Abstract
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.
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This study was partially funded by a University of the Sunshine Coast internal seed grant to HJW.
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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.
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Electronic supplementary material
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).
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).
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).
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).
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).
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Morris, K.M., Weaver, H.J., O’Meally, D. et al. Transcriptome sequencing of the long-nosed bandicoot (Perameles nasuta) reveals conservation and innovation of immune genes in the marsupial order Peramelemorphia. Immunogenetics 70, 327–336 (2018). https://doi.org/10.1007/s00251-017-1043-1
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DOI: https://doi.org/10.1007/s00251-017-1043-1