Biology subjects

David N Olivieri

Publications and source records attributed to David N Olivieri.

4 recordsLinked to original sources

bioRxiv2014

V genes in primates from whole genome shotgun data

The adaptive immune system uses V genes for antigen recognition. The evolutionary diversification and selection processes within and across species and orders are poorly understood. Here, we studied the amino acid (AA) sequences obtained of 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 clade. 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 co-evolutionary pressures can explain the phylogenetic results, as seen in genes of the TR loci. We describe how each of the 35 V genes clades of the TRA locus and 25 clades of the TRB locus must have specific and necessary roles for the viability of the species.

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↗