The Monodelphis domestica

Genomic Resources


As the only full-draft sequence of a marsupial genome, the M. domestica genome assembly, MonDom5 is the most widely used non-eutherian mammal genome for studying the evolution and functional attributes of coding and non-coding genomic elements among mammals and across vertebrates generally; it is also crucially important as a template for assembling genome structures and gene models for other marsupial species.  Current annotation of MonDom5 is based almost exclusively on automated predictive algorithms with virtually no assistance from expressed sequence data.  OpossumBase furnishes novel information on transcripts from a broad variety of tissues, organs, and life stages that will facilitate  refinement of MonDom5 annotation by determining the genomic coordinates of expressed sequences, evaluating and improving existing gene models, and discovering previously unknown genes.

The form and content of this website is a work in progress and we welcome helpful suggestions from the research community for its improvement and expansion.

  1. Genetic/Genomic Resources
  2. Polymorphisms
  3. Additional Resources
  4. Data Downloads
  5. Methods and Protocols
  6. Cell Culture Methods
  7. Microsatellite Primers
  8. Transcriptome
  9. Tools
  10. Getting Started
  11. GBrowse Tutorial
  12. JBrowse Tutorial
  13. BLAST
  14. Genome Browsers
  15. GBrowse
  16. JBrowse

About Us

The Monodelphis Genome Database is supported by grant R24 RR014214 from the National Institutes of Health (NCRR) and is hosted at the University of Missouri.  If you have comments or if you wish to report a problem, please contact the  Monodelphis Genome Database Administrator.

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The Monodelphis domestica

Genomic Resources


  1. Systematics, Natural History, and Characteristics of M. domestica
  2. Metatherian mammals; alternatives for biologic research
  3. The gray, short tailed opossum
  4. Systematics
  5. Range and habits
  6. Opossum genome characteristics
  7. Husbandry and reproduction in the laboratory
  8. M. domestica research colonies
  9. M. domestica Research Community:

Metatherian mammals; alternatives for biologic research: Metatheria comprise one of three major subdivisions of modern mammals. Better known as marsupials, they form the sister-group to our own subdivision, the Eutheria (Figure 1). Consequent of this close relationship, marsupial and eutherian mammals share fundamentally similar lifestyles, physiology, genetic structures, and molecular processes. However, during the ~170 million years since the two groups diverged, each group has evolved its own distinctive morphologic, physiologic, and genetic variations on these elemental mammalian themes.

Figure 1.   Phylogenetic Context of Metatherian Mammals. Splitting topology and approximate divergence dates for some representative vertebrates. Divergence dates are point estimates based on data from multiple sources (for details, see Samollow 2008; Hedges and Kumar 2009).

The most obvious differences between marsupial and eutherian mammals relate to their reproductive characteristics. Both groups bear live young, but marsupail gestation is brief and the young are born at a stage of development equivalent to mid-gestation of eutherian infants (see reviews by Behringer et al. 2006; Selwood and Johnson 2006). Newborn marsupials exhibit a mix of advanced and delayed developmental features. For example, they have well-developed jaws and forelimbs, and an fully operational gut, but these co-occur with hind limbs that are little more than buds (Figure 2), absence of adaptive immune function, and a rudimentary nervous system that possesses remarkable powers of regeneration, including the capacity to fully heal spinal cord transactions for nearly two weeks post-partum (references in Samollow 2006; Samollow 2008). Newborn marsupials complete the majority of their ‘fetal’ development external to the mother, receiving nutrition and protective antibodies from their mother’s milk. In some species this period of external developmental  occurs within a protective pouch, the marsupium. These distinctive reproductive and developmental characteristics make marsupials excellent models for examining sexual differentiation and development; hormonal effects on reproductive physiology and behavior; ontogeny and evolution of placental structure and function; development of immune-related structures and immumocompentece; evolution of developmental patterning; growth and maturation of neuromotor systems; and many other phenomena that take place in utero in eutherian species, but occur during early post-partum stages in marsupials. 

Figure 2. Monodelphis domestica. A. Adult female. B. Female with a litter of 10 pups. The newborns are ~36 hours post-partum age. Note that M. domestica does not have a pouch. C. Detail of litter from panel B. D. Newborn, less than 12 hours post-partum age. Scale is 1 mm between marks. Photos: Larry Wadsworth, TAMU Media Resources. [Figure reproduced by permission from Samollow (2008) Genome Research, copyright 2009, Cold Spring Harbor Laboratory Press]

  • With regard to genetic characteristics, the metatherian-eutherian sister-group relationship provides a powerful comparative system for examining relationships between the molecular structures and functional attributes of mammalian genes and genomes by providing clear phylogenetic polarity for assessing the novelty or antiquity of genomic features, and for elucidating how variations in genomic structural elements contribute to differences in gene regulation, expression, and function.

  • The gray, short tailed opossum: The gray, short-tailed opossum, Monodelphis domestica is a South American marsupial that is used extensively as an experimental model for basic comparative and biomedically oriented research applications (reviewed by VandeBerg and Robinson 1997; Samollow 2006; 2008; VandeBerg and Williams-Blangero 2010). It is the only non-eutherian mammal for which a high-quality draft genome sequence currently exists (Mikkelsen et al. 2007). Informally known as the 'laboratory opossum', M. domestica is small (70-160 grams), grows rapidly (maturity at 5-6 months), is highly prolific (mean litter size of ~8; up to 3 litters per year), and has simple husbandry requirements (rodent cages and commercial feed). Owing to such favorable physical and reproductive characteristics, M. domestica has been raised in pedigreed laboratory colonies in North America and elsewhere for more than 30 years and is the predominant laboratory-bred research marsupial in the world today.

  • Systematics: M. domestica belongs to the family Didelphidae, which comprises ~95 species in 19 genera distributed across the Americas (Gardner 2008). There are some 20 named and another 5-10 unnamed species in the genus Monodelphis (Pine and Handley 2008) which, as a whole, ranges from southern Panama southward throughout most of South America east of the Andes crest. All members of this genus are pouchless.

  • Range and habits: M. domestica ranges from eastern Brazil, southwest into Bolivia, Paraguay, and Northern Argentina (Pine and Handley 2008). Although reported to be primarily terrestrial in the wild, it is a good climber and likely utilizes arboreal habitats opportunistically. It is nocturnal, becoming active at sundown, and is omnivorous, eating a variety of invertebrates and plant materials.

  • Opossum genome characteristics: The opossum genome comprises ~3.5-3.6 gigabases (Gb) of DNA, distributed among eight large autosomes and an X or Y sex chromosome (Figure 3). The autosomes range in size from ~261 to ~748 megabases (Mb). The X and Y chromosomes are ~79 Mb and ~15 Mb, respectively. Detailed description of the opossum genome sequence and revelations therefrom can be found in Mikkelson (2007), several companion publications (e.g., Duke et al. 2007; Gentles et al. 2007; Goodstadt et al. 2007; Gu et al. 2007), and follow-up summaries (Samollow 2008; Samollow 2009).

  • Figure 3. The chromosomes of Monodelphis domestica. Main Panel A: Ideograms of M. domestica autosomes 1 – 8 and X and Y sex chromosomes, based on patterns modified from Pathak et al. (1993) (used by kind permission of Springer Science and Business Media). Orientation: p arm at top; q arm at bottom; centromere position indicated by constriction. Chromosome sizes are estimated total lengths (Mikkelesen et al 2007). Inset B. Inverted DAPI-banded mid-metaphase chromosomes from a female M. domestica peripheral lymphocyte (photograph courtesy of Matthew Breen, North Carolina State University). [Figure reproduced by permission from Samollow (2009) Encyclopedia of Life Sciences, copyright 2009, John Wiley & Sons, Ltd DOI: 10.1002/9780470015902.a2201781]

  • Husbandry and reproduction in the laboratory: M. domestica are easily maintained and bred in captivity under unremarkable conditions and are maintained in Research Colonies worldwide. Several descriptions of care and breeding in laboratory settings have been published. The most comprehensive and recent of these is by VandeBerg and Williams-Blangero (2010) who discuss life history, reproduction and growth, caging, nutrition, breeding, disease and veterinary care, laboratory practices, and the origins and histories of the various stocks and strains that have been developed for this species. Although each colony has it’s own variant procedures for care, feeding, and breeding of M. domestica, the paper by VandeBerg and Williams-Blangero is a good starting point for anyone planning to initiate their own colony. A recent description of general physiologic and bacteriologic parameters may be found in Evans et al. (2010) 

Monodelphis domestica research colonies: Please visit the Research Colonies page for more information.  

Monodelphis domestica users: Please visit the Research Community page for more information.  


Behringer, R.R., Eakin, G.S., and Renfree, M.B. 2006. Mammalian diversity: gametes, embryos and reproduction. Reprod., Fertil. and Dev. 18: 99-107.

Duke, S.E., Samollow, P.B., Mauceli, E., Lindblad-Toh, K., and Breen, M. 2007. Integrated cytogenetic BAC map of the genome of the gray, short-tailed opossum, Monodelphis domestica. Chromosome Res. 15: 361-370.

Evans, K.D., Hewett, T.A., Clayton, C.J., Krubitzer, L.A., and Griffey, S.M. 2010. Normal organ weights, serum chemistry, hematology, and cecal and nasopharyngeal bacterial cultures in the gray short-tailed opossum (Monodelphis domestica). J Am Assoc Lab Anim Sci 49: 401-406.

Gardner, A.L. 2008. Cohort Marsupialia. pp1-3. In Marsupials opf South America (ed. Gardner, A.L.). University of Chicago Press, Chicago.

Gentles, A.J., Wakefield, M.J., Kohany, O., Gu, W., Batzer, M.A., Pollock, D.D., and Jurka, J. 2007. Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica. Genome Res. 17: 992-1004.

Goodstadt, L., Heger, A., Webber, C., and Ponting, C.P. 2007. An analysis of the gene complement of a marsupial, Monodelphis domestica: evolution of lineage-specific genes and giant chromosomes. Genome Res. 17: 969-981.

Gu, W., Ray, D.A., Walker, J.A., Barnes, E.W., Gentles, A.J., Samollow, P.B., Jurka, J., Batzer, M.A., and Pollock, D.D. 2007. SINEs, evolution and genome structure in the opossum. Gene 396: 46-58.

Hedges, S.B. and Kumar, S. 2009. The Timetree of Life. The Oxford University Press., Oxford.

Mikkelsen, T.S., Wakefield, M.J., Aken, B., Amemiya, C.T., Chang, J.L., Duke, S., Garber, M., Gentles, A.J., Goodstadt, L., Heger, A. et al. 2007. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 447: 167-177.

Pathak, S., Ronne, M., Brown, N.M., Furlong, C.L., and VandeBerg, J.L. 1993. A high-resolution banding pattern idiogram of Monodelphis domestica chromosomes (Marsupialia, Mammalia). Cytogenet. Cell Genet. 63: 181-184.

Pine, R.H. and Handley, C.O., Jr. 2008. Genus Monodelphis. pp 82-107. In Marsupials of South America (ed. Gardner, A.L.), pp. 82-107. University of Chicago Press, Chicago.

Samollow, P.B. 2006. Status and applications of genomic resources for the gray, short-tailed opossum, Monodelphis domestica, an American marsupial model for comparative biology. Aust. J. Zool. 54: 173-196.

Samollow, P.B. 2008. The opossum genome: insights and opportunities from an alternative mammal. Genome Res. 18: 1199-1215.

Samollow, P.B. 2009. Evolution and characteristics of the opossum genome. In Encyclopedia of Life Sciences (ELS). John Wiley & Sons, Ltd., Chichester.

Selwood, L. and Johnson, M.H. 2006. Trophoblast and hypoblast in the monotreme, marsupial and eutherian mammal: evolution and origins. Bioessays 28: 128-145.

VandeBerg, J.L. and Robinson, E.S. 1997. The laboratory opossum (Monodelphis domestica) in laboratory research. ILAR Journal 38: 4-12.

VandeBerg, J.L. and Williams-Blangero, S. 2010. The laboratory opossum (Monodelphis domestica). Chapter 19. pp 246-261. In UFAW Handbook on the Care and Management of Laboratory and Other Research Animals. 8th edition. (eds. Hubrecht, R. and Kirkwood, J.). John Wiley & Sons, Ltd., Chichester.
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Building Polymorphisms

Genetic Polymorphisms of Monodelphis domestica: Several kinds of genetic polymorphisms have been described for the opossum model.  Polymorphisms are listed below by category and links are provided to tables and corresponding publications and websites where information about these polymorphisms can be obtained.

Coding-gene polymorphisms

Protein polymorphisms: Information and references for coding-gene polymorphisms detected by protein electrophoresis techniques. 

    Download Polymorphisms PROTEIN.xls

DNA polymorphisms: Information and references for coding gene polymorphisms detected by PCR-based analyses.

    Download Polymorphisms DNA.xls.

Anonymous polymorphisms

Short-tandem repeat (STR) polymorphisms: Information and references for short-tandem repeat (microsatellite) polymorphisms.

    Download Polymorphisms MICROSATS.xls

Non-repeat DNA polymorphisms: Information and references for unique sequence anonymous DNA polymorphisms.

     Download Polymorphisms NON_REPEAT.xls

Single nucleotide polymorphisms: A catalog of ~1.28 million potential single-nucleotide polymorphism (SNP) sites discovered in connection with the opossum genome project may be found at http://www.broad.mit.edu/mammals/opossum/snps.html. These putative SNPs were discovered by comparing reads from animals derived from different geographic origins with the sequence of the animal used to produce the genome assembly (MonDom5). The comparisons suggest an average SNP density in the range of one every 237 bp (1/237 bp) throughout the M. domestica genome, ranging from a low of 1/358 bp to a high of 1/140 bp depending on the animal compared. As expected, the frequency of SNPs correlates well with the geographic distance between the ancestral origins of test animals relative to that of the MonDom5 assembly animal.

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