Tracing the origin of fish immunoglobulins.

We have studied the origin of immunoglobulin genes in fish. There are two evolutionary lines of bony fish, Actinopterygii and Sarcopterygii. The former gave rise to most of the current fish and the latter to the animals that went to land.

Immunoglobulins genes in Neoceratodus forsteri and Protopterus annectens explain the origin of the immunoglobulins of the animals that passed ashore.

Sarcopterygian fishes are a taxon of bony fishes. They include lungfish and coelacanths (six species of lungfish and two species of coelacanths). Evolutionary adaptations arose with these fish, such as the appearance of lungs and paired lobed fins that help them move over the bottom of the sea.

Gouania willdenowi is a teleost fish without immunoglobulin genes.

Immunoglobulin (Ig) genes encode antibodies in jawed vertebrates. They are essential elements of the adaptive immune response. Ig exists in soluble form or as part of the B cell membrane antigen receptor (BCR).

Immunoglobulin T genes in Actinopterygii.

In teleost fishes, there are three immunoglobulin isotypes named immunoglobulin M (IgM), D (IgD), and T (IgT). IgT was the last to be described in teleost fishes, and it is specific to them. From recent fish genomes, we identified and studied the immunoglobulin heavy chain genes in Actinopterygii.

Insights into the evolution of IG genes in Amphibians and reptiles.

Immunoglobulins are essential proteins of the immune system to neutralize pathogens. Gene encoding B cell receptors and antibodies (Ig genes) first appeared with the emergence of early vertebrates having a jaw, and are now present in all extant jawed vertebrates, or Gnathostomata. The genes have undergone evolutionary changes.

Iterative Variable Gene Discovery from Whole Genome Sequencing with a Bootstrapped Multiresolution Algorithm.

In jawed vertebrates, variable (V) genes code for antigen-binding regions of B and T lymphocyte receptors, which generate a specific response to foreign pathogens. Obtaining the detailed repertoire of these genes across the jawed vertebrate kingdom would help to understand their evolution and function. However, annotations of V-genes are known for only a few model species since their extraction is not amenable to standard gene finding algorithms.

Immunoglobulin genes in Primates.

Five classes of immunoglobulins are known to exist in mammals. The number of isotypes of classes G, E and A varies among species for unknown reasons. Here, a study of the presence of immunoglobulin genes in Primates was carried out from the genomes and transcriptomes deposited in the NCBI repository.

Immunoglobulin and T cell receptor genes in Chinese crocodile lizard Shinisaurus crocodilurus.

Squamata are reptiles that diverged from mammals 300 million years ago. During this period, the immunoglobulin (IG) and T lymphocyte receptor (TCR) genes evolved parallel to mammals. However, unlike mammals whose IG/TCR locus has retained a constant structure throughout evolution, Squamata have witnessed duplications, losses, and/or gains in the domains of their immunoglobulin genes.

Genomic structure and expression of immunoglobulins in Squamata.

The Squamata order represents a major evolutionary reptile lineage, yet the structure and expression of immunoglobulins in this order has been scarcely studied in detail. From the genome sequences of four Squamata species (Gekko japonicus, Ophisaurus gracilis, Pogona vitticeps and Ophiophagus hannah) and RNA-seq datasets from 18 other Squamata species, we identified the immunoglobulins present in these animals as well as the tissues in which they are found. All Squamata have at least three immunoglobulin classes; namely, the immunoglobulins M, D, and Y.

Amphibians have immunoglobulins similar to ancestral IgD and IgA from Amniotes.

We studied the immunoglobulin genes from either the genomes or RNAs of amphibians. In particular, we obtained data from one frog genome (Nanorana parkeri) and three transcriptomes of the Caudata order (Andrias davidianus, Notophthalmus viridescens and Cynops pyrrhogaster). Apart from the immunoglobulins IgM and IgY previously described, we identified several IgD related immunoglobulins.

Evolution of V genes from the TRV loci of mammals.

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.

An automated algorithm for extracting functional immunologic V-genes from genomes in jawed vertebrates.

Variable (V) domains of immunoglobulins (Ig) and T cell receptors (TCR) are generated from genomic V gene segments (V-genes). At present, such V-genes have been annotated only within the genome of a few species. We have developed a bioinformatics tool that accelerates the task of identifying functional V-genes from genome datasets.

IgH loci of American alligator and saltwater crocodile shed light on IgA evolution.

Immunoglobulin loci of two representatives of the order Crocodylia were studied from full genome sequences. Both Alligator mississippiensis and Crocodylus porosus have 13 genes for the heavy chain constant regions of immunoglobulins. The IGHC locus contains genes encoding four immunoglobulins M (IgM), one immunoglobulin D (IgD), three immunoglobulins A (IgA), three immunoglobulins Y (IgY), and two immunoglobulins D2 (IgD2).

Immunoglobulin light chains in medaka (Oryzias latipes).

The gene segments encoding antibodies have been studied in many capacities and represent some of the best-characterized gene families in traditional animal disease models (mice and humans). To date, multiple immunoglobulin light chain (IgL) isotypes have been found in vertebrates and it is unclear as to which isotypes might be more primordial in nature. Sequence data emerging from an array of fish genome projects is a valuable resource for discerning complex multigene assemblages in this critical branch point of vertebrate phylogeny.

Immunoglobulin genes of the turtles.

The availability of reptile genomes for the use of the scientific community is an exceptional opportunity to study the evolution of immunoglobulin genes. The genome of Chrysemys picta bellii and Pelodiscus sinensis is the first one that has been reported for turtles. The scanning for immunoglobulin genes resulted in the presence of a complex locus for the immunoglobulin heavy chain (IGH).

Snakes antibodies.

Immunoglobulins are basic molecules of the immune system of vertebrates. In previous studies we described the immunoglobulins found in two squamata reptiles, Anolis carolinensis and Eublepharis macularius. Snakes are squamata reptiles too but they have undergone an extreme evolutionary process.

Immunoglobulin heavy chains in medaka (Oryzias latipes).

Background: Bony fish present an immunological system, which evolved independently from those of animals that migrated to land 400 million years ago. The publication of whole genome sequences and the availability of several cDNA libraries for medaka (Oryzias latipes) permitted us to perform a thorough analysis of immunoglobulin heavy chains present in this teleost.

Results: We identified IgM and IgD coding ESTs, mainly in spleen, kidney and gills using published cDNA libraries but we did not find any sequence that coded for IgT or other heavy chain isotypes described in fish.

Presence of an unique IgT on the IGH locus in three-spined stickleback fish (Gasterosteus aculeatus) and the very recent generation of a repertoire of VH genes.

This study describes the IGH locus in Gasterosteus aculeatus, with 10 genes encoding three immunoglobulin classes: IgT, IgM and IgD. These genes are organized into a structure with three repeats of IGHT-IGHM-IGHD separated by segments including the VH segments. There was also a fourth IGHT gene.

The immunoglobulin heavy chain locus in the reptile Anolis carolinensis.

We describe the entire immunoglobulin heavy chain (IgH) locus from the reptile Anolis carolinensis. The heavy chain constant (C(H)) region includes C mu, C delta and C upsilon genes. This is the first description of a C upsilon gene in the reptilian class.

IgD in the reptile leopard gecko.

Immunoglobulin D (IgD) has been a mysterious antibody ever since it was discovered in mammals 40 years ago. It shares with IgM the role of antigen-receptor in the membrane of mature B cells. The absence of IgD in birds and its description in bony fishes contributed to the confusion about its evolutionary origins.

A novel IgA-like immunoglobulin in the reptile Eublepharis macularius.

The appearance of antibody genes over evolution coincided with the origin of the vertebrates. Reptiles are of great interest in evolution since they are the link between the amphibians, birds, and mammals. This work describes the presence of a gene in the reptile leopard gecko (Eublepharis macularius) where phylogenetic studies suggest that it is the gene orthologue of immunoglobulin A (IgA) and immunoglobulin X (IgX) in Xenopus.