Data characterizing the genomic structure of the T cell receptor (TRB) locus in Camelus dromedarius

Antonacci, Rachele; Bellini, Mariagrazia; Castelli, Vito; Ciccarese, Salvatrice; Massari, Serafina

doi:10.1016/j.dib.2017.08.002

Cited by 9 publications

(60 citation statements)

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“…An analysis of the genomic sequence revealed that the general structural organization of the pig TRB locus follows that of the other mammalian species, with a library of TRBV genes positioned at the 5′ end of D-J-C clusters, followed by a single TRBV gene located at the 3′ end in an inverted transcriptional orientation (Figure 1 ). Specifically, analysis of the assembly confirmed the presence of three D-J-C clusters similar to the clusters found in other species of artiodactyls, where D-J-C cluster 3 lies between D-J-C cluster 1 and D-J-C cluster 2 ( 5 , 8 , 9 ) The pig D-J-C region covers approximately 27 kb. D-J-C cluster 1 spans 7,659 bp and contains one TRBD, seven TRBJ and one TRBC genes.…”

Section: Resultssupporting

confidence: 68%

“…The TRBD, TRBJ and TRBC genes were annotated, according to the similarity with the other artiodactyl species ( 5 , 8 , 9 ). Each TRBJ1, TRBJ2, and TRBJ3 gene was designed by a hyphen and a number corresponding to their position in the cluster.…”

Section: Methodsmentioning

confidence: 99%

“…The TRBV genes used for the phylogenetic analysis were retrieved from the following sequences deposited in the GEDI (for GenBank/ENA/DDBJ/IMGT/LIGM-DB) databases: NG_001333 (human TRB locus contig), NW_003726086 [dog TRB locus contig as characterized by 3 ); NW_011591622 , NW_011593440 , NW_011591151 , NW_011620189 , NW_011616084 , NW_011607149 , NW_011601111 , and LT837971 [dromedary TRB locus contig as characterized by ( 8 , 9 )]; NC_010460 (pig TRB locus contig, this work).…”

Section: Methodsmentioning

confidence: 99%

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Overview of the Germline and Expressed Repertoires of the TRB Genes in Sus scrofa

et al. 2018

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The α/β T cell receptor (TR) is a complex heterodimer that recognizes antigenic peptides and binds to major histocompatibility complex (MH) molecules. Both α and β chains are encoded by different genes localized on two distinct chromosomal loci: TRA and TRB. The present study employed the recent release of the swine genome assembly to define the genomic organization of the TRB locus. According to the sequencing data, the pig TRB locus spans approximately 400 kb of genomic DNA and consists of 38 TRBV genes belonging to 24 subgroups located upstream of three in tandem TRBD-J-C clusters, which are followed by a TRBV gene in an inverted transcriptional orientation. Comparative analysis confirms that the general organization of the TRB locus is similar among mammalian species, but the number of germline TRBV genes varies greatly even between species belonging to the same order, determining the diversity and specificity of the immune response. However, sequence analysis of the TRB locus also suggests the presence of blocks of conserved homology in the genomic region across mammals. Furthermore, by analysing a public cDNA collection, we identified the usage pattern of the TRBV, TRBD, and TRBJ genes in the adult pig TRB repertoire, and we noted that the expressed TRBV repertoire seems to be broader and more diverse than the germline repertoire, in line with the presence of a high level of TRBV gene polymorphisms. Because the nucleotide differences seems to be principally concentrated in the CDR2 region, it is reasonable to presume that most T cell β-chain diversity can be related to polymorphisms in pig MH molecules. Domestic pigs represent a valuable animal model as they are even more anatomically, genetically and physiologically similar to humans than are mice. Therefore, present knowledge on the genomic organization of the pig TRB locus allows the collection of increased information on the basic aspects of the porcine immune system and contributes to filling the gaps left by rodent models.

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Section: Resultssupporting

confidence: 68%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Overview of the Germline and Expressed Repertoires of the TRB Genes in Sus scrofa

et al. 2018

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“…(dromedary TRB locus contig as characterized by [14][15]; NC_010460 (pig TRB locus contig as characterized by [16]); and NC_030811.1 (this work) (goat TRB locus contig). We combined the nucleotide sequences of the V-REGION of the goat TRBV genes with the corresponding gene sequences of sheep, pig and dromedary.…”

Section: Phylogenetic Analysesmentioning

confidence: 99%

“…In human, mouse, and several other mammals (https://www.imgt.org/IMGTrepertoire/: Homo sapiens, Mus musculus; [7,8,9,10,11]), two TRBD-J-C clusters have been identi ed. In contrast, in the artiodactyl lineage [12,13,14,15,16,17], a duplication event within the 3′ end of the TRB locus has led to the generation of a third TRBD-J-C cluster. Moreover, ruminants appear to have an increased number of genes in the TRBV gene pool, which is the largest in cattle (134 TRBV genes) [13], and sheep (94 TRBV genes) [11] and resulted from massive expansion of mainly two TRBV gene subgroups.…”

Section: Introductionmentioning

confidence: 99%

The expansion of the TRB and TRG genes in domestic goats (Capra hircus) is characteristic of the ruminant species

Giannico

Massari

Jambrenghi

et al. 2020

Preprint

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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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The occurrence of three D-J-C clusters within the dromedary TRB locus highlights a shared evolution in Tylopoda, Ruminantia and Suina

Antonacci

Bellini

Pala

et al. 2017

Developmental & Comparative Immunology

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Data characterizing the genomic structure of the T cell receptor (TRB) locus in Camelus dromedarius

Cited by 9 publications

References 8 publications

Overview of the Germline and Expressed Repertoires of the TRB Genes in Sus scrofa

Overview of the Germline and Expressed Repertoires of the TRB Genes in Sus scrofa

The expansion of the TRB and TRG genes in domestic goats (Capra hircus) is characteristic of the ruminant species

The occurrence of three D-J-C clusters within the dromedary TRB locus highlights a shared evolution in Tylopoda, Ruminantia and Suina

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