Genomic V exons from whole genome shotgun data in reptiles

Olivieri, David N.; Haeften, B. von; Sánchez-Espinel, Christian; Faro, José; Gambón-Deza, Francisco

doi:10.1007/s00251-014-0784-3

Cited by 26 publications

(28 citation statements)

References 49 publications

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“…As mentioned, reptiles have fewer V genes in the TRBV locus than found in mammals (Olivieri et al 2014). Figure 4 (right) shows that of the four ancestral genes that gave rise to the mammalian V genes, the clades Vβ-I, -III, and -IV have clear representations in the diversification of reptiles; however, no orthologs were found for the Vβ-II.…”

Section: Gene From the Trav And Trbv Loci In Reptilesmentioning

confidence: 91%

“…We independently confirmed the loci assignment of each sequence with two separate methods, namely a BLASTP comparison against the NCBI NR protein database, and our random forest method trained with known reference sequences. As mentioned previously, more details of these methods are described elsewhere (Olivieri and Gambon-Deza 2015;Olivieri et al 2014).…”

Section: Methodsmentioning

confidence: 99%

“…Previously (Olivieri et al 2014), we showed that such a low number of TRB V genes is common among reptiles. Monotremes arose prior to marsupials and still retain reptilelike genes which are not found in other mammals (e.g., the IgD has ten domains (Gambon Deza et al 2009)).…”

Section: Gene From the Trav And Trbv Loci In Monotremes And Marsupialsmentioning

confidence: 95%

“…The details of the WGS assemblies and the number of TCR V genes obtained for each Reptile species are given in Table 3. In a previous publication (Olivieri et al 2014), we indicated that reptiles TRAV and TRBV clades contain gene sequences that share a common ancestor with mammals. These clades contain the majority of sequences found in reptiles.…”

Section: Gene From the Trav And Trbv Loci In Reptilesmentioning

confidence: 96%

“…Within each TCR locus, multiple V genes exist that constitute the TCR repertoire (Davis and Bjorkman 1988). Across species, the number of V genes in these loci varies considerably (i.e., ranging between 20 and 100 (Olivieri et al 2013(Olivieri et al , 2014; see also Fig. 1).…”

Section: Introductionmentioning

confidence: 99%

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Evolution of V genes from the TRV loci of mammals

2015

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Information concerning the evolution of T lymphocyte receptors (TCR) can be deciphered from that part of the molecule that recognizes antigen presented by major histocompatibility complex (MHC), namely the variable (V) regions. The genes that code for these variable regions are found within the TCR loci. Here, we describe a study of the evolutionary origin of V genes that code for the α and β chains of the TCR loci of mammals. In particular, we demonstrate that most of the 35 TRAV and 25 TRBV conserved genes found in Primates are also found in other Eutheria, while in Marsupials, Monotremes, and Reptiles, these genes diversified in a different manner. We also show that in mammals, all TRAV genes are derived from five ancestral genes, while all TRBV genes originate from four such genes. In Reptiles, the five TRAV and three out of the four TRBV ancestral genes exist, as well as other V genes not found in mammals. We also studied the TRGV and TRDV loci from all mammals, and we show a relationship of the TRDV to the TRAV locus throughout evolutionary time.

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Section: Gene From the Trav And Trbv Loci In Reptilesmentioning

confidence: 91%

Section: Methodsmentioning

confidence: 99%

Section: Gene From the Trav And Trbv Loci In Monotremes And Marsupialsmentioning

confidence: 95%

Section: Gene From the Trav And Trbv Loci In Reptilesmentioning

confidence: 96%

Section: Introductionmentioning

confidence: 99%

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Evolution of V genes from the TRV loci of mammals

2015

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V genes in primates from whole genome sequencing data

Olivieri

Gambón-Deza

2015

Immunogenetics

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The adaptive immune system uses V genes for antigen recognition. However, the evolutionary diversification and selection processes within and across species and orders remain poorly understood. Here, we studied the amino acid (AA) sequences obtained from the translated in-frame V exons of immunoglobulins (IG) and T cell receptors (TR) from 16 primate species whose genomes have been sequenced. Multi-species comparative analysis supports the hypothesis that V genes in the IG loci undergo birth/death processes, thereby permitting rapid adaptability over evolutionary time. We also show that multiple cladistic groupings exist in the TRA (35 clades) and TRB (25 clades) V gene loci and that each primate species typically contributes at least one V gene to each of these clades. The results demonstrate that IG V genes and TR V genes have quite different evolutionary pathways; multiple duplications can explain the IG loci results, while coevolutionary pressures can explain the phylogenetic results of the TR V gene loci. Our results suggest that there exist evolutionary relationships between V gene clades in the TRA and TRB loci. Due to the long-standing preservation of these clades, such genes may have specific and necessary roles for the viability of a species.

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Inter- and intraspecies comparison of phylogenetic fingerprints and sequence diversity of immunoglobulin variable genes

et al. 2020

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Protection and neutralization of a vast array of pathogens is accomplished by the tremendous diversity of the B cell receptor (BCR) repertoire. For jawed vertebrates, this diversity is initiated via the somatic recombination of immunoglobulin (Ig) germline elements. While it is clear that the number of these germline segments differs from species to species, the extent of cross-species sequence diversity remains largely uncharacterized. Here we use extensive computational and statistical methods to investigate the sequence diversity and evolutionary relationship between Ig variable (V), diversity (D), and joining (J) germline segments across nine commonly studied species ranging from zebrafish to human. Metrics such as guanine-cytosine (GC) content showed low redundancy across Ig germline genes within a given species. Other comparisons, including amino acid motifs, evolutionary selection, and sequence diversity revealed species-specific properties. Additionally, we showed that the germline-encoded diversity differs across antibody (recombined VDJ) repertoires of various B cell subsets. To facilitate future comparative immunogenomics analysis we created VDJgermlines, an R package that contains the germline sequences from multiple species. Our study informs strategies for the humanization and engineering of therapeutic antibodies.

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Genomic V exons from whole genome shotgun data in reptiles

Cited by 26 publications

References 49 publications

Evolution of V genes from the TRV loci of mammals

Evolution of V genes from the TRV loci of mammals

V genes in primates from whole genome sequencing data

Inter- and intraspecies comparison of phylogenetic fingerprints and sequence diversity of immunoglobulin variable genes

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