MHC Class II variability in bare-nosed wombats (Vombatus ursinus)
Julie M. Old A B , Eden M. Hermsen A and Lauren J. Young A
+ Author Affiliations
- Author Affiliations
A School of Science and Health, Hawkesbury, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia.
B Corresponding author. Email: j.old@westernsydney.edu.au
Australian Mammalogy 42(2) 135-143 https://doi.org/10.1071/AM19015
Submitted: 3 March 2019 Accepted: 14 May 2019 Published: 20 August 2019
Abstract
Studies of gene diversity are used to investigate population dynamics, including immunological fitness. Aside from the selection of an appropriate gene target, an important factor that underpins these studies is the ability to recover viable DNA samples from native animals that are protected, threatened or difficult to sample or locate such as the bare-nosed wombat (Vombatus ursinus). In this study, we used genomic DNA extracted from muscle tissue samples and also identified the optimal method to extract DNA from fresh wombat scat samples to enable further analyses to be performed using non-invasive techniques. The DNA was probed via the polymerase chain reaction using previously targeted marsupial Major Histocompatibility Complex (MHC) gene primers. These genes are highly variable and associated with binding and presentation of pathogens in the immune system. Twenty-three unique MHC Class II DAB V. ursinus gene sequences were translated to 21 unique predicted peptide sequences from 34 individual tissue or scat samples. Vombatus ursinus MHC Class II DAB gene and peptide sequences were most similar to other marsupial DNA and peptide sequences. Further analysis also indicated the likelihood of MHC Class II DAB family membership through motif identification. Additional sampling is required to assess the full level of diversity of MHC Class II DAB genes among V. ursinus populations; however, this study is the first to identify MHC genes in a wombat and will advance immunological and disease studies of the species.
Additional keywords: disease, immune system, marsupial, parasite.
References
Banks, S. C., Piggott, M. P., Hansen, B. D., Robinson, N. A., and Taylor, A. C. (2002). Wombat coprogenetics: enumerating a common wombat population by microsatellite analysis of faecal DNA. Australian Journal of Zoology 50, 193–204.| Wombat coprogenetics: enumerating a common wombat population by microsatellite analysis of faecal DNA.Crossref | GoogleScholarGoogle Scholar |
Bateson, Z. W., Hammerly, S. C., Johnson, J. A., Morrow, M. E., Whitingham, L. A., and Dunn, P. O. (2016). Specific alleles at immune genes, rather than genome-wide heterozygosity, are related to immunity and survival in the critically endangered Attwater’s prairie-chicken. Molecular Ecology 25, 4730–4744.
| Specific alleles at immune genes, rather than genome-wide heterozygosity, are related to immunity and survival in the critically endangered Attwater’s prairie-chicken.Crossref | GoogleScholarGoogle Scholar | 27485035PubMed |
Belov, K., Lam, M. K.-P., and Colgan, D. J. (2004). Marsupial MHC class II β genes are not orthologous to the eutherian b gene families. The Journal of Heredity 95, 338–345.
| Marsupial MHC class II β genes are not orthologous to the eutherian b gene families.Crossref | GoogleScholarGoogle Scholar | 15247314PubMed |
Belov, K., Deakin, J. E., Papenfuss, A. T., Baker, M. L., Melman, S. D., Siddle, H. V., Gouin, N., Goode, D. L., Sargeant, T. J., and Robinson, M. D. (2006). Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex. PLoS Biology 4, e46.
| Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex.Crossref | GoogleScholarGoogle Scholar | 16435885PubMed |
Belov, K., Miller, R. D., Old, J. M., and Young, L. J. (2013). Marsupial immunology bounding ahead. Australian Journal of Zoology 61, 24–40.
| Marsupial immunology bounding ahead.Crossref | GoogleScholarGoogle Scholar |
Benson, D. A., Cavanaugh, M., Clark, K., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., and Sayers, E. W. (2013). GenBank. Nucleic Acids Research 41, D36–D42.
| GenBank.Crossref | GoogleScholarGoogle Scholar | 23193287PubMed |
Bernatchez, L., and Landry, C. (2003). MHC studies in non model vertebrates: what have we learned about natural selection in 15 years? Journal of Evolutionary Biology 16, 363–377.
| MHC studies in non model vertebrates: what have we learned about natural selection in 15 years?Crossref | GoogleScholarGoogle Scholar | 14635837PubMed |
Brogden, J., Eckels, D., Davis, C., White, S., and Doyle, C. (1998). A site for CD4 binding in the β1 domain of the MHC Class II protein HLA-DR1. Journal of Immunology (Baltimore, Md.: 1950) 161, 5472–5480.
Brown, J. H., Jardetzky, T. S., Gorga, J. C., Stern, L. J., Urban, R. G., Strominger, J. L., and Wiley, D. C. (1993). Three-dimensional structure of the human Class II histocompatibility antigen HLA-DR1. Nature 364, 33–39.
| Three-dimensional structure of the human Class II histocompatibility antigen HLA-DR1.Crossref | GoogleScholarGoogle Scholar | 8316295PubMed |
Browning, T. L., Belov, K., Miller, R. D., and Eldridge, M. D. B. (2004). Molecular cloning and characterization of the polymorphic MHC Class II DBB from the tammar wallaby (Macropus eugenii). Immunogenetics 55, 791–795.
| Molecular cloning and characterization of the polymorphic MHC Class II DBB from the tammar wallaby (Macropus eugenii).Crossref | GoogleScholarGoogle Scholar | 14752580PubMed |
Cheng, Y., Sanderson, C., Jones, M., and Belov, K. (2012). Low MHC Class II diversity in the Tasmanian devil (Sarcophilus harrisii). Immunogenetics 64, 525–533.
| Low MHC Class II diversity in the Tasmanian devil (Sarcophilus harrisii).Crossref | GoogleScholarGoogle Scholar | 22460528PubMed |
Elbers, J. P., Brown, M. B., and Taylor, S. S. (2018). Identifying genome-wide immune gene variation underlying infectious disease in wildlife populations – a next generation sequencing approach in the gopher tortoise. BMC Genomics 19, 64.
| Identifying genome-wide immune gene variation underlying infectious disease in wildlife populations – a next generation sequencing approach in the gopher tortoise.Crossref | GoogleScholarGoogle Scholar | 29351737PubMed |
Ellison, A., Allainguillaume, J., Girdwood, S., Pachebat, J., Peat, K. M., Wright, P., and Consuegra, S. (2012). Maintaining functional major histocompatibility complex diversity under inbreeding: the case of a selfing vertebrate. Proceedings. Biological Sciences 279, 5004–5013.
| Maintaining functional major histocompatibility complex diversity under inbreeding: the case of a selfing vertebrate.Crossref | GoogleScholarGoogle Scholar | 23075838PubMed |
Fraser, T. A., Charleston, M., Martin, A., Polkinghorne, A., and Carver, S. (2016). The emergence of sarcoptic mange in Australian wildlife: an unresolved debate. Parasites & Vectors 9, 316.
| The emergence of sarcoptic mange in Australian wildlife: an unresolved debate.Crossref | GoogleScholarGoogle Scholar |
Gasteiger, E., Gattiker, A., Hoogland, C., Ivanyi, I., Appel, R. D., and Bairoch, A. (2003). ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Research 31, 3784–3788.
| ExPASy: the proteomics server for in-depth protein knowledge and analysis.Crossref | GoogleScholarGoogle Scholar | 12824418PubMed |
Gray, D. (1937). Sarcoptic mange affecting wild fauna in New South Wales. Australian Veterinary Journal 13, 154–155.
| Sarcoptic mange affecting wild fauna in New South Wales.Crossref | GoogleScholarGoogle Scholar |
Green, M. R., and Sambrook, J. (2012). ‘Molecular Cloning: A Laboratory Manual. Volume 1.’ (Cold Spring Harbour: New York.)
Gutierrez‐Espeleta, G. A., Hedrick, P. W., Kalinowski, S. T., Garrigan, D., and Boyce, W. M. (2001). Is the decline of desert bighorn sheep from infectious disease the result of low MHC variation? Heredity 86, 439–450.
| Is the decline of desert bighorn sheep from infectious disease the result of low MHC variation?Crossref | GoogleScholarGoogle Scholar | 11520344PubMed |
Hermsen, E. M., Young, L. J., and Old, J. M. (2017). Major Histocompatibility Complex Class II in the red-tailed phascogale (Phascogale calura). Australian Mammalogy 39, 28–32.
| Major Histocompatibility Complex Class II in the red-tailed phascogale (Phascogale calura).Crossref | GoogleScholarGoogle Scholar |
Holland, O. J., Cowan, P. E., Gleeson, D. M., and Chamley, L. W. (2008a). High variability in the MHC class II DA beta chain of the brushtail possum (Trichosurus vulpecula). Immunogenetics 60, 775–781.
| High variability in the MHC class II DA beta chain of the brushtail possum (Trichosurus vulpecula).Crossref | GoogleScholarGoogle Scholar | 18758765PubMed |
Holland, O. J., Cowan, P. E., Gleeson, D. M., and Chamley, L. W. (2008b). Novel alleles in classical major histocompatibility complex class II loci of the brushtail possum (Trichosurus vulpecula). Immunogenetics 60, 449–460.
| Novel alleles in classical major histocompatibility complex class II loci of the brushtail possum (Trichosurus vulpecula).Crossref | GoogleScholarGoogle Scholar | 18548245PubMed |
Kumar, S., Stecher, G., Li, M., Knyaz, C., and Tamura, K. (2018). MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Molecular Biology and Evolution 35, 1547–1549.
| MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms.Crossref | GoogleScholarGoogle Scholar | 29722887PubMed |
Lam, M. K. P., Belov, K., Harrison, G. A., and Cooper, D. W. (2001). Cloning of the MHC class II DRB cDNA from the brushtail possum (Trichosurus vulpecula). Immunology Letters 76, 31–36.
| Cloning of the MHC class II DRB cDNA from the brushtail possum (Trichosurus vulpecula).Crossref | GoogleScholarGoogle Scholar |
Lau, Q., Jobbins, S. E., Belov, K., and Higgins, D. P. (2013). Characterisation of four major histocompatibility complex class II genes of the koala (Phascolarctos cinereus). Immunogenetics 65, 37–46.
| Characterisation of four major histocompatibility complex class II genes of the koala (Phascolarctos cinereus).Crossref | GoogleScholarGoogle Scholar | 23089959PubMed |
Lau, Q., Jaratlerdsiri, W., Griffiths, J. E., Gongora, J., and Higgins, D. P. (2014). MHC Class II diversity of koala (Phascolarctos cinereus) populations across their range. Heredity 113, 287–296.
| MHC Class II diversity of koala (Phascolarctos cinereus) populations across their range.Crossref | GoogleScholarGoogle Scholar | 24690756PubMed |
Letunic, I., Doerks, T., and Bork, P. (2009). SMART 6: recent updates and new developments. Nucleic Acids Research 37, D229–D232.
| SMART 6: recent updates and new developments.Crossref | GoogleScholarGoogle Scholar | 18978020PubMed |
McIlroy, J. C. (1995). Common wombat. In ‘The Mammals of Australia’. (Eds S. Van Dyck, and R. Strahan.) pp. 204–205. (Australian Museum/Reed Books: Sydney.)
Meyer-Lucht, Y., Otten, C., Puttker, T., and Sommer, S. (2008). Selection, diversity and evolutionary patterns of the MHC class II DAB in free-ranging Neotropical marsupials. BMC Genetics 9, 39.
| Selection, diversity and evolutionary patterns of the MHC class II DAB in free-ranging Neotropical marsupials.Crossref | GoogleScholarGoogle Scholar | 18534008PubMed |
Meyer-Lucht, Y., Otten, C., Puttker, T., Pardini, R., Metzger, J. P., and Sommer, S. (2010). Variety matters: adaptive genetic diversity and parasite load in two mouse opossums from the Brazilian Atlantic forest. Conservation Genetics 11, 2001–2013.
| Variety matters: adaptive genetic diversity and parasite load in two mouse opossums from the Brazilian Atlantic forest.Crossref | GoogleScholarGoogle Scholar |
Morris, K., Austin, J. J., and Belov, K. (2013). Low major histocompatibility complex diversity in the Tasmanian devil predates European settlement and may explain susceptibility to disease epidemics. Biology Letters 9, 20120900.
| Low major histocompatibility complex diversity in the Tasmanian devil predates European settlement and may explain susceptibility to disease epidemics.Crossref | GoogleScholarGoogle Scholar | 23221872PubMed |
Morris, K. M., Wright, B., Grueber, C. E., Hogg, C., and Belov, K. (2015). Lack of genetic diversity across diverse immune genes in an endangered mammal, the Tasmanian devil (Sarcophilus harrisii). Molecular Ecology 24, 3860–3872.
| Lack of genetic diversity across diverse immune genes in an endangered mammal, the Tasmanian devil (Sarcophilus harrisii).Crossref | GoogleScholarGoogle Scholar | 26119928PubMed |
Nei, M., and Gojobori, T. (1986). Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Molecular Biology and Evolution 3, 418–426.
| 3444411PubMed |
Old, J. M., Hunter, N. E., and Wolfenden, J. (2018a). Who utilises bare-nosed wombat burrows? Australian Zoologist 39, 409–413.
| Who utilises bare-nosed wombat burrows?Crossref | GoogleScholarGoogle Scholar |
Old, J. M., Sengupta, C., Narayan, E., and Wolfenden, J. (2018b). Sarcoptic mange in wombats – a review and future research directions. Transboundary and Emerging Diseases 65, 399–407.
| Sarcoptic mange in wombats – a review and future research directions.Crossref | GoogleScholarGoogle Scholar | 29150905PubMed |
Pagni, M., Ioannidis, V., Cerutti, L., Zahn-Zabal, M., Jongeneel, C. V., and Falquet, L. (2004). MyHits: a new interactive resource for protein annotation and domain identification. Nucleic Acids Research 32, W332–W335.
| MyHits: a new interactive resource for protein annotation and domain identification.Crossref | GoogleScholarGoogle Scholar | 15215405PubMed |
Piggott, M. P., and Taylor, A. C. (2003). Remote collection of animal DNA and its application in conservation management and understanding the population biology of rare and cryptic species. Wildlife Research 30, 1–13.
| Remote collection of animal DNA and its application in conservation management and understanding the population biology of rare and cryptic species.Crossref | GoogleScholarGoogle Scholar |
Radwan, J., Biedrzycka, A., and Babik, W. (2010). Does reduced MHC diversity decrease viability of vertebrate populations? Biological Conservation 143, 537–544.
| Does reduced MHC diversity decrease viability of vertebrate populations?Crossref | GoogleScholarGoogle Scholar |
Roche, P. A., and Furuta, K. (2015). The ins and outs of MHC class II-mediated antigen processing and presentation. Nature Reviews. Immunology 15, 203–216.
| The ins and outs of MHC class II-mediated antigen processing and presentation.Crossref | GoogleScholarGoogle Scholar | 25720354PubMed |
Roger, E., Laffan, S.W., and Ramp, D. (2007). Habitat selection by the common wombat (Vombatus ursinus) in disturbed environments: implications for the conservation of a ‘common’ species. Biological Conservation 137, 437–449.
| Habitat selection by the common wombat (Vombatus ursinus) in disturbed environments: implications for the conservation of a ‘common’ species.Crossref | GoogleScholarGoogle Scholar |
Roger, E., Laffan, S. W., and Ramp, D. (2011). Road impacts a tipping point for wildlife populations in threatened landscapes. Population Ecology 53, 215–227.
| Road impacts a tipping point for wildlife populations in threatened landscapes.Crossref | GoogleScholarGoogle Scholar |
Saitou, N., and Nie, M. (1987). The neighbour-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4, 406–425.
| 3447015PubMed |
Schultz, J., Milpetz, F., Bork, P., and Ponting, C. P. (1998). SMART, a simple modular architecture research tool: identification of signaling domains. Proceedings of the National Academy of Sciences of the United States of America 95, 5857–5864.
| SMART, a simple modular architecture research tool: identification of signaling domains.Crossref | GoogleScholarGoogle Scholar | 9600884PubMed |
Siddle, H. V., Sanderson, C. E., and Belov, K. (2007). Characterization of major histocompatibility complex class I and class II genes from the Tasmanian devil (Sarcophilus harrisii). Immunogenetics 59, 753–760.
| Characterization of major histocompatibility complex class I and class II genes from the Tasmanian devil (Sarcophilus harrisii).Crossref | GoogleScholarGoogle Scholar | 17673996PubMed |
Siddle, H. V., Marzec, J., Cheng, Y., Jones, M., and Belov, K. (2010). MHC gene copy number variation in Tasmanian devils: implications for the spread of a contagious cancer. Proceedings. Biological Sciences 277, 2001–2006.
| MHC gene copy number variation in Tasmanian devils: implications for the spread of a contagious cancer.Crossref | GoogleScholarGoogle Scholar | 20219742PubMed |
Skerratt, L. F., Skerratt, J. H. L., Martin, R., and Handasyde, K. (2004). The effects of sarcoptic mange on the behaviour of wild common wombats (Vombatus ursinus). Australian Journal of Zoology 52, 331–339.
| The effects of sarcoptic mange on the behaviour of wild common wombats (Vombatus ursinus).Crossref | GoogleScholarGoogle Scholar |
Smith, S., Belov, K., and Hughes, J. (2010). MHC screening for marsupial conservation: extremely low levels of class II diversity indicate population vulnerability for an endangered Australian marsupial. Conservation Genetics 11, 269–278.
| MHC screening for marsupial conservation: extremely low levels of class II diversity indicate population vulnerability for an endangered Australian marsupial.Crossref | GoogleScholarGoogle Scholar |
Taggart, D., Martin, R., and Menkhorst, P. (2008). Vombatus ursinus. In ‘The IUCN Red List of Threatened Species. Vol. 24 March 2015’. Version 2014.3. (International Union for Conservation of Nature and Natural Resources.)
Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22, 4673–4680.
| CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.Crossref | GoogleScholarGoogle Scholar | 7984417PubMed |
Tsukamoto, K., Deakin, J. E., Graves, J. A. M., and Hashimoto, K. (2013). Exceptionally high conservation of the MHC class I-related gene, MR1, among mammals. Immunogenetics 65, 115–124.
| Exceptionally high conservation of the MHC class I-related gene, MR1, among mammals.Crossref | GoogleScholarGoogle Scholar | 23229473PubMed |
Weber, D. S., Stewart, B. S., Schienman, J., and Lehman, N. (2004). Major histocompatibility complex variation at three class II loci in the northern elephant seal. Molecular Ecology 13, 711–718.
| Major histocompatibility complex variation at three class II loci in the northern elephant seal.Crossref | GoogleScholarGoogle Scholar | 14871373PubMed |
Wedrowicz, F., Karsa, M., Mosse, J., and Hogan, F. E. (2013). Reliable genotyping of the koala (Phascolarctos cinereus) using DNA isolated from a single faecal pellet. Molecular Ecology Resources 13, 634–641.
| Reliable genotyping of the koala (Phascolarctos cinereus) using DNA isolated from a single faecal pellet.Crossref | GoogleScholarGoogle Scholar | 23582171PubMed |
Wolfenden, J., and Old, J.M. (2012). Taking action to improve wombat health on Emirates Estates Wolgan Conservation area. University of Western Sydney, Penrith.
Yuhki, N., and O’Brien, S. J. (1990). DNA variation of the mammalian major histocompatibility complex reflects genomic diversity and population history. Proceedings of the National Academy of Sciences of the United States of America 87, 836–840.
| DNA variation of the mammalian major histocompatibility complex reflects genomic diversity and population history.Crossref | GoogleScholarGoogle Scholar | 1967831PubMed |
