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PMID: 29967444 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Adaptation and conservation insights from the koala genome.

Nature genetics ·Vol. 50 ·No. 8 ·2018-00-00 ·Pages 1102-1111

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 AY, 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

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.

MeSH Terms
Adaptation, Physiological/genetics Animals Australia Chlamydia Infections/genetics Cytochrome P-450 Enzyme System/genetics,metabolism Female Genome Molecular Sequence Annotation/methods Phascolarctidae/genetics,metabolism Translocation, Genetic
Chemicals
Cytochrome P-450 Enzyme System
Authors & Affiliations
54 authors, click to expand affiliations / ORCID
Johnson Rebecca N ORCID
Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia. [email protected]. | School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia. [email protected].
O'Meally Denis
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.
Chen Zhiliang
School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, New South Wales, Australia.
Etherington Graham J
Earlham Institute, Norwich Research Park, Norwich, UK.
Ho Simon Y W ORCID
School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia.
Nash Will J
Earlham Institute, Norwich Research Park, Norwich, UK.
Grueber Catherine E ORCID
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.
Cheng Yuanyuan
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.
Whittington Camilla M
Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia.
Dennison Siobhan
Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia.
Peel Emma
School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia.
Haerty Wilfried
Earlham Institute, Norwich Research Park, Norwich, UK.
O'Neill Rachel J
Department of Molecular and Cell Biology and Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.
Colgan Don
Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia.
Russell Tonia L
Ramaciotti Centre for Genomics, University of New South Wales, Kensington, New South Wales, Australia.
Alquezar-Planas David E
Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia.
Attenbrow Val
Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia.
Bragg Jason G
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.
Brandies Parice A
School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia.
Chong Amanda Yoon-Yee
Earlham Institute, Norwich Research Park, Norwich, UK. | Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
Deakin Janine E
Institute for Applied Ecology, University of Canberra, Bruce, Australian Capital Territory, Australia.
Di Palma Federica
Earlham Institute, Norwich Research Park, Norwich, UK. | Department of Biological Sciences, University of East Anglia, Norwich, UK.
Duda Zachary
Department of Molecular and Cell Biology and Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.
Eldridge Mark D B
Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia.
Ewart Kyle M
Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia.
Hogg Carolyn J
School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia.
Frankham Greta J
Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia.
Georges Arthur
Institute for Applied Ecology, University of Canberra, Bruce, Australian Capital Territory, Australia.
Gillett Amber K
Australia Zoo Wildlife Hospital, Beerwah, Queensland, Australia.
Govendir Merran
Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia.
Greenwood Alex D
Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany. | Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany.
Hayakawa Takashi
Department of Wildlife Science (Nagoya Railroad Co., Ltd.), Primate Research Institute, Kyoto University, Inuyama, Japan. | Japan Monkey Centre, Inuyama, Japan.
Helgen Kristofer M
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.
Hobbs Matthew ORCID
Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia.
Holleley Clare E
Australian National Wildlife Collection, National Research Collections Australia, CSIRO, Canberra, Australian Capital Territory, Australia.
Heider Thomas N
Department of Molecular and Cell Biology and Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.
Jones Elizabeth A
Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia.
King Andrew
Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia.
Madden Danielle
Animal Research Centre, Faculty of Science, Health, Education & Engineering, University of the Sunshine Coast, Maroochydore, Queensland, Australia.
Graves Jennifer A Marshall
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.
Morris Katrina M
The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, UK.
Neaves Linda E ORCID
Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia. | Royal Botanic Garden Edinburgh, Edinburgh, UK.
Patel Hardip R
John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory, Australia.
Polkinghorne Adam
Animal Research Centre, Faculty of Science, Health, Education & Engineering, University of the Sunshine Coast, Maroochydore, Queensland, Australia.
Renfree Marilyn B ORCID
School of BioSciences, University of Melbourne, Melbourne, Victoria, Australia.
Robin Charles ORCID
School of BioSciences, University of Melbourne, Melbourne, Victoria, Australia.
Salinas Ryan
School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, New South Wales, Australia.
Tsangaras Kyriakos
Department of Translational Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.
Waters Paul D
School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, New South Wales, Australia.
Waters Shafagh A
School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, New South Wales, Australia.
Wright Belinda
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.
Wilkins Marc R
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.
Timms Peter
Faculty of Science, Health, Education & Engineering, University of the Sunshine Coast, Maroochydore, Queensland, Australia.
Belov Katherine
School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia.
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Article Info
Journal
Nature genetics
Abbr.
Nat Genet
ISSN
1546-1718
DOI
10.1038/s41588-018-0153-5
Email
[email protected]
Published
2018-00-00
Epub
2018-00-02
Pages
1102-1111
Language
English
Region
United States
NLM ID
9216904
PMCID
PMC6197426
Subset
IM
Grants
Biotechnology and Biological Sciences Research Council · BB/J004669/1 · United Kingdom
NIGMS NIH HHS · R01 GM092706 · United States
Corrections
CommentIn
PMID: 30042480
External Links
PubMed source DOI: 10.1038/s41588-018-0153-5 PMC Full Text View journal details
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