The Mouse Genome Database (MGD): integrating biology with the genome.

The Mouse Genome Database (MGD) is one component of the Mouse Genome Informatics (MGI) system (http://www.informatics.jax.org), a community database resource for the laboratory mouse. MGD strives to provide a comprehensive knowledgebase about the mouse with experiments and data annotated from both literature and online sources. MGD curates and presents consensus and experimental data representations of genetic, genotype (sequence) and phenotype information including highly detailed reports about genes and gene products. Primary foci of integration are through representations of relationships between genes, sequences and phenotypes. MGD collaborates with other bioinformatics groups to curate a definitive set of information about the laboratory mouse and to build and implement the data and semantic standards that are essential for comparative genome analysis. Recent developments in MGD discussed here include an extensive integration of the mouse sequence data and substantial revisions in the presentation, query and visualization of sequence data.

Taxonomic hierarchy of HLA class I allele sequences.

The markedly high levels of polymorphism present in classical class I loci of the human major histocompatibility complex have been implicated in infectious and immune disease recognition. The large numbers of alleles present at these loci have, however, limited efforts to verify associations between individual alleles and specific diseases. As an approach to reduce allele diversity to hierarchical evolutionarily related groups, we performed phylogenetic analyses of available HLA-A, B and C allele complete sequences (n = 216 alleles) using different approaches (maximum parsimony, distance-based minimum evolution and maximum likelihood). Full nucleotide and amino acid sequences were considered as well as abridged sequences from the hypervariable peptide binding region, known to interact in vivo, with HLA presented foreign peptide. The consensus analyses revealed robust clusters of 36 HLA-C alleles concordant for full and PBR sequence analyses. HLA-A alleles (n = 60) assorted into 12 groups based on full nucleotide and amino acid sequence which with few exceptions recapitulated serological groupings, however the patterns were largely discordant with clusters prescribed by PBR sequences. HLA-B which has the most alleles (n = 120) and which unlike HLA-A and -C is thought to be subject to frequent recombinational exchange, showed limited phylogenetic structure consistent with recent selection driven retention of maximum heterozygosity and population diversity. Those allele categories recognized offer an explicit phylogenetic criterion for grouping alleles potentially relevant for epidemiologic associations, for inferring the origin of MHC genome organization, and for comparing functional constraints in peptide presentation of HLA alleles.

Hybridization between tammar wallaby (Macropus eugenii) populations from Western and South Australia.

Populations of tammar wallabies (Macropus eugenii) occur in southwest Western Australia and on five Australian offshore islands, four in Western Australia and one in South Australia. The South Australia and Western Australia populations have probably been isolated from each other for 50,000-100,000 years. Studies have shown that there are morphological and genetic differences between these populations. Attempts at mating individuals from Garden Island (Western Australia) with individuals from Kangaroo Island (South Australia) indicate that while the two populations can hybridize in captivity and F1 hybrids of both sexes are fertile, a barrier to successful reproduction between these two populations is in the initial stages of development.

SRY and karyotypic status of one abnormal and two intersexual marsupials.

An intersexual agile wallaby (Macropus agilis) with a penis, a pouch and four teats had a sex-chromosome constitution of XXY in lymphocytes and cultured fibroblasts; the sex-determining region Y (SRY) gene was present, consistent with the presence of a testis. An intersexual eastern grey kangaroo (Macropus giganteus) with a small empty scrotum and no penis, and an abnormal red kangaroo (Macropus rufus) with no penis, pouch or teats, both had XX sex-chromosome complements; the SRY gene was not present, consistent with testis absence. The agile wallaby and grey kangaroo described here provide further evidence that scrotal development in marsupials is independent of the Y chromosome. The cause of the abnormalities in the XX individuals cannot be determined until candidate genes are identified. These animals provide a basis for further genetic studies into marsupial intersexuality and sex differentiation.

Close linkage between RNR and GPD genes on the tammar wallaby (Macropus eugenii) X chromosome.

No recombination was detected between two X-linked loci, RNR (Xp) and GPD (Xq), among 69 backcross progeny of two distantly related tammar wallaby (Macropus eugenii) subspecies. RNR loci are not dosage compensated, whereas the GPD locus is subject to the paternal X chromosome inactivation system that characterises female marsupials. The border of the region controlled by the marsupial X chromosome inactivation system has therefore been shown to lie between RNR and GPD.

Higher female than male recombination rates in a marsupial mammal, the tammar wallaby (Macropus eugenii).

Previous work has shown that females have lower recombination rates than males in two distinctly related marsupial species, an American didelphid and an Australian dasyurid. We report here that the tammar wallaby (Macropus eugenii), which belongs to a third major group, has higher female recombination rates in two linked pairs. The nature of the sex differences in recombination rates in this species is thus similar to the situation in eutherian mammals.

Phosphoglycerate kinase pseudogenes in the tammar wallaby and other macropodid marsupials.

Phosphoglycerate kinase (EC 2.7.2.3; PGK) exists in two forms in marsupials. PGK1 is an X-linked house-keeping enzyme, and PGK2 is a mainly testis-specific enzyme under autosomal control. We have used PGK1 probes derived from two closely related species of macropodid marsupials (kangaroos and wallabies) to demonstrate the existence of a large family of pseudogenes in the tammar wallaby (Macropus eugenii). Over 30 fragments are detectable after Taq digestion. We estimate that there are 25-30 copies per genome. Most are autosomally inherited and are apparently not closely linked. Only two restriction fragments that appeared to be sex linked could be detected. Varying degrees of hybridization of fragments to the probes suggest different levels of homology, and hence different ages of origin. The existence of two PGK1 homologous restriction fragments from the X and a large number from the autosomes was also demonstrated by somatic cell hybridization for two other macropodid species, the wallaroo (M. robustus) and the red kangaroo (M. rufus). These results are compared with those from human and mouse, and it is suggested that the propensity of PGK1 to form pseudogenes is an ancient (approximately 130 MYR BP) characteristic of mammals. The high level of polymorphism detected in the tammar makes these PGK1 probes potentially useful for measuring genetic variability in this species and other macropodids.

Low MHC class II variability in a marsupial.

The major histocompatibility complex (MHC) loci have been shown to be highly polymorphic in most eutherian ('placental') species studied. Several hypotheses have been advanced for the maintenance of this exceptional level of genetic variation, one of which suggests that it is necessary for successful eutherian reproduction. Marsupials (metatherians) and eutherians are the only two groups of viviparous mammals, but their modes of reproduction are quite distinct. Although marsupials have placentae, they are generally shorter lived and less invasive than in eutherians. Other investigations have shown that genetic variation at marsupial MHC class I loci is probably high. Weak or non-existent mixed lymphocyte culture responses previously reported in several marsupial species have suggested a lack of class II variation. Data have therefore been collected on the level of restriction fragment length polymorphism at MHC class II beta-chain encoding loci of a marsupial, Macropus eugenii (the tammar wallaby). This level is shown to be low, between the level of MHC variation found in cheetahs and a population of lions with a restricted genetic base. Attention is drawn to the need to collect more data on the level of class II variability in both eutherians and marsupials, and to the potential of marsupials for understanding the relation, if any, between mode of reproduction and MHC variability.

Use of a subspecies cross for efficient development of a linkage map for a marsupial mammal, the tammar wallaby (Macropus eugenii).

The tammar wallaby (Macropus eugenii) has a 2n = 16 karyotype with an XX/XY female/male sex dimorphism. Female reproduction can be manipulated to produce up to five offspring per year. We have crossed two genetically distant subspecies of tammars, one from Kangaroo Island in South Australia, the other from Garden Island in Western Australia, to produce fertile F1 offspring of both sexes. Male F1 hybrids were crossed with female Kangaroo Island tammars to produce over 80 phase-known backcross progeny for linkage studies. Here we report detection of two linkage groups derived from these male recombination values. The first consists of alpha-lactalbumin and an anonymous tammar cDNA clone, pB72; the second contains the gene for a marsupial-specific milk protein (late lactation protein), the gene for lipoprotein lipase, and an anonymous cDNA clone, pB65. The gene for late lactation protein has previously been assigned to tammar chromosome 3.