Twelve toll-like receptor (TLR) genes in the family Equidae – comparative genomics, selection and evolution.
Abstract: Toll-like receptors (TLRs) represent an important part of the innate immune system. While human and murine TLRs have been intensively studied, little is known about TLRs in non-model species. The order Perissodactyla comprises a variety of free-living and domesticated species exposed to different pathogens in different habitats and is therefore suitable for analyzing the diversity and evolution of immunity-related genes. We analyzed TLR genes in the order Perissodactyla with a focus on the family Equidae. Twelve TLRs were identified by bioinformatic analyses of online genomic resources; their sequences were confirmed in equids by genomic DNA re-sequencing of a panel of nine species. The expression of TLR11 and TLR12 was confirmed in the domestic horse by cDNA sequencing. Phylogenetic reconstruction of the TLR gene family in Perissodactyla identified six sub-families. TLR4 clustered together with TLR5; the TLR1-6-10 subfamily showed a high degree of sequence identity. The average estimated evolutionary divergence of all twelve TLRs studied was 0.3% among the Equidae; the most divergent CDS were those of Equus caballus and Equus hemionus kulan (1.34%) in the TLR3, and Equus africanus somaliensis and Equus quagga antiquorum (2.1%) in the TLR1 protein. In each TLR gene, there were haplotypes shared between equid species, most extensively in TLR3 and TLR9 CDS, and TLR6 amino acid sequence. All twelve TLR genes were under strong negative overall selection. Signatures of diversifying selection in specific codon sites were detected in all TLRs except TLR8. Differences in the selection patterns between virus-sensing and non-viral TLRs were observed.
© 2023. The Author(s).
Publication Date: 2023-10-24 PubMed ID: 37874499PubMed Central: 3552114DOI: 10.1007/s11259-023-10245-4Google Scholar: Lookup
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- Journal Article
Summary
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The research article focuses on studying the toll-like receptor (TLR) genes in the Equidae family, a group of mammals that includes horses and zebras, to understand their role in immunity and their evolution. The findings show that all TLR genes observed were under strong negative selection, with varying selection patterns recorded between virus-sensing and non-viral TLRs.
Objective of the Research
- This study aimed to explore the TLR genes in the order of Perissodactyla, particularly in the family of Equidae, which has direct relevance to their immunity system. This family of mammals includes horses and zebras, and they may often be exposed to varying pathogens in different environmental interactions. Therefore, studying their immunity-related genes opens enlightening ways in understanding diversity and evolutionary lines.
Methodology
- The research utilized bioinformatics to identify TLRs from online genomic resources and re-sequenced genomic DNA from nine different species to confirm these sequences.
- Expression of TLR11 and TLR12 was confirmed in domestic horses through sequencing.
- The team then carried out phylogenetic reconstruction of the TLR gene family in the organisms they were studying.
Findings
- A total of 12 TLRs were identified.
- Six sub-families were discovered in the TLR gene family in Perissodactyla.
- There was a high degree of sequence identity observed in the TLR1-6-10 subfamily.
- The most divergent CDS (coding sequences) were those of Equus caballus and Equus hemionus kulan with a divergence of 1.34% in the TLR3.
- Across all TLRs observed, there were instances of haplotypes shared between the different Equidae species.
Conclusion
- The researchers found that all twelve TLR genes were under strong negative overall selection, meaning that those gene variants that decreased the fitness of the organisms were eliminated by natural selection over time.
- The selection patterns differed between virus-sensing and non-viral TLRs, pointing towards possible different evolutionary trajectories and functions.
Cite This Article
APA
Stejskalova K, Janova E, Splichalova P, Futas J, Oppelt J, Vodicka R, Horin P.
(2023).
Twelve toll-like receptor (TLR) genes in the family Equidae – comparative genomics, selection and evolution.
Vet Res Commun.
https://doi.org/10.1007/s11259-023-10245-4 Publication
Researcher Affiliations
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, 61242, Czech Republic.
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, 61242, Czech Republic.
- RG Animal Immunogenomics, CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czech Republic.
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, 61242, Czech Republic.
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, 61242, Czech Republic.
- RG Animal Immunogenomics, CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czech Republic.
- RG Animal Immunogenomics, CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czech Republic.
- Zoo Prague, Prague, Czech Republic.
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, 61242, Czech Republic. horin@ics.muni.cz.
- RG Animal Immunogenomics, CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czech Republic. horin@ics.muni.cz.
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