To explore the origins and consequences of tetraploidy in the African clawed frog, we sequenced the Xenopus laevis genome and compared it to the related diploid X. tropicalis genome. We demonstrate the allotetraploid origin of X. laevis by partitioning its genome into two homeologous subgenomes, marked by distinct families of “fossil” transposable elements. Based on the activity of these elements and the age of hundreds of unitary pseudogenes, we estimate that the two diploid progenitor species diverged ~34 million years ago (Mya) and combined to form an allotetraploid ~17–18 Mya. 56% of all genes are retained in two homeologous copies. Protein function, gene expression, and the amount of flanking conserved sequence all correlate with retention rates. The subgenomes have evolved asymmetrically, with one chromosome set more often preserving the ancestral state and the other experiencing more gene loss, deletion, rearrangement, and reduced gene expression.

The western clawed frog Xenopus tropicalis is an important model for vertebrate development that combines experimental advantages of the African clawed frog Xenopus laevis with more tractable genetics. Here we present a draft genome sequence assembly of X. tropicalis. This genome encodes over 20,000 protein-coding genes, including orthologs of at least 1,700 human disease genes. Over a million expressed sequence tags validated the annotation. More than one-third of the genome consists of transposable elements, with unusually prevalent DNA transposons. Like other tetrapods, the genome contains gene deserts enriched for conserved non-coding elements. The genome exhibits remarkable shared synteny with human and chicken over major parts of large chromosomes, broken by lineage-specific chromosome fusions and fissions, mainly in the mammalian lineage.

The emergence of jawed vertebrates (gnathostomes) from jawless vertebrates was accompanied by major morphological and physiological innovations, such as hinged jaws, paired fins and immunoglobulin-based adaptive immunity. Gnathostomes subsequently diverged into two groups, the cartilaginous fishes and the bony vertebrates. Here we report the whole-genome analysis of a cartilaginous fish, the elephant shark (Callorhinchus milii). We find that the C. milii genome is the slowest evolving of all known vertebrates, including the ‘living fossil’ coelacanth, and features extensive synteny conservation with tetrapod genomes, making it a good model for comparative analyses of gnathostome genomes. Our functional studies suggest that the lack of genes encoding secreted calcium-binding phosphoproteins in cartilaginous fishes explains the absence of bone in their endoskeleton. Furthermore, the adaptive immune system of cartilaginous fishes is unusual: it lacks the canonical CD4 co-receptor and most transcription factors, cytokines and cytokine receptors related to the CD4 lineage, despite the presence of polymorphic major histocompatibility complex class II molecules. It thus presents a new model for understanding the origin of adaptive immunity.

Xenopus laevis is the model of choice for evolutionary, comparative, and developmental studies of immunity, and invaluable research tools including MHC-defined clones, inbred strains, cell lines, and monoclonal antibodies are available for these studies. Recent efforts to use Silurana (Xenopus) tropicalis for genetic analyses have led to the sequencing of the whole genome. Ongoing genome mapping and mutagenesis studies will provide a new dimension to the study of immunity. Here we review what is known about the immune system of X. laevis integrated with available genomic information from S. tropicalis. This review provides compelling evidence for the high degree of similarity and evolutionary conservation between Xenopus and mammalian immune systems. We propose to build a powerful and innovative comparative biomedical model based on modern genetic technologies that takes take advantage of X. laevis and S. tropicalis, as well as the whole Xenopus genus.

IgD has remained a mysterious Ig class and a bane to immunology students since its discovery >40 years ago. Its spotty occurrence in mammals and birds and the discovery of an isotype with similarities to IgD in bony fish are perplexing. We have identified IgD heavy (H) chain (␦) from the amphibian Xenopus tropicalis during examination of the IgH locus. The Xenopus ␦ gene is in the same position, immediately 3 of the IgM gene, as in mammals, and it is expressed only in the spleen at low levels, primarily as a transmembrane receptor by surface IgM ؉ cells. Our data suggest that frog IgD is expressed on mature B cells, like in mouse͞human. Unexpectedly, Xenopus IgD is orthologous to IgW, an Ig isotype found only in cartilaginous fish and lungfish, demonstrating that IgD͞W, like IgM, was present in the ancestor of all living jawed vertebrates. In striking contrast to IgM, IgD͞W is evolutionarily labile, showing many duplications͞deletions of domains, the presence of multiple splice forms, existence as predominantly a secretory or transmembrane form, or loss of the entire gene in a species-specific manner. Our study suggests that IgD͞W has played varied roles in different vertebrate taxa since the inception of the adaptive immune system, and it may have been preserved as a flexible locus over evolutionary time to complement steadfast IgM.evolution ͉ immune system S ince the pioneering work of comparative immunologists in the 1960s, IgM has been the Ig isotype believed to be primordial and most stable in vertebrate evolution (1). Despite differences in the degree of polymerization of the secretory form in different vertebrate groups (1, 2) and a major splice variant of the transmembrane (TM) form in teleost fish (3), IgM is renowned for its molecular, biochemical, and functional stability. Present in all living jawed vertebrates, IgM is the first isotype to be expressed both in ontogeny and during humoral adaptive immune responses and is found as the major TM receptor on the surface of both conventional and ''innate'' B cells (4).By contrast, IgD has remained an enigmatic isotype since its discovery long ago (5). Like IgM, IgD is expressed as a TM receptor on B cells of mouse and human, generated as a result of alternative splicing of pre-mRNA containing the transcribed variable (V) region and the IgM and IgD heavy (H) chain constant (C) regions ( and ␦, respectively). Because of its spotty presence in mammals and absence in birds, IgD was assumed to be a recently evolved isotype (6). However, the discovery of an isotype in ray-finned bony fish with sequence similarity to IgD (7) and its presence in some mammals previously believed to lack IgD (8) have greatly modified our view of Ig isotype evolution and suggested it may have arisen much earlier.A similarly strange phylogenetic jump surrounds the isotype IgW, which was discovered first in skates (9, 10) and later in sharks (11,12). The secreted version of the IgW H chain ( ) is present in long and short forms in all elasmobranchs tested to date, and the TM form is al...