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Massari S, Giannico F, Paolillo NV, Pala A, Jambrenghi AC, Antonacci R. Genomic and comparative analysis of the T cell receptor gamma locus in two Equus species. Front Immunol 2023; 14:1264949. [PMID: 37781375 PMCID: PMC10540303 DOI: 10.3389/fimmu.2023.1264949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 08/31/2023] [Indexed: 10/03/2023] Open
Abstract
The genus Equus 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 Equus genus, the horse (Equus caballus) and the donkey (Equus asinus), 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 Equus 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 Equus. These data is in agreement with the evolutionary idea of the existence of a Equus 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.
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Affiliation(s)
- Serafina Massari
- Department of Biological and Environmental Science and Technologies, University of Salento, Lecce, Italy
| | - Francesco Giannico
- Department of Veterinary Medicine, University of Bari "Aldo Moro", Bari, Italy
| | - Nunzia Valentina Paolillo
- Department of Biosciences, Biotechnologies and Environment, University of Bari "Aldo Moro", Bari, Italy
| | - Angela Pala
- Department of Biosciences, Biotechnologies and Environment, University of Bari "Aldo Moro", Bari, Italy
| | | | - Rachele Antonacci
- Department of Biosciences, Biotechnologies and Environment, University of Bari "Aldo Moro", Bari, Italy
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Giannico F, Massari S, Caputi Jambrenghi A, Soriano A, Pala A, Linguiti G, Ciccarese S, Antonacci R. The expansion of the TRB and TRG genes in domestic goats (Capra hircus) is characteristic of the ruminant species. BMC Genomics 2020; 21:623. [PMID: 32912163 PMCID: PMC7488459 DOI: 10.1186/s12864-020-07022-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/24/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Goats (Capra hircus), one of the first domesticated species, are economically important for milk and meat production, and their broad geographical distribution reflects their successful adaptation to diverse environmental conditions. Despite the relevance of this species, the genetic research on the goat traits is limited compared to other domestic species. Thanks to the latest goat reference genomic sequence (ARS1), which is considered to be one of the most continuous assemblies in livestock, we deduced the genomic structure of the T cell receptor beta (TRB) and gamma (TRG) loci in this ruminant species. RESULTS Our analyses revealed that although the organization of the goat TRB locus is broadly similar to that of the other artiodactyl species, with three in-tandem D-J-C clusters located at the 3' end, a complex and extensive series of duplications have occurred in the V genes at the 5' end, leading to a marked expansion in the number of the TRBV genes. This phenomenon appears to be a feature of the ruminant lineage since similar gene expansions have also occurred in sheep and cattle. Likewise, the general organization of the goat TRG genes is typical of ruminant species studied so far, with two paralogous TRG loci, TRG1 and TRG2, located in two distinct and distant positions on the same chromosome as result of a split in the ancestral locus. Each TRG locus consists of reiterated V-J-J-C cassettes, with the goat TRG2 containing an additional cassette relative to the corresponding sheep and cattle loci. CONCLUSIONS Taken together, these findings demonstrate that strong evolutionary pressures in the ruminant lineage have selected for the development of enlarged sets of TRB and TRG genes that contribute to a diverse T cell receptor repertoire. However, differences observed among the goat, sheep and cattle TRB and TRG genes indicate that distinct evolutionary histories, with independent expansions and/or contractions, have also affected each ruminant species.
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Affiliation(s)
- Francesco Giannico
- Department of Veterinary Medicine, University of Bari "Aldo Moro", Bari, Italy
| | - Serafina Massari
- Department of Biological and Environmental Science and Technologies, University of Salento, Lecce, Italy
| | - Anna Caputi Jambrenghi
- Department of Agricultural and Environmental Science, University of Bari "Aldo Moro", Bari, Italy
| | - Adriano Soriano
- Department of Biology, University of Bari "Aldo Moro", 70124, Bari, Italy
| | - Angela Pala
- Department of Biology, University of Bari "Aldo Moro", 70124, Bari, Italy
| | - Giovanna Linguiti
- Department of Biology, University of Bari "Aldo Moro", 70124, Bari, Italy
| | | | - Rachele Antonacci
- Department of Biology, University of Bari "Aldo Moro", 70124, Bari, Italy.
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Antonacci R, Massari S, Linguiti G, Caputi Jambrenghi A, Giannico F, Lefranc MP, Ciccarese S. Evolution of the T-Cell Receptor (TR) Loci in the Adaptive Immune Response: The Tale of the TRG Locus in Mammals. Genes (Basel) 2020; 11:E624. [PMID: 32517024 PMCID: PMC7349638 DOI: 10.3390/genes11060624] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/28/2020] [Accepted: 06/02/2020] [Indexed: 12/16/2022] Open
Abstract
T lymphocytes are the principal actors of vertebrates' cell-mediated immunity. Like B cells, they can recognize an unlimited number of foreign molecules through their antigen-specific heterodimer receptors (TRs), which consist of αβ or γδ chains. The diversity of the TRs is mainly due to the unique organization of the genes encoding the α, β, γ, and δ chains. For each chain, multi-gene families are arranged in a TR locus, and their expression is guaranteed by the somatic recombination process. A great plasticity of the gene organization within the TR loci exists among species. Marked structural differences affect the TR γ (TRG) locus. The recent sequencing of multiple whole genome provides an opportunity to examine the TR gene repertoire in a systematic and consistent fashion. In this review, we report the most recent findings on the genomic organization of TRG loci in mammalian species in order to show differences and similarities. The comparison revealed remarkable diversification of both the genomic organization and gene repertoire across species, but also unexpected evolutionary conservation, which highlights the important role of the T cells in the immune response.
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Affiliation(s)
- Rachele Antonacci
- Department of Biology, University of Bari “Aldo Moro”, 70124 Bari, Italy; (G.L.); (S.C.)
| | - Serafina Massari
- Department of Biological and Environmental Science and Technologies, University of Salento, 73100 Lecce, Italy;
| | - Giovanna Linguiti
- Department of Biology, University of Bari “Aldo Moro”, 70124 Bari, Italy; (G.L.); (S.C.)
| | - Anna Caputi Jambrenghi
- Department of Agricultural and Environmental Science, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.C.J.); (F.G.)
| | - Francesco Giannico
- Department of Agricultural and Environmental Science, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.C.J.); (F.G.)
| | - Marie-Paule Lefranc
- IMGT, the International ImMunoGeneTics Information System, Laboratoire d’ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UMR9002 CNRS, Université de Montpellier, CEDEX 5, 34396 Montpellier, France;
| | - Salvatrice Ciccarese
- Department of Biology, University of Bari “Aldo Moro”, 70124 Bari, Italy; (G.L.); (S.C.)
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Wang X, Wang P, Wang R, Wang C, Bai J, Ke C, Yu D, Li K, Ma Y, Han H, Zhao Y, Zhou X, Ren L. Analysis of TCRβ and TCRγ genes in Chinese alligator provides insights into the evolution of TCR genes in jawed vertebrates. Dev Comp Immunol 2018; 85:31-43. [PMID: 29574022 DOI: 10.1016/j.dci.2018.01.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 01/12/2018] [Accepted: 01/12/2018] [Indexed: 06/08/2023]
Abstract
All jawed vertebrates have four T cell receptor (TCR) chains that are expressed by thymus-derived lymphocytes and play a major role in animal immune defence. However, few studies have investigated the TCR chains of crocodilians compared with those of birds and mammals, despite their key evolutionary position linking amphibians, reptiles, birds and mammals. Here, employing an Alligator sinensis genomic bacterial artificial chromosome (BAC) library and available genome data, we characterized the genomic organization, evolution and expression of TRB and TRG loci in Alligator sinensis. According to the sequencing data, the Alligator sinensis TRB locus spans approximately 500 Kb of genomic DNA containing two D-J-C clusters and 43 V gene segments and is organized as Vβ(39)-pJβ1-pCβ1-pDβ1-Dβ2- Jβ2(12)-Cβ2-Vβ(4), whereas the TRG locus spans 115 Kb of DNA genomic sequence consisting of 18 V gene segments, nine J gene segments and one C gene segment and is organized in a classical translocon pattern as Vγ(18)-Jγ(9)-Cγ. Moreover, syntenic analysis of TRB and TRG chain loci suggested a high degree of conserved synteny in the genomic regions across mammals, birds and Alligator sinensis. By analysing the cloned TRB/TRG cDNA, we identified the usage pattern of V families in the expressed TRB and TRG. An analysis of the junctions of the recombined VJ revealed the presence of N and P nucleotides in both expressed TRB and TRG sequences. Phylogenetic analysis revealed that TRB and TRG loci possess distinct evolutionary patterns. Most Alligator sinensis V subgroups have closely related orthologues in chicken and duck, and a small number of Alligator sinensis V subgroups have orthologues in mammals, which supports the hypothesis that crocodiles are the closest relatives of birds and mammals. Collectively, these data provide insights into TCR gene evolution in vertebrates and improve our understanding of the Alligator sinensis immune system.
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Affiliation(s)
- Xifeng Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Peng Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Renping Wang
- Administration Bureau of Chinese Alligator National Nature Reserve Protection, Anhui, People's Republic of China
| | - Chaolin Wang
- Administration Bureau of Chinese Alligator National Nature Reserve Protection, Anhui, People's Republic of China
| | - Jianhui Bai
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Cuncun Ke
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Di Yu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Kongpan Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Yonghe Ma
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Haitang Han
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Yaofeng Zhao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Xin Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100193, People's Republic of China; College of Plant Protection, China Agricultural University, Beijing, People's Republic of China.
| | - Liming Ren
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China.
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