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Hogg CJ, Edwards RJ, Farquharson KA, Silver LW, Brandies P, Peel E, Escalona M, Jaya FR, Thavornkanlapachai R, Batley K, Bradford TM, Chang JK, Chen Z, Deshpande N, Dziminski M, Ewart KM, Griffith OW, Marin Gual L, Moon KL, Travouillon KJ, Waters P, Whittington CM, Wilkins MR, Helgen KM, Lo N, Ho SYW, Ruiz Herrera A, Paltridge R, Marshall Graves JA, Renfree M, Shapiro B, Ottewell K, Belov K. Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial. Nat Ecol Evol 2024; 8:1311-1326. [PMID: 38945974 PMCID: PMC11239497 DOI: 10.1038/s41559-024-02436-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 05/03/2024] [Indexed: 07/02/2024]
Abstract
Ninu (greater bilby, Macrotis lagotis) are desert-dwelling, culturally and ecologically important marsupials. In collaboration with Indigenous rangers and conservation managers, we generated the Ninu chromosome-level genome assembly (3.66 Gbp) and genome sequences for the extinct Yallara (lesser bilby, Macrotis leucura). We developed and tested a scat single-nucleotide polymorphism panel to inform current and future conservation actions, undertake ecological assessments and improve our understanding of Ninu genetic diversity in managed and wild populations. We also assessed the beneficial impact of translocations in the metapopulation (N = 363 Ninu). Resequenced genomes (temperate Ninu, 6; semi-arid Ninu, 6; and Yallara, 4) revealed two major population crashes during global cooling events for both species and differences in Ninu genes involved in anatomical and metabolic pathways. Despite their 45-year captive history, Ninu have fewer long runs of homozygosity than other larger mammals, which may be attributable to their boom-bust life history. Here we investigated the unique Ninu biology using 12 tissue transcriptomes revealing expression of all 115 conserved eutherian chorioallantoic placentation genes in the uterus, an XY1Y2 sex chromosome system and olfactory receptor gene expansions. Together, we demonstrate the holistic value of genomics in improving key conservation actions, understanding unique biological traits and developing tools for Indigenous rangers to monitor remote wild populations.
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Affiliation(s)
- Carolyn J Hogg
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia.
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia.
| | - Richard J Edwards
- Minderoo OceanOmics Centre at UWA, Oceans Institute, The University of Western Australia, Perth, Western Australia, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Katherine A Farquharson
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Luke W Silver
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Parice Brandies
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Emma Peel
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Merly Escalona
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Frederick R Jaya
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Rujiporn Thavornkanlapachai
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Kimberley Batley
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Tessa M Bradford
- Evolutionary Biology Unit, South Australian Museum, Adelaide, South Australia, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - J King Chang
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | | | - Nandan Deshpande
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
- Ramaciotti Centre for Genomics and School of Biotechnology and Biomolecular Science, UNSW, Sydney, New South Wales, Australia
| | - Martin Dziminski
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Kyle M Ewart
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Oliver W Griffith
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Laia Marin Gual
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Katherine L Moon
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Kenny J Travouillon
- Collections and Research, Western Australian Museum, Welshpool, Western Australia, Australia
| | - Paul Waters
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Camilla M Whittington
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
- Ramaciotti Centre for Genomics and School of Biotechnology and Biomolecular Science, UNSW, Sydney, New South Wales, Australia
| | - Kristofer M Helgen
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Aurora Ruiz Herrera
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Rachel Paltridge
- Indigenous Desert Alliance, Alice Springs, Northern Territory, Australia
| | | | - Marilyn Renfree
- School of BioSciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Kym Ottewell
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
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Peel E, Silver L, Brandies P, Zhu Y, Cheng Y, Hogg CJ, Belov K. Best genome sequencing strategies for annotation of complex immune gene families in wildlife. Gigascience 2022; 11:giac100. [PMID: 36310247 PMCID: PMC9618407 DOI: 10.1093/gigascience/giac100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 08/10/2022] [Accepted: 09/29/2022] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND The biodiversity crisis and increasing impact of wildlife disease on animal and human health provides impetus for studying immune genes in wildlife. Despite the recent boom in genomes for wildlife species, immune genes are poorly annotated in nonmodel species owing to their high level of polymorphism and complex genomic organisation. Our research over the past decade and a half on Tasmanian devils and koalas highlights the importance of genomics and accurate immune annotations to investigate disease in wildlife. Given this, we have increasingly been asked the minimum levels of genome quality required to effectively annotate immune genes in order to study immunogenetic diversity. Here we set out to answer this question by manually annotating immune genes in 5 marsupial genomes and 1 monotreme genome to determine the impact of sequencing data type, assembly quality, and automated annotation on accurate immune annotation. RESULTS Genome quality is directly linked to our ability to annotate complex immune gene families, with long reads and scaffolding technologies required to reassemble immune gene clusters and elucidate evolution, organisation, and true gene content of the immune repertoire. Draft-quality genomes generated from short reads with HiC or 10× Chromium linked reads were unable to achieve this. Despite mammalian BUSCOv5 scores of up to 94.1% amongst the 6 genomes, automated annotation pipelines incorrectly annotated up to 59% of manually annotated immune genes regardless of assembly quality or method of automated annotation. CONCLUSIONS Our results demonstrate that long reads and scaffolding technologies, alongside manual annotation, are required to accurately study the immune gene repertoire of wildlife species.
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Affiliation(s)
- Emma Peel
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, University of Sydney, Sydney NSW 2006, Australia
| | - Luke Silver
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Parice Brandies
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Ying Zhu
- Sichuan Provincial Academy of Natural Resource Sciences, Chengdu, Sichuan 610000, China
| | - Yuanyuan Cheng
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, University of Sydney, Sydney NSW 2006, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, University of Sydney, Sydney NSW 2006, Australia
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Quigley BL, Timms P. Helping koalas battle disease - Recent advances in Chlamydia and koala retrovirus (KoRV) disease understanding and treatment in koalas. FEMS Microbiol Rev 2020; 44:583-605. [PMID: 32556174 PMCID: PMC8600735 DOI: 10.1093/femsre/fuaa024] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/14/2020] [Indexed: 12/31/2022] Open
Abstract
The iconic Australian marsupial, the koala (Phascolarctos cinereus), has suffered dramatic population declines as a result of habitat loss and fragmentation, disease, vehicle collision mortality, dog attacks, bushfires and climate change. In 2012, koalas were officially declared vulnerable by the Australian government and listed as a threatened species. In response, research into diseases affecting koalas has expanded rapidly. The two major pathogens affecting koalas are Chlamydia pecorum, leading to chlamydial disease and koala retrovirus (KoRV). In the last eight years, these pathogens and their diseases have received focused study regarding their sources, genetics, prevalence, disease presentation and transmission. This has led to vast improvements in pathogen detection and treatment, including the ongoing development of vaccines for each as a management and control strategy. This review will summarize and highlight the important advances made in understanding and combating C. pecorum and KoRV in koalas, since they were declared a threatened species. With complementary advances having also been made from the koala genome sequence and in our understanding of the koala immune system, we are primed to make a significant positive impact on koala health into the future.
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Affiliation(s)
- Bonnie L Quigley
- Genecology Research Centre, University of the Sunshine Coast,
90 Sippy Downs Drive, Sippy Downs, Queensland, 4556, Australia
| | - Peter Timms
- Genecology Research Centre, University of the Sunshine Coast,
90 Sippy Downs Drive, Sippy Downs, Queensland, 4556, Australia
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Johnson RN, O'Meally D, Chen Z, Etherington GJ, Ho SYW, Nash WJ, Grueber CE, Cheng Y, Whittington CM, Dennison S, Peel E, Haerty W, O'Neill RJ, Colgan D, Russell TL, Alquezar-Planas DE, Attenbrow V, Bragg JG, Brandies PA, Chong AYY, Deakin JE, Di Palma F, Duda Z, Eldridge MDB, Ewart KM, Hogg CJ, Frankham GJ, Georges A, Gillett AK, Govendir M, Greenwood AD, Hayakawa T, Helgen KM, Hobbs M, Holleley CE, Heider TN, Jones EA, King A, Madden D, Graves JAM, Morris KM, Neaves LE, Patel HR, Polkinghorne A, Renfree MB, Robin C, Salinas R, Tsangaras K, Waters PD, Waters SA, Wright B, Wilkins MR, Timms P, Belov K. Adaptation and conservation insights from the koala genome. Nat Genet 2018; 50:1102-1111. [PMID: 29967444 PMCID: PMC6197426 DOI: 10.1038/s41588-018-0153-5] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 04/30/2018] [Indexed: 11/16/2022]
Abstract
The koala, the only extant species of the marsupial family Phascolarctidae, is classified as 'vulnerable' due to habitat loss and widespread disease. We sequenced the koala genome, producing a complete and contiguous marsupial reference genome, including centromeres. We reveal that the koala's ability to detoxify eucalypt foliage may be due to expansions within a cytochrome P450 gene family, and its ability to smell, taste and moderate ingestion of plant secondary metabolites may be due to expansions in the vomeronasal and taste receptors. We characterized novel lactation proteins that protect young in the pouch and annotated immune genes important for response to chlamydial disease. Historical demography showed a substantial population crash coincident with the decline of Australian megafauna, while contemporary populations had biogeographic boundaries and increased inbreeding in populations affected by historic translocations. We identified genetically diverse populations that require habitat corridors and instituting of translocation programs to aid the koala's survival in the wild.
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Affiliation(s)
- Rebecca N Johnson
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia.
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia.
| | - Denis O'Meally
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
- Animal Research Centre, Faculty of Science, Health, Education & Engineering, University of the Sunshine Coast, Maroochydore, Queensland, Australia
| | - Zhiliang Chen
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, New South Wales, Australia
| | | | - Simon Y W Ho
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
| | - Will J Nash
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Catherine E Grueber
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
- San Diego Zoo Global, San Diego, CA, USA
| | - Yuanyuan Cheng
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
- UQ Genomics Initiative, University of Queensland, St Lucia, Queensland, Australia
| | - Camilla M Whittington
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
| | - Siobhan Dennison
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Emma Peel
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
| | | | - Rachel J O'Neill
- Department of Molecular and Cell Biology and Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - Don Colgan
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Tonia L Russell
- Ramaciotti Centre for Genomics, University of New South Wales, Kensington, New South Wales, Australia
| | | | - Val Attenbrow
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Jason G Bragg
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
- National Herbarium of New South Wales, Royal Botanic Gardens & Domain Trust, Sydney, New South Wales, Australia
| | - Parice A Brandies
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
| | - Amanda Yoon-Yee Chong
- Earlham Institute, Norwich Research Park, Norwich, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Janine E Deakin
- Institute for Applied Ecology, University of Canberra, Bruce, Australian Capital Territory, Australia
| | - Federica Di Palma
- Earlham Institute, Norwich Research Park, Norwich, UK
- Department of Biological Sciences, University of East Anglia, Norwich, UK
| | - Zachary Duda
- Department of Molecular and Cell Biology and Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - Mark D B Eldridge
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Kyle M Ewart
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
| | - Greta J Frankham
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Bruce, Australian Capital Territory, Australia
| | - Amber K Gillett
- Australia Zoo Wildlife Hospital, Beerwah, Queensland, Australia
| | - Merran Govendir
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
| | - Alex D Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
- Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Takashi Hayakawa
- Department of Wildlife Science (Nagoya Railroad Co., Ltd.), Primate Research Institute, Kyoto University, Inuyama, Japan
- Japan Monkey Centre, Inuyama, Japan
| | - Kristofer M Helgen
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
- School of Biological Sciences, Environment Institute, Centre for Applied Conservation Science, and ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, South Australia, Australia
| | - Matthew Hobbs
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Clare E Holleley
- Australian National Wildlife Collection, National Research Collections Australia, CSIRO, Canberra, Australian Capital Territory, Australia
| | - Thomas N Heider
- Department of Molecular and Cell Biology and Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - Elizabeth A Jones
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
| | - Andrew King
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Danielle Madden
- Animal Research Centre, Faculty of Science, Health, Education & Engineering, University of the Sunshine Coast, Maroochydore, Queensland, Australia
| | - Jennifer A Marshall Graves
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
- Institute for Applied Ecology, University of Canberra, Bruce, Australian Capital Territory, Australia
- School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - Katrina M Morris
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, UK
| | - Linda E Neaves
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
- Royal Botanic Garden Edinburgh, Edinburgh, UK
| | - Hardip R Patel
- John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory, Australia
| | - Adam Polkinghorne
- Animal Research Centre, Faculty of Science, Health, Education & Engineering, University of the Sunshine Coast, Maroochydore, Queensland, Australia
| | - Marilyn B Renfree
- School of BioSciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Charles Robin
- School of BioSciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Ryan Salinas
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, New South Wales, Australia
| | - Kyriakos Tsangaras
- Department of Translational Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Paul D Waters
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, New South Wales, Australia
| | - Shafagh A Waters
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, New South Wales, Australia
| | - Belinda Wright
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, New South Wales, Australia
- Ramaciotti Centre for Genomics, University of New South Wales, Kensington, New South Wales, Australia
| | - Peter Timms
- Faculty of Science, Health, Education & Engineering, University of the Sunshine Coast, Maroochydore, Queensland, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
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Transcriptome sequencing of the long-nosed bandicoot (Perameles nasuta) reveals conservation and innovation of immune genes in the marsupial order Peramelemorphia. Immunogenetics 2017; 70:327-336. [PMID: 29159447 DOI: 10.1007/s00251-017-1043-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 10/30/2017] [Indexed: 12/22/2022]
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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Hing S, Currie A, Broomfield S, Keatley S, Jones K, Thompson RCA, Narayan E, Godfrey SS. Host stress physiology and Trypanosoma haemoparasite infection influence innate immunity in the woylie (Bettongia penicillata). Comp Immunol Microbiol Infect Dis 2016; 46:32-9. [PMID: 27260808 DOI: 10.1016/j.cimid.2016.04.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 04/08/2016] [Accepted: 04/13/2016] [Indexed: 11/26/2022]
Abstract
Understanding immune function is critical to conserving wildlife in view of infectious disease threats, particularly in threatened species vulnerable to stress, immunocompromise and infection. However, few studies examine stress, immune function and infection in wildlife. We used a flow cytometry protocol developed for human infants to assess phagocytosis, a key component of innate immunity, in a critically endangered marsupial, the woylie (Bettongia penicillata). The effects of stress physiology and Trypanosoma infection on phagocytosis were investigated. Blood and faecal samples were collected from woylies in a captive facility over three months. Trypanosoma status was determined using PCR. Faecal cortisol metabolites (FCM) were quantified by enzyme-immunoassay. Mean phagocytosis measured was >90%. An interaction between sex and FCM influenced the percentage of phagocytosing leukocytes, possibly reflecting the influence of sex hormones and glucocorticoids. An interaction between Trypanosoma status and FCM influenced phagocytosis index, suggesting that stress physiology and infection status influence innate immunity.
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Affiliation(s)
- Stephanie Hing
- Murdoch University, School of Veterinary and Life Sciences, 90 South Street, Murdoch, Western Australia 6150, Australia.
| | - Andrew Currie
- Murdoch University, School of Veterinary and Life Sciences, 90 South Street, Murdoch, Western Australia 6150, Australia
| | - Steven Broomfield
- Health Innovation Research Institute, Curtin University, Kent Street, Bentley, Western Australia 6102, Australia
| | - Sarah Keatley
- Murdoch University, School of Veterinary and Life Sciences, 90 South Street, Murdoch, Western Australia 6150, Australia
| | - Krista Jones
- Murdoch University, School of Veterinary and Life Sciences, 90 South Street, Murdoch, Western Australia 6150, Australia
| | - R C Andrew Thompson
- Murdoch University, School of Veterinary and Life Sciences, 90 South Street, Murdoch, Western Australia 6150, Australia
| | - Edward Narayan
- Charles Sturt University, School of Animal and Veterinary Science, Boorooma Street, Wagga Wagga, NSW 2678, Australia
| | - Stephanie S Godfrey
- Murdoch University, School of Veterinary and Life Sciences, 90 South Street, Murdoch, Western Australia 6150, Australia
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7
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Morris KM, Cheng Y, Warren W, Papenfuss AT, Belov K. Identification and analysis of divergent immune gene families within the Tasmanian devil genome. BMC Genomics 2015; 16:1017. [PMID: 26611146 PMCID: PMC4662006 DOI: 10.1186/s12864-015-2206-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 11/12/2015] [Indexed: 02/01/2023] Open
Abstract
Background The Tasmanian devil (Sarcophilus harrisii) is being threatened with extinction in the wild by a disease known as devil facial tumour disease (DFTD). In order to prevent the spread of this disease a thorough understanding of the Tasmanian devil immune system and its response to the disease is required. In 2011 and 2012 two genome sequencing projects of the Tasmania devil were released. This has provided us with the raw data required to begin to investigate the Tasmanian devil immunome in depth. In this study we characterise immune gene families of the Tasmanian devil. We focus on immunoglobulins, T cell receptors and cytokine families. Results We identify and describe 119 cytokines including 40 interleukins, 39 chemokines, 8 interferons, 18 tumour necrosis family cytokines and 14 additional cytokines. Constant regions for immunoglobulins and T cell receptors were also identified. The repertoire of genes in these families was similar to the opossum, however devil specific duplications were seen and orthologs to eutherian genes not previously identified in any marsupial were also identified. Conclusions By using multiple data sources as well as targeted search methods, highly divergent genes across the Tasmanian devil immune system were identified and characterised. This understanding will allow for the development of devil specific assays and reagents and allow for future studies into the immune response of the Tasmanian devil immune system to DFTD. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2206-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katrina M Morris
- Faculty of Veterinary Science, University of Sydney, Camperdown, NSW, Australia.
| | - Yuanyuan Cheng
- Faculty of Veterinary Science, University of Sydney, Camperdown, NSW, Australia.
| | - Wesley Warren
- Washington University School of Medicine, 4444 Forest Park Ave, St Louis, MO, 63108, USA.
| | - Anthony T Papenfuss
- Bioinformatics Division, The Walter and Eliza Hall Institute for Medical Research, Parkville, VIC, Australia. .,Bioinformatics and Cancer Genomics, Research Division, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia.
| | - Katherine Belov
- Faculty of Veterinary Science, University of Sydney, Camperdown, NSW, Australia.
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8
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Morris KM, Mathew M, Waugh C, Ujvari B, Timms P, Polkinghorne A, Belov K. Identification, characterisation and expression analysis of natural killer receptor genes in Chlamydia pecorum infected koalas (Phascolarctos cinereus). BMC Genomics 2015; 16:796. [PMID: 26471184 PMCID: PMC4608214 DOI: 10.1186/s12864-015-2035-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Accepted: 10/08/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Koalas (Phascolarctos cinereus), an iconic Australian marsupial, are being heavily impacted by the spread of Chlamydia pecorum, an obligate intracellular bacterial pathogen. Koalas vary in their response to this pathogen, with some showing no symptoms, while others suffer severe symptoms leading to infertility, blindness or death. Little is known about the pathology of this disease and the immune response against it in this host. Studies have demonstrated that natural killer (NK) cells, key components of the innate immune system, are involved in the immune response to chlamydial infections in humans. These cells can directly lyse cells infected by intracellular pathogens and their ability to recognise these infected cells is mediated through NK receptors on their surface. These are encoded in two regions of the genome, the leukocyte receptor complex (LRC) and the natural killer complex (NKC). These two families evolve rapidly and different repertoires of genes, which have evolved by gene duplication, are seen in different species. METHODS In this study we aimed to characterise genes belonging to the NK receptor clusters in the koala by searching available koala transcriptomes using a combination of search methods. We developed a qPCR assay to quantify relative expression of four genes, two encoded within the NK receptor cluster (CLEC1B, CLEC4E) and two known to play a role in NK response to Chalmydia in humans (NCR3, PRF1). RESULTS We found that the NK receptor repertoire of the koala closely resembles that of the Tasmanian devil, with minimal genes in the NKC, but with lineage specific expansions in the LRC. Additional genes important for NK cell activity, NCR3 and PRF1, were also identified and characterised. In a preliminary study to investigate whether these genes are involved in the koala immune response to infection by its chlamydial pathogen, C. pecorum, we investigated the expression of four genes in koalas with active chlamydia infection, those with past infection and those without infection using qPCR. This analysis revealed that one of these four, CLEC4E, may be upregulated in response to chlamydia infection. CONCLUSION We have characterised genes of the NKC and LRC in koalas and have discovered evidence that one of these genes may be upregulated in koalas with chlamydia, suggesting that these receptors may play a role in the immune response of koalas to chlamydia infection.
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Affiliation(s)
- Katrina M Morris
- Faculty of Veterinary Science, University of Sydney, Camperdown, NSW, Australia.
| | - Marina Mathew
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, Brisbane, QLD, Australia.
| | - Courtney Waugh
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, Brisbane, QLD, Australia. .,Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia.
| | - Beata Ujvari
- Faculty of Veterinary Science, University of Sydney, Camperdown, NSW, Australia. .,Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Waurn Ponds, Geelong, VIC, Australia.
| | - Peter Timms
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, Brisbane, QLD, Australia. .,Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia.
| | - Adam Polkinghorne
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, Brisbane, QLD, Australia. .,Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia.
| | - Katherine Belov
- Faculty of Veterinary Science, University of Sydney, Camperdown, NSW, Australia.
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9
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Abstract
Toll-like receptors (TLRs) play a crucial role in the early defence against invading pathogens, yet our understanding of TLRs in marsupial immunity is limited. Here, we describe the characterisation of nine TLRs from a koala immune tissue transcriptome and one TLR from a draft sequence of the koala genome and the subsequent development of an assay to study genetic diversity in these genes. We surveyed genetic diversity in 20 koalas from New South Wales, Australia and showed that one gene, TLR10 is monomorphic, while the other nine TLR genes have between two and 12 alleles. 40 SNPs (16 non-synonymous) were identified across the ten TLR genes. These markers provide a springboard to future studies on innate immunity in the koala, a species under threat from two major infectious diseases.
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10
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Abts KC, Ivy JA, DeWoody JA. Immunomics of the koala (Phascolarctos cinereus). Immunogenetics 2015; 67:305-21. [PMID: 25761531 DOI: 10.1007/s00251-015-0833-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 02/19/2015] [Indexed: 12/20/2022]
Abstract
The study of the koala transcriptome has the potential to advance our understanding of its immunome--immunological reaction of a given host to foreign antigens--and to help combat infectious diseases (e.g., chlamydiosis) that impede ongoing conservation efforts. We used Illumina sequencing of cDNA to characterize genes expressed in two different koala tissues of immunological importance, blood and spleen. We generated nearly 600 million raw sequence reads, and about 285 million of these were subsequently assembled and condensed into ~70,000 subcomponents that represent putative transcripts. We annotated ~16% of these subcomponents and identified those related to infection and the immune response, including Toll-like receptors (TLRs), RIG-I-like receptors (RLRs), major histocompatibility complex (MHC) genes, and koala retrovirus (KoRV). Using phylogenetic analyses, we identified 29 koala genes in these target categories and report their concordance with currently accepted gene groups. By mapping multiple sequencing reads to transcripts, we identified 56 putative SNPs in genes of interest. The distribution of these SNPs indicates that MHC genes (34 SNPs) are more diverse than KoRV (12 SNPs), TLRs (8 SNPs), or RLRs (2 SNPs). Our sequence data also indicate that KoRV sequences are highly expressed in the transcriptome. Our efforts have produced full-length sequences for potentially important immune genes in koala, which should serve as targets for future investigations that aim to conserve koala populations.
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Affiliation(s)
- Kendra C Abts
- Department of Forestry and Natural Resources, Purdue University, 195 Marsteller St, West Lafayette, IN, 47907, USA,
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11
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Comparison of subcutaneous versus intranasal immunization of male koalas (Phascolarctos cinereus) for induction of mucosal and systemic immunity against Chlamydia pecorum. Vaccine 2015; 33:855-60. [PMID: 25562793 DOI: 10.1016/j.vaccine.2014.12.052] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 11/20/2014] [Accepted: 12/19/2014] [Indexed: 01/04/2023]
Abstract
Chlamydia pecorum infections are debilitating in the koala, contributing significantly to morbidity and mortality, with current antibiotic treatments having minimal success and adversely affecting gut microflora. This, combined with the sometimes-asymptomatic nature of the infection, suggests that an efficacious anti-chlamydial vaccine is required to control chlamydial infections in the koala. To date vaccination studies have focused primarily on female koalas, however, given the physiological differences between male and female reproductive tracts, we tested the efficacy of a vaccine in 12 captive male koalas. We evaluated the potential of both subcutaneous and intranasal vaccine delivery to elicit mucosal immunity in male koalas. Our results showed that both intranasal and subcutaneous delivery of a vaccine consisting of C. pecorum major outer membrane protein (MOMP) and the adjuvant immunostimulating complex (ISC) induced significant immune responses in male koalas. Subcutaneous immunization elicited stronger cell-mediated responses in peripheral blood lymphocytes (PBL), and greater plasma antibody levels whereas the intranasal immunization elicited stronger humoral responses in urogenital tract (UGT) secretions. This is the first time a Chlamydia vaccine has been tested in the male koala and the first assessment of a mucosal vaccination route in this species. Our results suggest that vaccination of male koalas can elicit mucosal immunity and could contribute to the long-term survivability of wild populations of the koala.
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12
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Robinson RT. IL12Rβ1: the cytokine receptor that we used to know. Cytokine 2014; 71:348-59. [PMID: 25516297 DOI: 10.1016/j.cyto.2014.11.018] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 11/15/2014] [Accepted: 11/17/2014] [Indexed: 12/22/2022]
Abstract
Human IL12RB1 encodes IL12Rβ1, a type I transmembrane receptor that is an essential component of the IL12- and IL23-signaling complex. IL12RB1 is well-established as being a promoter of delayed type hypersensitivity (DTH), the immunological reaction that limits tuberculosis. However, recent data demonstrate that in addition to promoting DTH, IL12RB1 also promotes autoimmunity. The contradictory roles of IL12RB1 in human health raises the question, what are the factors governing IL12RB1 function in a given individual, and how is inter-individual variability in IL12RB1 function introduced? Here we review recent data that demonstrate individual variability in IL12RB1 function is introduced at the epigenetic, genomic polymorphism, and mRNA splicing levels. Where and how these differences contribute to disease susceptibility and outcome are also reviewed. Collectively, recent data support a model wherein IL12RB1 sequence variability - whether introduced at the genomic or post-transcriptional level - contributes to disease, and that human IL12RB1 is not as simple a gene as we once believed.
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Affiliation(s)
- Richard T Robinson
- Department of Microbiology and Molecular Genetics, The Medical College of Wisconsin, Milwaukee, WI 53226, United States.
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13
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Mathew M, Waugh C, Beagley KW, Timms P, Polkinghorne A. Interleukin 17A is an immune marker for chlamydial disease severity and pathogenesis in the koala (Phascolarctos cinereus). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2014; 46:423-429. [PMID: 24915607 DOI: 10.1016/j.dci.2014.05.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 05/22/2014] [Accepted: 05/22/2014] [Indexed: 06/03/2023]
Abstract
The koala (Phascolarctos cinereus) is an iconic Australian marsupial species that is facing many threats to its survival. Chlamydia pecorum infections are a significant contributor to this ongoing decline. A major limiting factor in our ability to manage and control chlamydial disease in koalas is a limited understanding of the koala's cell-mediated immune response to infections by this bacterial pathogen. To identify immunological markers associated with chlamydial infection and disease in koalas, we used koala-specific Quantitative Real Time PCR (qrtPCR) assays to profile the cytokine responses of Peripheral Blood Mononuclear Cells (PBMCs) collected from 41 koalas with different stages of chlamydial disease. Target cytokines included the principal Th1 (Interferon gamma; IFNγ), Th2 (Interleukin 10; IL10), and pro-inflammatory cytokines (Tumor Necrosis Factor alpha; TNFα). A novel koala-specific IL17A qrtPCR assay was also developed as part of this study to quantitate the gene expression of this Th17 cytokine in koalas. A statistically significant higher IL17A gene expression was observed in animals with current chlamydial disease compared to animals with asymptomatic chlamydial infection. A modest up-regulation of pro-inflammatory cytokines, such as TNFα and IFNγ, was also observed in these animals with signs of current chlamydial disease. IL10 gene expression was not evident in the majority of animals from both groups. Future longitudinal studies are now required to confirm the role played by cytokines in pathology and/or protection against C. pecorum infection in the koala.
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Affiliation(s)
- Marina Mathew
- Institute of Health & Biomedical Innovation, Queensland University of Technology, 60 Musk Avenue, Kelvin Grove 4059, Brisbane, Australia
| | - Courtney Waugh
- Institute of Health & Biomedical Innovation, Queensland University of Technology, 60 Musk Avenue, Kelvin Grove 4059, Brisbane, Australia; Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, 90 Sippy Downs Dr, Sippy Downs 4558, QLD, Australia
| | - Kenneth W Beagley
- Institute of Health & Biomedical Innovation, Queensland University of Technology, 60 Musk Avenue, Kelvin Grove 4059, Brisbane, Australia
| | - Peter Timms
- Institute of Health & Biomedical Innovation, Queensland University of Technology, 60 Musk Avenue, Kelvin Grove 4059, Brisbane, Australia; Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, 90 Sippy Downs Dr, Sippy Downs 4558, QLD, Australia
| | - Adam Polkinghorne
- Institute of Health & Biomedical Innovation, Queensland University of Technology, 60 Musk Avenue, Kelvin Grove 4059, Brisbane, Australia; Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, 90 Sippy Downs Dr, Sippy Downs 4558, QLD, Australia.
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