Biology subjects

Francisco Gambón-Deza

Publications and source records attributed to Francisco Gambón-Deza.

4 recordsLinked to original sources

bioRxiv2014

V genes in rodents from whole genome sequencing data

We studied the V exons of 14 rodent species obtained from whole genome sequencing (WGS) datasets. Compared to other mammals, we found an increase in the number of immunoglobulin (IG) V genes in the heavy (IGH) and kappa chain (IGK) loci. We provide evidence for a reduction genes in lambda chain (IGL) locus, disappearing entirely in one of the species(Dipodomys ordii). We show relationships amongst the V genes of the T-cell receptors (TR) found in primates, possessing ortholog sequences between them. As compared with other mammals, there is an increase in the number of TRAV genes within rodents. Such an increase within this locus is caused by duplication events involving a few putative V genes. This duplication phenomenon does not occur in the TRBV locus. In those species that underwent an expansion of TRAV genes, we found that they also have a correspondingly larger number of MHC Class I genes. The results suggest that selective pressures have conditioned the expansion of V genomic repertoire the TRA, IGK and IGH loci during the diversification process of rodents.

Immunology↗

bioRxiv2014

The immunologic V-gene repertoire in mammals

From recent whole genome shotgun data of 48 mammalian species, we have used our software VgenExtractor to obtain the functional V-gene sequence repertoire in order to conduct comparative phylogenetic studies. These studies reveal a large variation in the number of V-genes across mammalian species, ranging from a mere 36 V-genes in dolphins to nearly 600 V-genes in rats. Monotremes and marsupials are the only mammals possessing an additional locus, the TRMV, apart from the seven common loci found in mammals. Also, we show evidence for the loss of the light chain loci, specifically the V{kappa} chain in one microbat, and the V{lambda} chain in one rodent species. Finally, we suggest different features related to the evolution of immunoglobulin and T cell receptor loci, where frequent sequence duplications are seen in the former, while preserved and undiversified lineages are observed in the latter. All the V-gene sequences described in this study are available in the public database repository vgenerepertoire.org.

Immunology↗

bioRxiv2014

Genomic V-gene repertoire in reptiles

Reptiles and mammals diverged over 300 million years ago, creating two parallel evolutionary lineages amongst terrestrial vertebrates. In reptiles, two main evolutionary lines emerged, one gave rise to Squamata, while the other gave rise to Testudines, Crocodylia and birds. In this study, we determined the genomic variable (V)-gene repertoire in reptiles corresponding to the three main immunoglobulin (Ig) loci and the four main T-cell receptor (TCR) loci. We show that squamata lack the TCR{gamma} /{delta} genes and snakes lack the V{kappa} genes. In representative species of testudines and crocodiles, the seven major Ig and TCR loci are maintained. As in mammals, genes of the Ig loci can be grouped into well-defined clans through a multi-species phylogenetic analysis. We show that the reptile VH and V{lambda} genes are distributed amongst the established mammalian clans, while their V{kappa} genes are found within a single clan, nearly exclusive from the mammalian sequences. The reptile and mammal V-genes of the TRA locus cluster into six common evolutionary clans. In contrast, the reptile V-genes from the TRB locus cluster into three clans, which have few mammalian members. In this locus, the V-gene sequences from mammals appear to have undergone different evolutionary diversification processes that occurred outside these shared reptile clans.

Immunology↗

bioRxiv2014

VgeneRepertoire.org identifies and stores variable genes of immunoglobulins and T-cell receptors from the genomes of jawed vertebrates

The VgeneRepertoire.org platform (http://vgenerepertoire.org) is a new public database repository for variable (V) gene sequences that encode immunoglobulin and T-cell receptor molecules. It identifies the nucleic and amino acid sequences of more than 20,000 genes, providing their exon location in either the contig, scaffold, or chromosome region, as well as locus information for more than 100 jawed vertebrate taxa whose genomes have been sequenced. This web repository provides support to immunologists interested in these molecules and aids in comparative phylogenetic studies.

Immunology↗