The Organization of the Pig T-Cell Receptor γ (TRG) Locus Provides Insights into the Evolutionary Patterns of the TRG Genes across Cetartiodactyla

Linguiti, Giovanna; Giannico, Francesco; D’Addabbo, Pietro; Pala, Angela; Jambrenghi, Anna Caputi; Ciccarese, Salvatrice; Massari, Serafina; Antonacci, Rachele

doi:10.3390/genes13020177

Cited by 3 publications

(5 citation statements)

References 50 publications

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“…The pig TCR gamma chain (TRG) region (Babraham Chr 9: 108,295,979 – 108,409,334) has recently been described in detail for the Babraham, Sscrofa11.1, and USMARCv1.0 assemblies (Le Page et al 2021; Linguiti et al 2022). In the Babraham, this region is intact and in the middle of a 41.7 Mb contig.…”

Section: Resultsmentioning

confidence: 99%

“…The pig reference genome assembly (Groenen et al 2012; Warr et al 2020) has greatly contributed to our understanding of porcine immunology (Dawson et al 2013; Schwartz et al 2017; Massari et al 2018; Morgan et al 2018; Schwartz and Hammond 2018; Hammer et al 2020; Zhang et al 2020; Le Page et al 2021; Linguiti et al 2022) and has helped researchers better utilize the pig as a model of disease (Groenen et al 2012; Nicholls et al 2016; Perleberg et al 2018). It has also facilitated the generation of genome-edited pigs, such as, for example, for resistance to porcine reproductive and respiratory syndrome virus (PRRSV) infection (Whitworth et al 2014; Burkard et al 2018), or for the inactivation of porcine endogenous retroviruses in order to improve the safety of xenotransplantation (Niu et al 2017; Niu et al 2021).…”

Section: Introductionmentioning

confidence: 99%

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A highly-contiguous genome assembly of the inbred Babraham pig (Sus scrofa) quantifies breed homozygosity and illuminates porcine immunogenetic variation

Schwartz,

Farrell,

Freimanis

et al. 2023

Preprint

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The inbred Babraham pig serves as a valuable biomedical model for research due to its high level of homozygosity, including in the major histocompatibility complex (MHC) loci and likely other important immune-related gene complexes, which are generally highly diverse in outbred populations. As the ability to control for this diversity using inbred organisms is of great utility, we sought to improve this resource by generating a long-read whole genome assembly of a Babraham pig. The Babraham genome wasde novoassembled using PacBio long-reads and error-corrected using Illumina short-reads. The assembled contigs were then mapped to the current porcine reference assembly, Sscrofa11.1, to generate chromosome-level scaffolds. The resulting Babraham pig assembly is nearly as contiguous as Sscrofa11.1 with a contig N50 of 34.95 Mb and contig L50 of 23. The remaining sequence gaps are generally the result of poor assembly across large and highly repetitive regions such as the centromeres and tandemly duplicated gene families, including immune-related gene complexes, that often vary in gene content between haplotypes. We also further confirm homozygosity across the Babraham pig MHC and characterize the allele content across several immune-related gene complexes, including the contiguous assemblies of the antibody heavy chain locus and leukocyte receptor complex. The Babraham pig genome assembly provides an alternate highly contiguous porcine genome assembly as a resource for the livestock genomics community. The assembly will also aid biomedical and veterinary research that utilizes this animal model such as when controlling for genetic variation is critical.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A highly-contiguous genome assembly of the inbred Babraham pig (Sus scrofa) quantifies breed homozygosity and illuminates porcine immunogenetic variation

Schwartz,

Farrell,

Freimanis

et al. 2023

Preprint

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“…The recovered sequence comprises also the AMPH and the STARD3NL genes, which represent the IMGT 5’ and 3’ bornes (IMGT, https://www.imgt.org/IMGTrepertoire/LocusGenes/bornes/bornesTRG.html ) since located, respectively, upstream of the first and downstream of the last gene of the TRG locus in all mammalian species in which this locus maps in a single position ( 6 , 22 – 25 , 29 ). This ensures that we have recovered the entire horse TRG genomic region.…”

Section: Resultsmentioning

confidence: 99%

“…Overall, the deduced genomic structure of the horse TRG locus reflects the organization of the TRG genes in V-J-J-C unit or TRGC “cassettes”, which is a peculiarity of artiodactyl (ruminants, pigs and camels), carnivore (dogs and cats) and mouse species ( 6 , 25 ). In the horse TRG region, we identified and annotated 45 TRGV, 25 TRGJ and 17 TRGC genes distributed in 17 V-J-(J)-C cassettes, arranged in the same transcriptional orientation, which were classified from TRGC1 to TRGC17 proceeding from the 5’ to the 3’ end of the locus.…”

Section: Resultsmentioning

confidence: 99%

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

Massari,

Giannico,

Paolillo

et al. 2023

Front. Immunol.

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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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A genome assembly and transcriptome atlas of the inbred Babraham pig to illuminate porcine immunogenetic variation

Schwartz,

Farrell,

Freimanis

et al. 2024

Immunogenetics

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The inbred Babraham pig serves as a valuable biomedical model for research due to its high level of homozygosity, including in the major histocompatibility complex (MHC) loci and likely other important immune-related gene complexes, which are generally highly diverse in outbred populations. As the ability to control for this diversity using inbred organisms is of great utility, we sought to improve this resource by generating a long-read whole genome assembly and transcriptome atlas of a Babraham pig. The genome was de novo assembled using PacBio long reads and error-corrected using Illumina short reads. Assembled contigs were then mapped to the porcine reference assembly, Sscrofa11.1, to generate chromosome-level scaffolds. The resulting TPI_Babraham_pig_v1 assembly is nearly as contiguous as Sscrofa11.1 with a contig N50 of 34.95 Mb and contig L50 of 23. The remaining sequence gaps are generally the result of poor assembly across large and highly repetitive regions such as the centromeres and tandemly duplicated gene families, including immune-related gene complexes, that often vary in gene content between haplotypes. We also further confirm homozygosity across the Babraham MHC and characterize the allele content and tissue expression of several other immune-related gene complexes, including the antibody and T cell receptor loci, the natural killer complex, and the leukocyte receptor complex. The Babraham pig genome assembly provides an alternate highly contiguous porcine genome assembly as a resource for the livestock genomics community. The assembly will also aid biomedical and veterinary research that utilizes this animal model such as when controlling for genetic variation is critical.

show abstract

The Organization of the Pig T-Cell Receptor γ (TRG) Locus Provides Insights into the Evolutionary Patterns of the TRG Genes across Cetartiodactyla

Cited by 3 publications

References 50 publications

A highly-contiguous genome assembly of the inbred Babraham pig (Sus scrofa) quantifies breed homozygosity and illuminates porcine immunogenetic variation

A highly-contiguous genome assembly of the inbred Babraham pig (Sus scrofa) quantifies breed homozygosity and illuminates porcine immunogenetic variation

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

A genome assembly and transcriptome atlas of the inbred Babraham pig to illuminate porcine immunogenetic variation

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