Adaptation and conservation insights from the koala genome

Rebecca N. Johnson; Denis O’Meally; Zhiliang Chen; Graham J. Etherington; Simon Y.W. Ho; Will J. Nash; Catherine E. Grueber; Yuanyuan Cheng; Camilla M. Whittington; Siobhan Dennison; Emma Peel; Wilfried Haerty; Rachel J. O’Neill; Don Colgan; Tonia L. Russell; David E. Alquezar-Planas; Val Attenbrow; Jason G. Bragg; Parice A. Brandies; Amanda Yoon Yee Chong; Janine E. Deakin; Federica Di Palma; Zachary Duda; Mark D.B. Eldridge; Kyle M. Ewart; Carolyn J. Hogg; Greta J. Frankham; Arthur Georges; Amber K. Gillett; Merran Govendir; Alex D. Greenwood; Takashi Hayakawa; Kristofer M. Helgen; Matthew Hobbs; Clare E. Holleley; Thomas N. Heider; Elizabeth A. Jones; Andrew King; Danielle Madden; Jennifer A.Marshall Graves; Katrina M. Morris; Linda E. Neaves; Hardip R. Patel; Adam Polkinghorne; Marilyn B. Renfree; Charles Robin; Ryan Salinas; Kyriakos Tsangaras; Paul D. Waters; Shafagh A. Waters; Belinda Wright; Marc R. Wilkins; Peter Timms; Katherine Belov

doi:10.1038/s41588-018-0153-5

Adaptation and conservation insights from the koala genome

Rebecca N. Johnson^*, Denis O’Meally, Zhiliang Chen, Graham J. Etherington, Simon Y.W. Ho, Will J. Nash, Catherine E. Grueber, Yuanyuan Cheng, Camilla M. Whittington, Siobhan Dennison, Emma Peel, Wilfried Haerty, Rachel J. O’Neill, Don Colgan, Tonia L. Russell, David E. Alquezar-Planas, Val Attenbrow, Jason G. Bragg, Parice A. Brandies, Amanda Yoon Yee ChongJanine E. Deakin, Federica Di Palma, Zachary Duda, Mark D.B. Eldridge, Kyle M. Ewart, Carolyn J. Hogg, Greta J. Frankham, Arthur Georges, Amber K. Gillett, Merran Govendir, Alex D. Greenwood, Takashi Hayakawa, Kristofer M. Helgen, Matthew Hobbs, Clare E. Holleley, Thomas N. Heider, Elizabeth A. Jones, Andrew King, Danielle Madden, Jennifer A.Marshall Graves, Katrina M. Morris, Linda E. Neaves, Hardip R. Patel, Adam Polkinghorne, Marilyn B. Renfree, Charles Robin, Ryan Salinas, Kyriakos Tsangaras, Paul D. Waters, Shafagh A. Waters, Belinda Wright, Marc R. Wilkins, Peter Timms, Katherine Belov

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

146 Citations (Scopus)

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.

Original language	English
Pages (from-to)	1102-1111
Number of pages	10
Journal	Nature Genetics
Volume	50
Issue number	8
DOIs	https://doi.org/10.1038/s41588-018-0153-5
Publication status	Published - 1 Aug 2018

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Johnson, R. N., O’Meally, D., Chen, Z., Etherington, G. J., Ho, S. Y. W., Nash, W. J., Grueber, C. E., Cheng, Y., Whittington, C. M., Dennison, S., Peel, E., Haerty, W., O’Neill, R. J., Colgan, D., Russell, T. L., Alquezar-Planas, D. E., Attenbrow, V., Bragg, J. G., Brandies, P. A., ... Belov, K. (2018). Adaptation and conservation insights from the koala genome. Nature Genetics, 50(8), 1102-1111. https://doi.org/10.1038/s41588-018-0153-5

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title = "Adaptation and conservation insights from the koala genome",

abstract = "The koala, the only extant species of the marsupial family Phascolarctidae, is classified as {\textquoteleft}vulnerable{\textquoteright} 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{\textquoteright}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{\textquoteright}s survival in the wild.",

author = "Johnson, {Rebecca N.} and Denis O{\textquoteright}Meally and Zhiliang Chen and Etherington, {Graham J.} and Ho, {Simon Y.W.} and Nash, {Will J.} and Grueber, {Catherine E.} and Yuanyuan Cheng and Whittington, {Camilla M.} and Siobhan Dennison and Emma Peel and Wilfried Haerty and O{\textquoteright}Neill, {Rachel J.} and Don Colgan and Russell, {Tonia L.} and Alquezar-Planas, {David E.} and Val Attenbrow and Bragg, {Jason G.} and Brandies, {Parice A.} and Chong, {Amanda Yoon Yee} and Deakin, {Janine E.} and {Di Palma}, Federica and Zachary Duda and Eldridge, {Mark D.B.} and Ewart, {Kyle M.} and Hogg, {Carolyn J.} and Frankham, {Greta J.} and Arthur Georges and Gillett, {Amber K.} and Merran Govendir and Greenwood, {Alex D.} and Takashi Hayakawa and Helgen, {Kristofer M.} and Matthew Hobbs and Holleley, {Clare E.} and Heider, {Thomas N.} and Jones, {Elizabeth A.} and Andrew King and Danielle Madden and Graves, {Jennifer A.Marshall} and Morris, {Katrina M.} and Neaves, {Linda E.} and Patel, {Hardip R.} and Adam Polkinghorne and Renfree, {Marilyn B.} and Charles Robin and Ryan Salinas and Kyriakos Tsangaras and Waters, {Paul D.} and Waters, {Shafagh A.} and Belinda Wright and Wilkins, {Marc R.} and Peter Timms and Katherine Belov",

note = "Publisher Copyright: {\textcopyright} 2018, The Author(s).",

year = "2018",

month = aug,

day = "1",

doi = "10.1038/s41588-018-0153-5",

language = "English",

volume = "50",

pages = "1102--1111",

journal = "Nature Genetics",

issn = "1061-4036",

publisher = "Nature Publishing Group",

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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 2018, 'Adaptation and conservation insights from the koala genome', Nature Genetics, vol. 50, no. 8, pp. 1102-1111. https://doi.org/10.1038/s41588-018-0153-5

TY - JOUR

T1 - Adaptation and conservation insights from the koala genome

AU - Johnson, Rebecca N.

AU - O’Meally, Denis

AU - Chen, Zhiliang

AU - Etherington, Graham J.

AU - Ho, Simon Y.W.

AU - Nash, Will J.

AU - Grueber, Catherine E.

AU - Cheng, Yuanyuan

AU - Whittington, Camilla M.

AU - Dennison, Siobhan

AU - Peel, Emma

AU - Haerty, Wilfried

AU - O’Neill, Rachel J.

AU - Colgan, Don

AU - Russell, Tonia L.

AU - Alquezar-Planas, David E.

AU - Attenbrow, Val

AU - Bragg, Jason G.

AU - Brandies, Parice A.

AU - Chong, Amanda Yoon Yee

AU - Deakin, Janine E.

AU - Di Palma, Federica

AU - Duda, Zachary

AU - Eldridge, Mark D.B.

AU - Ewart, Kyle M.

AU - Hogg, Carolyn J.

AU - Frankham, Greta J.

AU - Georges, Arthur

AU - Gillett, Amber K.

AU - Govendir, Merran

AU - Greenwood, Alex D.

AU - Hayakawa, Takashi

AU - Helgen, Kristofer M.

AU - Hobbs, Matthew

AU - Holleley, Clare E.

AU - Heider, Thomas N.

AU - Jones, Elizabeth A.

AU - King, Andrew

AU - Madden, Danielle

AU - Graves, Jennifer A.Marshall

AU - Morris, Katrina M.

AU - Neaves, Linda E.

AU - Patel, Hardip R.

AU - Polkinghorne, Adam

AU - Renfree, Marilyn B.

AU - Robin, Charles

AU - Salinas, Ryan

AU - Tsangaras, Kyriakos

AU - Waters, Paul D.

AU - Waters, Shafagh A.

AU - Wright, Belinda

AU - Wilkins, Marc R.

AU - Timms, Peter

AU - Belov, Katherine

PY - 2018/8/1

Y1 - 2018/8/1

N2 - 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.

AB - 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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U2 - 10.1038/s41588-018-0153-5

DO - 10.1038/s41588-018-0153-5

M3 - Article

SN - 1061-4036

VL - 50

SP - 1102

EP - 1111

JO - Nature Genetics

JF - Nature Genetics

IS - 8

ER -

Adaptation and conservation insights from the koala genome

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