Comparative Analysis of the TRB Locus in the Camelus Genus

Abstract

T cells can be separated into two major subsets based on the heterodimer that forms their T cell receptors. αβ T cells have receptors consisting of α and β chains, while γδ T cells are composed of γ and δ chains. αβ T cells play an essential role within the adaptive immune responses against pathogens. The recent genomic characterization of the Camelus dromedarius T cell receptor β (TRB) locus has allowed us to infer the structure of this locus from the draft genome sequences of its wild and domestic Bactrian congeners, Camelus ferus and Camelus bactrianus . The general structural organization of the wild and domestic Bactrian TRB locus is similar to that of the dromedary, with a pool of TRBV genes positioned at the 5′ end of D-J-C clusters, followed by a single TRBV gene located at the 3′ end with an inverted transcriptional orientation. Despite the fragmented nature of the assemblies, comparative genomics reveals the existence of a perfect co-linearity between the three Old World camel TRB genomic sequences, which enables the transfer of information from one sequence to another and the filling of gaps in the genomic sequences. A virtual camelid TRB locus is hypothesized with the presence of 33 TRBV genes distributed in 26 subgroups. Likewise, in the artiodactyl species, three in-tandem D-J-C clusters, each composed of one TRBD gene, six or seven TRBJ genes, and one TRBC gene, are placed at the 3′ end of the locus. As reported in the ruminant species, a group of four functional TRY genes at the 5′ end and only one gene at the 3′ end, complete the camelid TRB locus. Although the gene content is similar, differences are observed in the TRBV functional repertoire, and genes that are functional in one species are pseudogenes in the other species. Hence, variations in the functional repertoire between dromedary, wild and domestic Bactrian camels, rather than differences in the gene content, may represent the molecular basis explaining the disparity in the TRB repertoire between the Camelus species. Finally, our data contribute to the knowledge about the evolutionary history of Old World camelids.

Chromosome‐level assembly of wild Bactrian camel genome reveals organization of immune gene loci

“…functional TRBV genes were distributed on five sequential contigs (Figure 4c). The tandem organization of three TRBD-J-C clusters was in agreement with that observed in camelids and other artiodactyls (Antonacci et al, 2019(Antonacci et al, , 2017.…”

“…Although several draft genome assemblies of camelids were previously released (Bactrian Camels Genome Sequencing & Analysis Consortium et al, 2012;Wu et al, 2014), they were primarily constructed based on short-read sequencing with limited contiguity and quality. Because of the high repetition and large size of many of the immune gene loci, attempts to annotate the loci often resulted in numerous fragments that required further labour-intensive work to complete (Antonacci, Bellini, Linguiti, Ciccarese, & Massari, 2019;Antonacci et al, 2017;Liang et al, 2015;Plasil et al, 2016Plasil et al, , 2019a. The recent development of long-read sequencing technology, such as that provided by Pacific Biosciences (PacBio) and Oxford Nanopore, has resulted in the ability to produce reads that are tens of kilobases in size.…”

Old World camels in a modern world – a balancing act between conservation and genetic improvement

“…They have not been identified in mammalian species so far and could enhance the acquirement of new antigenic specificity (Ciccarese et al 2014). On the contrary, a and b T-cells show a reduced repertoire with great sequence identity between orthologous genes in all three Old World camel species (Antonacci et al 2019). This might be due to equally limited requirements of the ab CDR1 and CDR2 domains, which bind to the MHC molecules; these in return show low levels of genetic diversity (Plasil et al 2016(Plasil et al , 2019.…”

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

“…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.…”