The opossum genome: Insights and opportunities from an alternative mammal

Abstract

The strategic importance of the genome sequence of the gray, short-tailed opossum, Monodelphis domestica, accrues from both the unique phylogenetic position of metatherian (marsupial) mammals and the fundamental biologic characteristics of metatherians that distinguish them from other mammalian species. Metatherian and eutherian (placental) mammals are more closely related to one another than to other vertebrate groups, and owing to this close relationship they share fundamentally similar genetic structures and molecular processes. However, during their long evolutionary separation these alternative mammals have developed distinctive anatomical, physiologic, and genetic features that hold tremendous potential for examining relationships between the molecular structures of mammalian genomes and the functional attributes of their components. Comparative analyses using the opossum genome have already provided a wealth of new evidence regarding the importance of noncoding elements in the evolution of mammalian genomes, the role of transposable elements in driving genomic innovation, and the relationships between recombination rate, nucleotide composition, and the genomic distributions of repetitive elements. The genome sequence is also beginning to enlarge our understanding of the evolution and function of the vertebrate immune system, and it provides an alternative model for investigating mechanisms of genomic imprinting. Equally important, availability of the genome sequence is fostering the development of new research tools for physical and functional genomic analyses of M. domestica that are expanding its versatility as an experimental system for a broad range of research applications in basic biology and biomedically oriented research.Compilation and publication of the genome sequence of the gray short-tailed opossum, Monodelphis domestica, a metatherian (marsupial) mammal (Mikkelsen et al. 2007b), create unique opportunities for investigating the evolutionary processes that have shaped the structural and functional attributes of mammalian and other vertebrate genomes. These opportunities arise from both the unique phylogenetic position of metatherians in the vertebrate scheme and some fundamental characteristics of metatherians that distinguish them from other mammalian species.Modern mammals comprise three major lineages (Fig. 1). Judged from multiple nuclear sequence and mtDNA alignments, the most closely related of these, the Metatheria and Eutheria (placental mammals), diverged from their most recent common ancestor ∼173-190 million years ago (Mya) (Kumar and Hedges 1998;Woodburne et al. 2003;van Rheede et al. 2006). The other major clade, the Prototheria, of which the egg-laying monotremes (platypus and four species of echidnas) are the only living representatives, branched off 20-35 million years (Myr) prior to the metatherian-eutherian divergence (Phillips and Penny 2003;Woodburne et al. 2003;van Rheede et al. 2006). 2 By way of reference, the separation of mammals and birds occurred at least 310 Mya (d...

Genome-wide histone state profiling of fibroblasts from the opossum, Monodelphis domestica, identifies the first marsupial-specific imprinted gene

“…This creates "conflict" between paternal and maternal genomes for genes that influence resource allocation and is generally couched in terms of fetal growth regulation, and/or in neurologic development that can enhance or inhibit postnatal growth rates through variation in feeding competence [75,77-79]. The Conflict Model is pleasingly consistent with the known roles of several imprinted genes in fetal growth and postnatal nutritionally related behaviors, but for most imprinted genes agreement with the Conflict Model has been assumed rather than demonstrated [12]. …”

The opossum MHC genomic region revisited

“…The gray short-tailed opossum (Monodelphis domestica) is arguably one of the better-developed model marsupial species and has been useful for comparative immunology and biomedical research (Samollow 2008). M. domestica is currently used as a model for melanoma, developmental biology, spinal cord injury, and genetics of cholesterol regulation (Samollow 2008). Significantly, it is one of the few non-eutherian mammals for which a well-annotated whole genome sequence is available (Mikkelsen et al 2007).…”

“…Marsupials represent a lineage of mammals that diverged from the eutherians (placental mammals) over 150 million years ago and have provided insights into the evolution of mammalian MHC (Baker et al 2009;Belov et al 2006;Gouin et al 2006). The gray short-tailed opossum (Monodelphis domestica) is arguably one of the better-developed model marsupial species and has been useful for comparative immunology and biomedical research (Samollow 2008). M. domestica is currently used as a model for melanoma, developmental biology, spinal cord injury, and genetics of cholesterol regulation (Samollow 2008).…”

Genome Size Evolution: Sizing Mammalian Genomes

“…It appears quite clear that TEs constitute from at least 30% to more than half of the sequences of mammalian genomes [Lander et al, 2001;Han et al, 2007;Mikkelsen et al, 2007;Pontius et al, 2007]. Recently published genomes of 3 early diverged mammals, the platypus (Ornithorhynchus anatinus) [O'Brien, 2008;Warren et al ., 2008], the short-tailed opossum (Monodelphis domestica) [Mikkelsen et al, 2007;Samollow, 2008], and the tammar wallaby (Macropus eugenii) [Renfree et al, 2011] allow us to get a scent of the mode/tempo of the TE relationship in a well time-frameworked specific example of the evolution process. The platypus genome is composed of a large proportion ( ϳ 50%) of interspersed repeats [O'Brien, 2008;Warren et al, 2008] mostly represented by the still active LINE-2 and its non-autonomous companion, the mammalian-wide interspersed repeat (MIR).…”