, Volume 70, Issue 5, pp 327–336 | Cite as

Transcriptome sequencing of the long-nosed bandicoot (Perameles nasuta) reveals conservation and innovation of immune genes in the marsupial order Peramelemorphia

  • Katrina M. Morris
  • Haylee J. Weaver
  • Denis O’Meally
  • Marion Desclozeaux
  • Amber Gillett
  • Adam Polkinghorne
Short Communication


Bandicoots are omnivorous marsupials of the order Peramelemorphia. Conservation concerns and their unique biological characteristics suggest peramelomorphs are worthy research subjects, but knowledge of their genetics and immunology has lagged behind that of other high-profile marsupials. Here, we characterise the transcriptome of the long-nose bandicoot (Perameles nasuta), the first high-throughput data set from any peramelomorph. We investigate the immune gene repertoire of the bandicoot, with a focus on key immune gene families, and compare to previously characterised marsupial and mammalian species. We find that the immune gene complement in bandicoot is often conserved with respect to other marsupials; however, the diversity of expressed transcripts in several key families, such as major histocompatibility complex, T cell receptor μ and natural killer cell receptors, appears greater in the bandicoot than other Australian marsupials, including devil and koala. This transcriptome is an important first step for future studies of bandicoots and the bilby, allowing for population level analysis and construction of bandicoot-specific immunological reagents and assays. Such studies will be critical to understanding the immunology and physiology of Peramelemorphia and to inform the conservation of these unique marsupials.


Marsupial Metatherian Immunity Transcriptome 



This study was partially funded by a University of the Sunshine Coast internal seed grant to HJW.

Compliance with ethical standards

Ethical approval

All applicable international, national, and/or institutional guidelines for the care and use of animals were followed. All procedures performed in studies involving animals were in accordance with the ethical standards of the institution or practice at which the studies were conducted.

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

251_2017_1043_MOESM1_ESM.xlsx (35 kb)
Online Resource 1 List of all bandicoot transcripts analysed in this study (Sheet 1), number of genes mapping to GOSlim terms (Sheet 2), number of genes mapping to GO terms under the ‘immune system process’ category (Sheet 3) and accession numbers of sequences used in phylogenies (Sheets 4–11). (XLSX 34 kb).
251_2017_1043_MOESM2_ESM.pdf (387 kb)
Online Resource 2 Phylogeny of XCL chemokine sequences. The phylogenetic tree was constructed using the maximum-likelihood method and the Jones-Thornton-Taylor (JTT) model (Jones et al. 1992), and evaluation through 500 bootstrap replicates in MEGA6. Bootstrap values <%50 not displayed. Pena = bandicoot (Perameles nasuta; red circles); Saha = devil (Sarcophilus harrisii; green triangles; Modo = opossum (Monodelphis domestica; yellow diamonds); Hosa = human (Homo sapiens; blue squares); Accession numbers for sequences used can be found in Online Resource 1. (PDF 387 kb).
251_2017_1043_MOESM3_ESM.pdf (120 kb)
Online Resource 3 Phylogeny of CCL chemokine sequences. The phylogenetic tree was constructed using the maximum-likelihood method and the Jones-Thornton-Taylor (JTT) model (Jones et al. 1992), and evaluation through 500 bootstrap replicates in MEGA6. Bootstrap values <%50 not displayed. Pena = bandicoot (Perameles nasuta; red circles); Saha = devil (Sarcophilus harrisii; green triangles; Modo = opossum (Monodelphis domestica; yellow diamonds); Hosa = human (Homo sapiens; blue squares). Accession numbers for sequences used can be found in Online Resource 1. (PDF 120 kb).
251_2017_1043_MOESM4_ESM.pdf (467 kb)
Online Resource 4 Phylogeny of LRC sequences. Individual Ig domains from each LRC sequence were extracted and aligned using MUSCLE. The phylogenetic tree was constructed using the maximum-likelihood method and the Jones-Thornton-Taylor (JTT) model (Jones et al. 1992), and evaluation through 500 bootstrap replicates in MEGA6. Bootstrap values <%50 not displayed. Pena = bandicoot (Perameles nasuta; red circles); Saha = devil (Sarcophilus harrisii; green triangles; Modo = opossum (Monodelphis domestica; yellow circles); Hosa = human (Homo sapiens; blue squares); Phci = koala (Phascolarctus cinerius; pink triangles); Mumu = mouse (Mus musculus; purple squares). Accession numbers for sequences used can be found in Online Resource 1. (PDF 467 kb).
251_2017_1043_MOESM5_ESM.pdf (21 kb)
Online Resource 5 Phylogeny of UT sequences. The phylogenetic tree was constructed using the maximum-likelihood method and the Jones-Thornton-Taylor (JTT) model (Jones et al. 1992), and evaluation through 500 bootstrap replicates in MEGA6. Bootstrap values <%50 not displayed. Pena = bandicoot (Perameles nasuta; red circles); Saha = devil (Sarcophilus harrisii; green triangles; Modo = opossum (Monodelphis domestica; yellow diamonds); Maeu = wallaby (Notamacropus eugenii; cyan triangles); Oran = platypus (Ornithorhynchus anatinus; black diamonds). Accession numbers for sequences used can be found in Online Resource 1. (PDF 20 kb).


  1. Abts KC, Ivy JA, DeWoody JA (2015) Immunomics of the koala (Phascolarctos cinereus). Immunogenetics 67(5-6):305–321. CrossRefPubMedGoogle Scholar
  2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410. CrossRefPubMedGoogle Scholar
  3. Beck RMD (2008) A dated phylogeny of marsupials using a molecular supermatrix and multiple fossil constraints. J Mammal 89(1):175–189. CrossRefGoogle Scholar
  4. Belov K, Deakin JE, Papenfuss AT, Baker ML, Melman SD, Siddle HV, Gouin N, Goode DL, Sargeant TJ, Robinson MD, Wakefield MJ, Mahony S, Cross JG, Benos PV, Samollow PB, Speed TP, Graves JA, Miller RD (2006) Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex. PLoS Biol 4:e46CrossRefPubMedPubMedCentralGoogle Scholar
  5. Belov K, Sanderson CE, Deakin JE, Wong ES, Assange D, McColl KA, Gout A, de Bono B, Barrow AD, Speed TP, Trowsdale J (2007) Characterization of the opossum immune genome provides insights into the evolution of the mammalian immune system. Genome Res 17:982–991CrossRefPubMedPubMedCentralGoogle Scholar
  6. Bennett MD, Woolford L, O'Hara AJ, Nicholls PK, Warren K, Hobbs RP (2006) A new Eimeria species parasitic in western barred bandicoots, Perameles bougainville (Marsupialia: Peramelidae), in western Australia. J Parasitol 92(6):1292–1294. CrossRefPubMedGoogle Scholar
  7. Bennett MD, Woolford L, O'Hara AJ, Nicholls PK, Warren KS, Friend JA, Swan RA (2007) Klossiella quimrensis (Apicomplexa: Klossiellidae) causes renal coccidiosis in western barred bandicoots Perameles bougainville (Marsupialia: Peramelidae) in Western Australia. J Parasitol 93(1):89–92. CrossRefPubMedGoogle Scholar
  8. Boyle EI, Weng S, Gollub J, Jin H, Botstein D, Cherry JM, Sherlock G (2004) GO::TermFinder—open source software for accessing gene ontology information and finding significantly enriched gene ontology terms associated with a list of genes. Bioinformatics 20(18):3710–3715. CrossRefPubMedPubMedCentralGoogle Scholar
  9. Brocker C, Thompson D, Matsumoto A, Nebert DW, Vasiliou V (2010) Evolutionary divergence and functions of the human interleukin (IL) gene family. Hum Genomics 5(1):30–55. CrossRefPubMedPubMedCentralGoogle Scholar
  10. Cheng Y, Sanderson C, Jones M, Belov K (2012a) Low MHC class II diversity in the Tasmanian devil (Sarcophilus harrisii). Immunogenetics 64(7):525–533. CrossRefPubMedGoogle Scholar
  11. Cheng Y, Stuart A, Morris K, Taylor R, Siddle H, Deakin J, Jones M, Amemiya CT, Belov K (2012b) Antigen-presenting genes and genomic copy number variations in the Tasmanian devil MHC. BMC Genomics 13(1):87. CrossRefPubMedPubMedCentralGoogle Scholar
  12. Cui J, Cheng Y, Belov K (2015) Diversity in the toll-like receptor genes of the Tasmanian devil (Sarcophilus harrisii). Immunogenetics 67(3):195–201. CrossRefPubMedGoogle Scholar
  13. Delneste Y, Beauvillain C, Jeannin P (2007) Innate immunity: structure and function of TLRs. Med Sci 23:67–73Google Scholar
  14. DoEE (2017) EPBC Act List of Threatened Fauna. Department of Environment and Energy, CanberraGoogle Scholar
  15. Franchi L, Warner N, Viani K, Nuñez G (2009) Function of nod-like receptors in microbial recognition and host defense. Immunol Rev 227(1):106–128. CrossRefPubMedPubMedCentralGoogle Scholar
  16. Gemmell RT, Cepon G, Green PE, Stewart NP (1991) Some effects of tick infestations on juvenile northern brown bandicoot (Isoodon macrourus). J Wildl Dis 27(2):269–275. CrossRefPubMedGoogle Scholar
  17. Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, MacManes MD (2013) De novo transcript sequence reconstruction from RNA-seq using the trinity platform for reference generation and analysis. Nat Protoc 8(8):1494–1512. CrossRefPubMedGoogle Scholar
  18. Hayman DL, Martin PG (1965) Sex chromosome mosaicism in the marsupial genera Isoodon and Perameles. Genetics 52(6):1201–1206PubMedPubMedCentralGoogle Scholar
  19. Herberman RB (1986) Natural killer cells. Annu Rev Med 37(1):347–352. CrossRefPubMedGoogle Scholar
  20. Hewavisenti RV, Morris KM, O'Meally D, Cheng Y, Papenfuss AT, Belov K (2016) The identification of immune genes in the milk transcriptome of the Tasmanian devil (Sarcophilus harrisii). PeerJ 4:e1569. CrossRefPubMedPubMedCentralGoogle Scholar
  21. Hobbs M, Pavasovic A, King A, Prentis P, Eldridge M, Chen Z, Colgan D, Polkinghorne A, Wilkins M, Flanagan C, Gillett A, Hanger J, Johnson R, Timms P (2014) A transcriptome resource for the koala (Phascolarctos cinereus): insights into koala retrovirus transcription and sequence diversity. BMC Genomics 15(1):786. CrossRefPubMedPubMedCentralGoogle Scholar
  22. Janeway CA, Travers P, Walport M, Shlomchik MJ (2001) Immunobiology, 5th edn. Garland Science, New York and LondonGoogle Scholar
  23. Jones DT, Taylor WR, Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Bioinformatics 8(3):275-282Google Scholar
  24. Klein J, Hoøejsí V (1997) Immunology. Blackwell Science, OxfordGoogle Scholar
  25. Laing KJ, Secombes CJ (2004) Chemokines. Dev Comp Immunol 28(5):443–460. CrossRefPubMedGoogle Scholar
  26. Leary T, Wright D, Hamilton Z, Singadan R et al (2016) IUCN red list of threatened species. Version 2016. International Union for Conservation of Nature. Accessed 01 July 2017
  27. Mackerras IM, Mackerras MJ, Sandars DF (1953) Parasites of the bandicoot, Isoodon obesulus. Proc R Soc Queensl 63:61–63Google Scholar
  28. Marsh SGE, Albert ED, Bodmer WF, Bontrop RE, Dupont B, Erlich HA, Fernández-Viña M, Geraghty DE, Holdsworth R, Hurley CK, Lau M, Lee KW, Mach B, Maiers M, Mayr WR, Müller CR, Parham P, Petersdorf EW, Sasazuki T, Strominger JL, Svejgaard A, Terasaki PI, Tiercy JM, Trowsdale J (2010) Nomenclature for factors of the HLA system. Tiss Ant 75(4):291–455. CrossRefGoogle Scholar
  29. Miller RD (2010) Those other mammals: the immunoglobulins and T cell receptors of marsupials and monotremes. Semin Immunol 22(1):3–9. CrossRefPubMedGoogle Scholar
  30. Mitchell KJ, Pratt RC, Watson LN, Gibb GC, Llamas B, Kasper M, Edson J, Hopwood B, Mlae D, Armstrong KN, Meyer M, Hofreiter M, Austin J, Donnellan SC, Lee MSY, Phillips MJ, Cooper A (2014) Molecular phylogeny, biogeography and habitat preference evolution of marsupials. Mol Biol Evol 31(9):2322–2330. CrossRefPubMedGoogle Scholar
  31. Morris K, Prentis PJ, O’Meally D, Pavasovic A, Brown AT, Timms P, Belov K, Polkinghorne A (2014) The koala immunological toolkit: sequence identification and comparison of key markers of the koala (Phascolarctos cinereus) immune response. Aust J Zool 62(3):195–199. CrossRefGoogle Scholar
  32. Morris KM, Cheng Y, Warren W, Papenfuss AT, Belov K (2015a) Identification and analysis of divergent immune gene families within the Tasmanian devil genome. BMC Genomics 16(1):1017. CrossRefPubMedPubMedCentralGoogle Scholar
  33. Morris KM, Mathew M, Waugh C, Ujvari B, Timms P, Polkinghorne A, Belov K (2015b) Identification, characterisation and expression analysis of natural killer receptor genes in chlamydia pecorum infected koalas (Phascolarctos cinereus). BMC Genomics 16(1):796. CrossRefPubMedPubMedCentralGoogle Scholar
  34. Morris KM, Wright B, Grueber CE, Hogg C, Belov K (2015c) Lack of genetic diversity across diverse immune genes in an endangered mammal, the Tasmanian devil (Sarcophilus harrisii). Mol Ecol 24(15):3860–3872. CrossRefPubMedGoogle Scholar
  35. Morris KM, O'Meally D, Zaw T, Song X, Gillett A, Molloy MP, Polkinghorne A, Belov K (2016) Characterisation of the immune compounds in koala milk using a combined transcriptomic and proteomic approach. Sci Rep 6(1):35011. CrossRefPubMedPubMedCentralGoogle Scholar
  36. Obendorf DL, Munday BL (1990) Toxoplasmosis in wild eastern barred bandicoots, Perameles gunnii. In: Seebeck JH (ed) Bandicoots and bilbies. Surrey Beatty and Sons, Sydney, pp 193–197Google Scholar
  37. Padykula HA, Taylor JM (1982) Marsupial placentation and its evolutionary significance. J Reprod Fertil Suppl 31:95–104PubMedGoogle Scholar
  38. Papenfuss AT, Baker ML, Feng ZP, Tachedjian M, Crameri G, Cowled C, Ng J, Janardhana V, Field HE, Wang LF (2012) The immune gene repertoire of an important viral reservoir, the Australian black flying fox. BMC Genomics 13(1):261. CrossRefPubMedPubMedCentralGoogle Scholar
  39. Papenfuss AT, Feng ZP, Krasnec K, Deakin JE, Baker ML, Miller RD (2015) Marsupials and monotremes possess a novel family of MHC class I genes that is lost from the eutherian lineage. BMC Genomics 16(1):535. CrossRefPubMedPubMedCentralGoogle Scholar
  40. Parra ZE, Baker ML, Schwarz R, Deakin JE, Lindblad-Toh K, Miller RD (2007) Discovery of a new T cell receptor in marsupials. Proc Natl Acad Sci U S A 104(23):9776–9781. CrossRefPubMedPubMedCentralGoogle Scholar
  41. Parra ZE, Baker ML, Hathaway J, Lopez AM, Trujillo J, Sharp A, Miller RD (2008) Comparative genomic analysis and evolution of the T cell receptor loci in the opossum Monodelphis domestica. BMC Genomics 9(1):111. CrossRefPubMedPubMedCentralGoogle Scholar
  42. Schroder K, Hertzog PJ, Ravasi T, Hume DA (2004) Interferon-gamma: an overview of signals, mechanisms and functions. J Leukoc Biol 75(2):163–189. CrossRefPubMedGoogle Scholar
  43. Siddle HV, Deakin JE, Coggill P, Hart E, Cheng Y, Wong ES, Harrow J, Beck S, Belov K (2009) MHC-linked and un-linked class I genes in the wallaby. BMC Genomics 10:310CrossRefPubMedPubMedCentralGoogle Scholar
  44. Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM (2015) BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31:3210–3212CrossRefPubMedGoogle Scholar
  45. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Mol Biol Evol 30(12):2725-2729Google Scholar
  46. Thomas PD, Campbell MJ, Kejariwal A, Mi H, Karlak B, Daverman R, Diemer K, Muruganujan A, Narechania A (2003) PANTHER: a library of protein families and subfamilies indexed by function. Genome Res 13(9):2129–2141. CrossRefPubMedPubMedCentralGoogle Scholar
  47. Ting JP, Lovering RC, Alnemri ES, Bertin J, Boss JM, Davis BK, Flavell RA, Girardin SE, Godzik A, Harton JA, Hoffman HM (2008) The NLR gene family: a standard nomenclature. Immunity 28(3):285–287. CrossRefPubMedPubMedCentralGoogle Scholar
  48. van der Kraan LE, Wong ES, Lo N, Ujvari B, Belov K (2013) Identification of natural killer cell receptor genes in the genome of the marsupial Tasmanian devil (Sarcophilus harrisii). Immunogenetics 65(1):25–35.
  49. Villadangos JA (2001) Presentation of antigens by MHC class II molecules: getting the most out of them. Mol Immunol 38(5):329–346. CrossRefPubMedGoogle Scholar
  50. Warren K, Swan R, Bodetti T, Friend T, Hill S, Timms P (2005) Ocular Chlamydiales infections of western barred bandicoots (Perameles bougainville) in Western Australia. J Zoo Wildl Med 36(1):100–102. CrossRefPubMedGoogle Scholar
  51. Williams A, Peh CA, Elliott T (2002) The cell biology of MHC class I antigen presentation. Tiss Ant 59(1):3–17. CrossRefGoogle Scholar
  52. Wong ES, Papenfuss AT, Belov K (2011a) Genomic identification of chemokines and cytokines in opossum. J Interf Cytokine Res 31(3):317–330. CrossRefGoogle Scholar
  53. Wong ES, Papenfuss AT, Belov K (2011b) Immunome database for marsupials and monotremes. BMC Immunol 12(1):48. CrossRefPubMedPubMedCentralGoogle Scholar
  54. Woolford L, Rector A, Van Ranst M, Ducki A, Bennett MD, Nicholls PK, Warren KS, Swan RA, Wilcox GE, O'Hara AJ (2007) A novel virus detected in papillomas and carcinomas of the endangered western barred bandicoot (Perameles bougainville) exhibits genomic features of both the Papillomaviridae and Polyomaviridae. J Virol 81(24):13280–13290. CrossRefPubMedPubMedCentralGoogle Scholar
  55. Yoneyama M, Kikuchi M, Matsumoto K, Imaizumi T, Miyagishi M, Taira K, Foy E, Loo YM, Gale M, Akira S, Yonehara S (2005) Shared and unique functions of the DExD/H-Box Helicases RIG-I, MDA5, and LGP2 in antiviral innate immunity. J Immunol 175(5):2851–2858. CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2017

Authors and Affiliations

  • Katrina M. Morris
    • 1
  • Haylee J. Weaver
    • 2
    • 3
  • Denis O’Meally
    • 4
  • Marion Desclozeaux
    • 4
  • Amber Gillett
    • 5
  • Adam Polkinghorne
    • 4
  1. 1.The Roslin Institute and R(D)SVSUniversity of EdinburghMidlothianUK
  2. 2.School of Science and EngineeringUniversity of the Sunshine CoastSippy DownsAustralia
  3. 3.Australian Biological Resources Study, Department of the Environment & EnergyCanberraAustralia
  4. 4.Centre for Animal Health InnovationUniversity of the Sunshine CoastSippy DownsAustralia
  5. 5.Australia Zoo Wildlife HospitalBeerwahAustralia

Personalised recommendations