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Frontiers in immunology2023; 14; 1264949; doi: 10.3389/fimmu.2023.1264949

Genomic and comparative analysis of the T cell receptor gamma locus in two Equus species.

Abstract: The genus is the only extant genus of the Equidae family, which belongs to Perissodactyla, an order of mammals characterized by an odd number of toes (odd-toes ungulates). Taking advantage of the latest release of the genome assembly, we studied, for the first time in two organisms belonging to the genus, the horse () and the donkey (), the T cell receptor gamma (TRG) locus encoding the gamma chain of the γδ T cell receptor. Forty-five Variable (TRGV) genes belonging to the seven IMGT-NC validated mammalian TRGV subgroups, 25 Joining (TRGJ) and 17 Constant (TRGC) genes organized in 17 V-J-(J)-C cassettes, in tandem on about 1100 Kb, characterize the horse TRG locus, making the horse TRG locus the one with the greatest extension and with a significantly higher number of genes than the orthologous loci of the other mammalian species. A clonotype analysis of an RNA-seq transcriptomic dataset derived from spleen of an adult healthy horse, using the complete set of the horse TRGJ germline gene sequences as a probe, revealed that, in addition to the most prominent V-J rearrangements within each cassette, there is a relevant proportion of trans-cassette V-J recombination, whereby the same TRGV genes can recombine with different TRGJ genes spliced to the corresponding TRGC genes. This recombinant event strongly contributes to the diversity of the γ chain repertoire. In the donkey TRG locus, 34 TRGV, 21 TRGJ and 14 TRGC genes distributed in 14 V-J-(J)-C cassettes were found in a region of approximately 860 kb. Although the donkey's TRG is smaller than that of the horse, in genus, this is still the second largest locus so far found in any mammalian species. Finally, the comparative analysis highlighted differences in size and gene content between the horse and donkey TRG loci, despite belonging to the same genus, indicating a good level of diversification within . These data is in agreement with the evolutionary idea of the existence of a recent common ancestor in rapid evolution, for which a mutation rate between horses and donkeys is more comparable to that between species belonging to different genera rather than to species of the same genus.
Copyright © 2023 Massari, Giannico, Paolillo, Pala, Jambrenghi and Antonacci.
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Publication Date: 2023-09-15 PubMed ID: 37781375PubMed Central: PMC10540303DOI: 10.3389/fimmu.2023.1264949Google Scholar: Lookup
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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 explores the T cell receptor gamma (TRG) locus, responsible for encoding the gamma chain of the γδ T cell receptor, in two species of the Equus genus: horses and donkeys. The horses’ TRG locus has the greatest extension and significantly more genes than other mammals, contributing to the diversity of the γ chain repertoire. However, despite being of the same genus, the TRG loci of horses and donkeys showed noticeable differences in size and gene content.

Investigation of the T Cell Receptor Gamma Locus in the Horse and Donkey Genomes

  • The research used the most recent genome assembly to study the T cell receptor gamma (TRG) locus in both horses and donkeys, an exploration that has never been done before. Frequently referred to as odd-toed ungulates, these species are part of the Equidae family and are characterized by an odd number of toes.
  • In horses, the TRG locus spans around 1100 kilobases (Kb) and includes 45 Variable (TRGV), 25 Joining (TRGJ), and 17 Constant (TRGC) genes. These genes are sorted into 17 V-J-(J)-C cassettes. The size and gene content of the horse TRG locus make it the most extensive among other mammals’ orthologous loci.
  • Analysis of transcriptomic data from the spleen of an adult horse showed a significant proportion of trans-cassette V-J recombination events, in which the same TRGV genes combine with varying TRGJ genes spliced to corresponding TRGC genes, contributing to the diversity of the γ chain repertoire.

Differences in the TRG Loci of Horses and Donkeys

  • The TRG locus in the donkey’s genome is smaller than that of the horse, spanning approximately 860 kb. This locus encompasses 34 TRGV, 21 TRGJ, and 14 TRGC genes sorted into 14 V-J-(J)-C cassettes.
  • While the donkey’s TRG locus is smaller, it remains the second-largest locus discovered in any mammalian species within the Equus genus.

Comparative Analysis Between Horse and Donkey TRG Loci

  • Despite belonging to the same Equus genus, the TRG loci of horses and donkeys have noticeable differences in size and gene content.
  • The difference suggests a high level of diversification within the Equus genus, in line with evolutionary hypothesis postulating a recent common ancestor rapidly evolving between horses and donkeys.
  • This rapid evolution implies the mutation rate between horses and donkeys is more akin to that between species from different genera, not species within the same genus.

Cite This Article

APA
(2023). Genomic and comparative analysis of the T cell receptor gamma locus in two Equus species. Front Immunol, 14, 1264949. https://doi.org/10.3389/fimmu.2023.1264949

Publication

Frontiers in immunology
ISSN: 1664-3224
NlmUniqueID: 101560960
Country: Switzerland
Language: English
Volume: 14
Pages: 1264949
PII: 1264949

Researcher Affiliations

MeSH Terms

  • Horses / genetics
  • Animals
  • Amino Acid Sequence
  • Genome
  • Receptors, Antigen, T-Cell, gamma-delta / genetics
  • Genomics
  • Equidae / genetics

Conflict of Interest Statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

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Citations

This article has been cited 2 times.
  1. Antonacci R, Giannico F, Moschetti R, Pala A, Jambrenghi AC, Massari S. A Comprehensive Analysis of the Genomic and Expressed Repertoire of the T-Cell Receptor Beta Chain in Equus caballus. Animals (Basel) 2024 Sep 29;14(19).
    doi: 10.3390/ani14192817pubmed: 39409766google scholar: lookup
  2. Ren H, Wen X, He Q, Yi M, Dugarjaviin M, Bou G. Comparative Study on the Sperm Proteomes of Horses and Donkeys. Animals (Basel) 2024 Jul 31;14(15).
    doi: 10.3390/ani14152237pubmed: 39123763google scholar: lookup
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