FREE SHIPPING over $40
OVER 10000 FIVE-STAR REVIEWS
5% OFF ALL SUBSCRIPTIONS
100% HAPPINESS GUARANTEE
Analyze Diet
0
Veterinary research communications2023; doi: 10.1007/s11259-023-10245-4

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).
Get Full Text
Publication Date: 2023-10-24 PubMed ID: 37874499PubMed Central: 3552114DOI: 10.1007/s11259-023-10245-4Google Scholar: Lookup
The Equine Research Bank provides access to a large database of publicly available scientific literature. Inclusion in the Research Bank does not imply endorsement of study methods or findings by Mad Barn.
LinkedInCopy
  • Journal Article

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 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

Veterinary research communications
ISSN: 1573-7446
NlmUniqueID: 8100520
Country: Switzerland
Language: English

Researcher Affiliations

Stejskalova, K
  • Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, 61242, Czech Republic.
Janova, E
  • 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.
Splichalova, P
  • Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, 61242, Czech Republic.
Futas, J
  • 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.
Oppelt, J
  • RG Animal Immunogenomics, CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czech Republic.
Vodicka, R
  • Zoo Prague, Prague, Czech Republic.
Horin, P
  • 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.

References

This article includes 59 references
  1. Anderson KV, Bokla L, Nüsslein-Volhard C. Establishment of dorsal-ventral polarity in the Drosophila embryo: the induction of polarity by the toll gene product. Cell 42:791–798.
    doi: 10.1016/0092-8674(85)90275-2pubmed: 3931919google scholar: lookup
  2. Andrade WA, Souza M do C, Martinez ER. Combined action of nucleic acid-sensing toll-like receptors (TLRs) and TLR11/TLR12 heterodimers imparts resistance to Toxoplasma Gondii in mice. Cell Host Microbe 13:42–53.
    doi: 10.1016/j.chom.2012.12.003pubmed: 23290966pmc: 3552114google scholar: lookup
  3. Areal H, Abrantes J, Esteves PJ. Signatures of positive selection in toll-like receptor (TLR) genes in mammals. BMC Evol Biol 11:368.
    doi: 10.1186/1471-2148-11-368pubmed: 22185391pmc: 3276489google scholar: lookup
  4. Astakhova NM, Perelygin AA, Zharkikh AA. Characterization of equine and other vertebrate TLR3, TLR7, and TLR8 genes. Immunogenetics 61:529–539.
    doi: 10.1007/s00251-009-0381-zpubmed: 19568743google scholar: lookup
  5. Azevedo L, Serrano C, Amorim A, Cooper DN. Trans-species polymorphism in humans and the great apes is generally maintained by balancing selection that modulates the host immune response. Hum Genomics 9:21.
    doi: 10.1186/s40246-015-0043-1pubmed: 26337052pmc: 4559023google scholar: lookup
  6. Bai B, Wang Y-Q, Meng J. The divergence and dispersal of early perissodactyls as evidenced by early Eocene equids from Asia. Commun Biol 1:115.
    doi: 10.1038/s42003-018-0116-5pubmed: 30271995pmc: 6123789google scholar: lookup
  7. Barreiro LB, Ben-Ali M, Quach H. Evolutionary dynamics of human toll-like receptors and their different contributions to host defense. PLoS Genet 5:e1000562.
    doi: 10.1371/journal.pgen.1000562pubmed: 19609346pmc: 2702086google scholar: lookup
  8. Bayerova Z, Janova E, Matiasovic J. Positive selection in the SLC11A1 gene in the family Equidae. Immunogenetics 68:353–364.
    doi: 10.1007/s00251-016-0905-2pubmed: 26846480google scholar: lookup
  9. Behzadi P, García-Perdomo HA, Karpiński TM. Toll-Like Receptors: General Molecular and Structural Biology. J Immunol Res 2021:9914854.
    doi: 10.1155/2021/9914854google scholar: lookup
  10. Brennan JJ, Gilmore TD. Evolutionary origins of toll-like receptor signaling. Mol Biol Evol 35:1576–1587.
    doi: 10.1093/molbev/msy050pubmed: 29590394google scholar: lookup
  11. Darfour-Oduro KA, Megens H-J, Roca AL. Evolutionary patterns of toll-like receptor signaling pathway genes in the Suidae. BMC Evol Biol 16:33.
    doi: 10.1186/s12862-016-0602-7pubmed: 26860534pmc: 4748524google scholar: lookup
  12. Downing T, Lloyd AT, O’Farrelly C, Bradley DG. The differential evolutionary dynamics of avian cytokine and TLR gene classes. J Immunol 184:6993–7000.
    doi: 10.4049/jimmunol.0903092pubmed: 20483729google scholar: lookup
  13. Dubey JP, Murata FHA, Cerqueira-Cézar CK, Kwok OCH. Toxoplasma gondii Infections in horses, donkeys, and other equids: the last decade. Res Vet Sci 132:492–499.
    doi: 10.1016/j.rvsc.2020.07.005pubmed: 32799174google scholar: lookup
  14. Dugovich BS, Crane LL, Alcantar BB. Multiple innate antibacterial immune defense elements are correlated in diverse ungulate species. PLoS ONE 14:e0225579.
    doi: 10.1371/journal.pone.0225579pubmed: 31774834pmc: 6881064google scholar: lookup
  15. Fisher CA, Bhattarai EK, Osterstock JB. Evolution of the Bovine TLR Gene Family and Member associations with Mycobacterium avium subspecies paratuberculosis Infection. PLoS ONE 6:e27744.
    doi: 10.1371/journal.pone.0027744pubmed: 22164200pmc: 3227585google scholar: lookup
  16. Fitzgerald KA, Kagan JC. Toll-like receptors and the control of immunity. Cell 180:1044–1066.
    doi: 10.1016/j.cell.2020.02.041pubmed: 32164908pmc: 9358771google scholar: lookup
  17. Futas J, Horin P. Natural killer cell receptor genes in the family Equidae: not only Ly49. PLoS ONE 8:e64736.
    doi: 10.1371/journal.pone.0064736pubmed: 23724088pmc: 3665701google scholar: lookup
  18. Gazzinelli RT, Mendonça-Neto R, Lilue J. Innate resistance against Toxoplasma Gondii: an evolutionary tale of mice, cats and men. Cell Host Microbe 15:132–138.
    doi: 10.1016/j.chom.2014.01.004pubmed: 24528860pmc: 4006104google scholar: lookup
  19. Ghosh M, Basak S, Dutta S. Natural selection shaped the evolution of amino acid usage in mammalian toll like receptor genes. Comput Biol Chem 97:107637.
    doi: 10.1016/j.compbiolchem.2022.107637pubmed: 35131622google scholar: lookup
  20. Halldórsdóttir K, Árnason E. Trans-species polymorphism at antimicrobial innate immunity cathelicidin genes of Atlantic Cod and related species. PeerJ 3:e976.
    doi: 10.7717/peerj.976pubmed: 26038731pmc: 4451034google scholar: lookup
  21. Hatai H, Lepelley A, Zeng W. Toll-like receptor 11 (TLR11) interacts with Flagellin and Profilin through disparate mechanisms. PLoS ONE 11:e0148987.
    doi: 10.1371/journal.pone.0148987pubmed: 26859749pmc: 4747465google scholar: lookup
  22. Janova E, Matiasovic J, Vahala J. Polymorphism and selection in the major histocompatibility complex DRA and DQA genes in the family Equidae. Immunogenetics 61:513–527.
    doi: 10.1007/s00251-009-0380-0pubmed: 19557406google scholar: lookup
  23. Johnson CM, Lyle EA, Omueti KO. Cutting edge: a common polymorphism impairs cell surface trafficking and functional responses of TLR1 but protects against Leprosy. J Immunol 178:7520–7524.
    doi: 10.4049/jimmunol.178.12.7520pubmed: 17548585google scholar: lookup
  24. Kawai T, Akira S. Toll-like receptors and their crosstalk with other innate receptors in Infection and immunity. Immunity 34:637–650.
    doi: 10.1016/j.immuni.2011.05.006pubmed: 21616434google scholar: lookup
  25. Kesh S, Mensah NY, Peterlongo P. TLR1 and TLR6 polymorphisms are associated with susceptibility to invasive aspergillosis after allogeneic stem cell transplantation. Ann N Y Acad Sci 1062:95–103.
    doi: 10.1196/annals.1358.012pubmed: 16461792google scholar: lookup
  26. Khan I, Maldonado E, Silva L. The Vertebrate TLR Supergene Family Evolved dynamically by gene Gain/Loss and positive selection revealing a host–Pathogen Arms race in birds. Diversity 11:131.
    doi: 10.3390/d11080131google scholar: lookup
  27. Kimble KM, Gomez G, Szule JA. Systemic toxoplasmosis in a horse. J Comp Pathol 182:27–31.
    doi: 10.1016/j.jcpa.2020.11.004pubmed: 33494904google scholar: lookup
  28. Klumplerova M, Splichalova P, Oppelt J. Genetic diversity, evolution and selection in the major histocompatibility complex DRB and DQB loci in the family Equidae. BMC Genomics 21:677.
    doi: 10.1186/s12864-020-07089-6pubmed: 32998693pmc: 7525986google scholar: lookup
  29. Koblansky AA, Jankovic D, Oh H. Recognition of Profilin by toll-like receptor 12 is critical for Host Resistance to Toxoplasma Gondii. Immunity 38:119–130.
    doi: 10.1016/j.immuni.2012.09.016pubmed: 23246311google scholar: lookup
  30. Kruithof EK, Satta N, Liu JW. Gene conversion limits divergence of mammalian TLR1 and TLR6. BMC Evol Biol 7:148.
    doi: 10.1186/1471-2148-7-148pubmed: 17727694pmc: 2077338google scholar: lookup
  31. Kumar V. Toll-like receptors in adaptive immunity. Handb Exp Pharmacol 276:95–131.
    doi: 10.1007/164_2021_543pubmed: 34510306google scholar: lookup
  32. Librado P, Orlando L. Genomics and the Evolutionary history of Equids. Annu Rev Anim Biosci 9:81–101.
    doi: 10.1146/annurev-animal-061220-023118pubmed: 33197207google scholar: lookup
  33. Liu G, Zhang H, Sun G. Characterization of the peripheral blood transcriptome and adaptive evolution of the MHC I and TLR gene families in the wolf (Canis lupus). BMC Genomics 18:584.
    doi: 10.1186/s12864-017-3983-0pubmed: 28784091pmc: 5545864google scholar: lookup
  34. Liu G, Zhang H, Zhao C, Zhang H. Evolutionary history of the toll-like receptor gene family across vertebrates. Genome Biol Evol 12:3615–3634.
    doi: 10.1093/gbe/evz266pubmed: 31800025google scholar: lookup
  35. Ma X, Liu Y, Gowen BB. Full-exon resequencing reveals toll-like receptor variants contribute to human susceptibility to Tuberculosis Disease. PLoS ONE 2:e1318.
    doi: 10.1371/journal.pone.0001318pubmed: 18091991pmc: 2117342google scholar: lookup
  36. Manuja A, Manuja BK, Singha H. Sequence and functional variability of toll-like receptor 9 gene in equines. Mol Immunol 105:276–282.
    doi: 10.1016/j.molimm.2018.10.010pubmed: 30503611google scholar: lookup
  37. Mathur R, Oh H, Zhang D. A mouse model of Salmonella typhi Infection. Cell 151:590–602.
    doi: 10.1016/j.cell.2012.08.042pubmed: 23101627pmc: 3500584google scholar: lookup
  38. Meyer CG, Reiling N, Ehmen C. TLR1 variant H305L Associated with Protection from Pulmonary Tuberculosis. PLoS ONE 11:e0156046.
    doi: 10.1371/journal.pone.0156046pubmed: 27214039pmc: 4877073google scholar: lookup
  39. Minias P, Vinkler M. Selection balancing at Innate Immune genes: adaptive polymorphism maintenance in toll-like receptors. Mol Biol Evol 39:msac102.
    doi: 10.1093/molbev/msac102pubmed: 35574644pmc: 9132207google scholar: lookup
  40. Mukherjee S, Huda S, Sinha Babu SP. Toll-like receptor polymorphism in host immune response to infectious Diseases: a review. Scand J Immunol 90:e12771.
    doi: 10.1111/sji.12771pubmed: 31054156google scholar: lookup
  41. Neves F, Marques JP, Areal H. TLR7 and TLR8 evolution in lagomorphs: different patterns in the different lineages. Immunogenetics 74:475–485.
    doi: 10.1007/s00251-022-01262-9pubmed: 35419618google scholar: lookup
  42. Novák K. Functional polymorphisms in toll-like receptor genes for innate immunity in farm animals. Vet Immunol Immunopathol 157:1–11.
    doi: 10.1016/j.vetimm.2013.10.016pubmed: 24268689google scholar: lookup
  43. Oosting M, Cheng S-C, Bolscher JM. Human TLR10 is an anti-inflammatory pattern-recognition receptor. Proc Natl Acad Sci U S A 111:E4478–E4484.
    doi: 10.1073/pnas.1410293111pubmed: 25288745pmc: 4210319google scholar: lookup
  44. Opsal MAa, Våge DI, Hayes B. Genomic organization and transcript profiling of the bovine toll-like receptor gene cluster TLR6-TLR1-TLR10. Gene 384:45–50.
    doi: 10.1016/j.gene.2006.06.027google scholar: lookup
  45. Price SA, Bininda-Emonds ORP. A comprehensive phylogeny of extant horses, rhinos and tapirs (Perissodactyla) through data combination. Zoosyst Evol 85:277–292.
    doi: 10.1002/zoos.200900005google scholar: lookup
  46. Roach JC, Glusman G, Rowen L. The evolution of vertebrate toll-like receptors. Proc Natl Acad Sci U S A 102:9577–9582.
    doi: 10.1073/pnas.0502272102pubmed: 15976025pmc: 1172252google scholar: lookup
  47. Silva MJA, Santana DS, de Oliveira LG. The relationship between 896A/G (rs4986790) polymorphism of TLR4 and infectious Diseases: a meta-analysis. Front Genet 13:1045725.
    doi: 10.3389/fgene.2022.1045725pubmed: 36506333pmc: 9729345google scholar: lookup
  48. Smith RM, Kotzé A, Grobler JP, Dalton DL. Molecular characterization in the toll-like receptor 9 gene of Cape Mountain Zebra (Equus zebra zebra) from three populations. Infect Genet Evol 78:104118.
    doi: 10.1016/j.meegid.2019.104118pubmed: 31734289google scholar: lookup
  49. STEINER CC, RYDER OA. Molecular phylogeny and evolution of the Perissodactyla. Zoo j Linn Soc-Lond 163:1289–1303.
    doi: 10.1111/j.1096-3642.2011.00752.xgoogle scholar: lookup
  50. Stejskalova K, Janova E, Horecky C. Associations between the presence of specific antibodies to the West Nile Virus Infection and candidate genes in Romanian horses from the Danube delta. Mol Biol Rep 46:4453–4461.
    doi: 10.1007/s11033-019-04900-wpubmed: 31175514google scholar: lookup
  51. Su S-B, Tao L, Deng Z-P. TLR10: insights, controversies and potential utility as a therapeutic target. Scand J Immunol 93:e12988.
    doi: 10.1111/sji.12988pubmed: 33047375google scholar: lookup
  52. Tarlinton RE, Alder L, Moreton J. RNA expression of TLR10 in normal equine tissues. BMC Res Notes 9:353.
    doi: 10.1186/s13104-016-2161-9pubmed: 27435589pmc: 4952062google scholar: lookup
  53. Uddin MJ, Suen WW, Bosco-Lauth A. Kinetics of the West Nile virus induced transcripts of selected cytokines and toll-like receptors in equine peripheral blood mononuclear cells. Vet Res 47:61.
    doi: 10.1186/s13567-016-0347-8pubmed: 27267361pmc: 4895877google scholar: lookup
  54. Velová H, Gutowska-Ding MW, Burt DW, Vinkler M. Toll-like receptor evolution in birds: gene duplication, pseudogenization, and diversifying selection. Mol Biol Evol 35:2170–2184.
    doi: 10.1093/molbev/msy119pubmed: 29893911pmc: 6107061google scholar: lookup
  55. Vijay K. Toll-like receptors in immunity and inflammatory Diseases: past, present, and future. Int Immunopharmacol 59:391–412.
    doi: 10.1016/j.intimp.2018.03.002pubmed: 29730580pmc: 7106078google scholar: lookup
  56. Walsh C, Gangloff M, Monie T. Elucidation of the MD-2/TLR4 interface required for signaling by lipid IVa1. J Immunol 181:1245–1254.
    doi: 10.4049/jimmunol.181.2.1245pubmed: 18606678google scholar: lookup
  57. Werners AH, Bull S, Vendrig JC. Genotyping of toll-like receptor 4, myeloid differentiation factor 2 and CD-14 in the horse: an investigation into the influence of genetic polymorphisms on the LPS induced TNF-alpha response in equine whole blood. Vet Immunol Immunopathol 111:165–173.
    doi: 10.1016/j.vetimm.2005.12.003pubmed: 16476493google scholar: lookup
  58. Xu Y, Tao X, Shen B. Structural basis for signal transduction by the Toll/interleukin-1 receptor domains. Nature 408:111–115.
    doi: 10.1038/35040600pubmed: 11081518google scholar: lookup
  59. Yarovinsky F, Zhang D, Andersen JF. TLR11 activation of dendritic cells by a protozoan profilin-like protein. Science 308:1626–1629.
    doi: 10.1126/science.1109893pubmed: 15860593google scholar: lookup

Citations

This article has been cited 3 times.
  1. Wuyun B, Liu J, Wu R, Li Y, Liu F, Zhao H, Hao C, Zhao G, Sun W, Song Y, Wang W, Wang Y, Ma C, Xu F, He J, Wang P, Bao X, Cao G, Zhang Y, Lu Y, Li X. A telomere-to-telomere gapless genome assembly of the Tibetan wild ass (Equus kiang). Sci Data 2026 Jan 6;13(1):182.
    doi: 10.1038/s41597-025-06494-4pubmed: 41495097google scholar: lookup
  2. Stejskalova K, Vychodilova L, Janova E, Oppelt J, Horin P. Innate Immunity Toll-Like Triad TLR6-1-10 and Its Diversity in Distinct Horse Breeds. Vet Med Sci 2025 Mar;11(2):e70230.
    doi: 10.1002/vms3.70230pubmed: 39918481google scholar: lookup
  3. Moghaddam MM, Behzadi E, Sedighian H, Goleij Z, Kachuei R, Heiat M, Fooladi AAI. Regulation of immune responses to infection through interaction between stem cell-derived exosomes and toll-like receptors mediated by microRNA cargoes. Front Cell Infect Microbiol 2024;14:1384420.
    doi: 10.3389/fcimb.2024.1384420pubmed: 38756232google scholar: lookup
Subscribe to our newsletter
Join 99,850 horse owners like you who receive our email updates on horse health and nutrition.