER  -

BAYEROVÁ, Zuzana; Eva JÁNOVÁ; Ján MATIAŠOVIC; Ludovic ORLANDO a Petr HOŘÍN. Positive selection in the SLC11A1 gene in the family Equidae. \textit{Immunogenetics}. Springer, 2016, roč.~68, č.~5, s.~353–364, 11 s. ISSN~0093-7711. Dostupné z: https://doi.org/10.1007/s00251-016-0905-2.

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