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

Antonacci, Rachele; Bellini, Mariagrazia; Pala, Angela; Mineccia, Micaela; Hassanane, M. S.; Ciccarese, Salvatrice; Massari, Serafina

doi:10.1016/j.dci.2017.05.021

Cited by 16 publications

(60 citation statements)

References 60 publications

(129 reference statements)

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“… These data are presented in support of structural and evolutionary analysis of the published article entitled “The occurrence of three D-J-C clusters within the dromedary TRB locus highlights a shared evolution in Tylopoda, Ruminantia and Suina” (Antonacci et al, 2017) [1] . Here we describe the genomic structure and the gene content of the T cell receptor beta chain (TRB) locus in Camelus dromedarius.…”

supporting

confidence: 66%

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

et al. 2017

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These data are presented in support of structural and evolutionary analysis of the published article entitled “The occurrence of three D-J-C clusters within the dromedary TRB locus highlights a shared evolution in Tylopoda, Ruminantia and Suina” (Antonacci et al., 2017) [1]. Here we describe the genomic structure and the gene content of the T cell receptor beta chain (TRB) locus in Camelus dromedarius. As in the other species of mammals, the general genomic organization of the dromedary TRB locus consists of a pool of TRBV genes located upstream of in tandem TRBD-J-C clusters, followed by a TRBV gene with an inverted transcriptional orientation. A peculiarity of the dromedary TRB locus structure is the presence of three TRBD-J-C clusters, which is a common feature of sheep, cattle and pig sequences.

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supporting

confidence: 66%

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

et al. 2017

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“…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.…”

Section: Tcr Gene Locisupporting

confidence: 88%

“…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.…”

Section: Introductionmentioning

confidence: 99%

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

Liang

Wang

et al. 2020

Molecular Ecology Resources

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Camelids are characterized by their unique adaptive immune system that exhibits the generation of homodimeric heavy-chain immunoglobulins, somatic hypermutation of T-cell receptors, and low genetic diversity of major histocompatibility complex (MHC) genes. However, short-read assemblies are typically highly fragmented in these gene loci owing to their repetitive and polymorphic nature. Here, we constructed a chromosome-level assembly of wild Bactrian camel genome based on high-coverage long-read sequencing and chromatin interaction mapping. The assembly with a contig N50 of 5.37 Mb and a scaffold N50 of 76.03 Mb, represents the most contiguous camelid genome to date. The genomic organization of immunoglobulin heavy-chain locus was similar between the wild Bactrian camel and alpaca, and genes encoding for conventional and heavy-chain antibodies were intermixed. The organizations of two immunoglobulin light-chain loci and four T cell receptor loci were also fully deciphered using the new assembly. Additionally, the complete classical MHC region was resolved into a single contig. The high-quality assembly presented here provides an essential reference for future investigations examining the camelid immune system. K E Y W O R D S chromosome assembly, immunoglobin, long-read sequencing, major histocompatibility complex, T cell receptor, wild Bactrian camel | 771 MING et al.

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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

Cited by 16 publications

References 60 publications

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

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

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

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

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