Genome analysis of the platypus reveals unique signatures of evolution

Wesley Warren; LaDeana Hillier; Jenny Marshall Graves; Ewan Birney; Chris Ponting; Frank Grutzner; Katherine Belov; Webb Miller; Laura Clarke; Asif Chinwalla; Shiaw-Pyng Yang; Andreas Heger; Devin Locke; Pat Miethke; Paul Waters; Frederick Veyrunes; Lucinda Fulton; Bob Fulton; Tina Graves; John Wallis; Xose Puente; Carlos Lopez-Otin; Gonzalo Ordonez; Evan Eichler; L Chen; Ze Cheng; Janine DEAKIN; Amber Alsop; Katherine Thompson; Patrick Kirby; Anthony Papenfuss; Matthew Wakefield; Tsviya Olender; Doron Lancet; Gavin Huttley; Arian Smit; Andrew Pask; Peter Temple-Smith; Mark Batzer; Jerilyn Walker; Miriam K. Konkel; Harris S. Robert; Camilla Whittington; Emily Wong; Neil Gemmell; Emmanuel Buschiazzo; Iris Jentzsch; Angelika Merkel; Juergen Schmitz; Anja Zemann; Gennady Churakov; Jan Kriegs; Juergen Brosius; Elizabeth Murchison; Ravi Sachidanandam; Carly Smith; Gregory Hannon; Enkhjargal Tsend-Ayush; Daniel McMillan; Rosalind Attenborough; Willem Rens; Malcolm Ferguson-Smith; Christophe Lefevre; Julie Sharp; Kevin R. Nicholas; David A. Ray; Michael Kube; reinhardt Reinhardt; Thomas Pringle; James Taylor; Russell Jones; Brett Nixon; Jean-Louis Dacheux; Hitoshi Niwa; Yoko Sekita; Xiaoqiu Huang; Alexander Stark; Pouya Kheradpour; Manolis Kellis; Paul Flicek; Yuan Chen; Caleb Webber; Ross Hardison; Joanne Nelson; Kym Hallsworth-Pepin; Kim Delehaunty; Chris Markovic; Pat Minx; Yucheng Feng; Colin Kremitzki; Makedonka Mitreva; Jarret Glasscock; Todd Wylie; Patricia Wohldmann; Prathapan Thiru; Michael Nhan; Craig Pohl; Scott M. Smith; Shunfeng Hou; M. B. Renfree; Elaine Mardis; Richard Wilson

doi:10.1038/nature06936

Genome analysis of the platypus reveals unique signatures of evolution

Wesley Warren, LaDeana Hillier, Jenny Marshall Graves, Ewan Birney, Chris Ponting, Frank Grutzner, Katherine Belov, Webb Miller, Laura Clarke, Asif Chinwalla, Shiaw-Pyng Yang, Andreas Heger, Devin Locke, Pat Miethke, Paul Waters, Frederick Veyrunes, Lucinda Fulton, Bob Fulton, Tina Graves, John WallisXose Puente, Carlos Lopez-Otin, Gonzalo Ordonez, Evan Eichler, L Chen, Ze Cheng, Janine DEAKIN, Amber Alsop, Katherine Thompson, Patrick Kirby, Anthony Papenfuss, Matthew Wakefield, Tsviya Olender, Doron Lancet, Gavin Huttley, Arian Smit, Andrew Pask, Peter Temple-Smith, Mark Batzer, Jerilyn Walker, Miriam K. Konkel, Harris S. Robert, Camilla Whittington, Emily Wong, Neil Gemmell, Emmanuel Buschiazzo, Iris Jentzsch, Angelika Merkel, Juergen Schmitz, Anja Zemann, Gennady Churakov, Jan Kriegs, Juergen Brosius, Elizabeth Murchison, Ravi Sachidanandam, Carly Smith, Gregory Hannon, Enkhjargal Tsend-Ayush, Daniel McMillan, Rosalind Attenborough, Willem Rens, Malcolm Ferguson-Smith, Christophe Lefevre, Julie Sharp, Kevin R. Nicholas, David A. Ray, Michael Kube, reinhardt Reinhardt, Thomas Pringle, James Taylor, Russell Jones, Brett Nixon, Jean-Louis Dacheux, Hitoshi Niwa, Yoko Sekita, Xiaoqiu Huang, Alexander Stark, Pouya Kheradpour, Manolis Kellis, Paul Flicek, Yuan Chen, Caleb Webber, Ross Hardison, Joanne Nelson, Kym Hallsworth-Pepin, Kim Delehaunty, Chris Markovic, Pat Minx, Yucheng Feng, Colin Kremitzki, Makedonka Mitreva, Jarret Glasscock, Todd Wylie, Patricia Wohldmann, Prathapan Thiru, Michael Nhan, Craig Pohl, Scott M. Smith, Shunfeng Hou, M. B. Renfree, Elaine Mardis, Richard Wilson

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

558 Citations (Scopus)

Abstract

We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venomsimilar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation.

Original language	English
Pages (from-to)	175-256
Number of pages	82
Journal	Nature
Volume	453
DOIs	https://doi.org/10.1038/nature06936
Publication status	Published - 2008
Externally published	Yes

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Warren, W., Hillier, L., Marshall Graves, J., Birney, E., Ponting, C., Grutzner, F., Belov, K., Miller, W., Clarke, L., Chinwalla, A., Yang, S.-P., Heger, A., Locke, D., Miethke, P., Waters, P., Veyrunes, F., Fulton, L., Fulton, B., Graves, T., ... Wilson, R. (2008). Genome analysis of the platypus reveals unique signatures of evolution. Nature, 453, 175-256. https://doi.org/10.1038/nature06936

@article{7b1e961a20fe4381a1d15edd015b5ad1,

title = "Genome analysis of the platypus reveals unique signatures of evolution",

abstract = "We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venomsimilar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation.",

author = "Wesley Warren and LaDeana Hillier and {Marshall Graves}, Jenny and Ewan Birney and Chris Ponting and Frank Grutzner and Katherine Belov and Webb Miller and Laura Clarke and Asif Chinwalla and Shiaw-Pyng Yang and Andreas Heger and Devin Locke and Pat Miethke and Paul Waters and Frederick Veyrunes and Lucinda Fulton and Bob Fulton and Tina Graves and John Wallis and Xose Puente and Carlos Lopez-Otin and Gonzalo Ordonez and Evan Eichler and L Chen and Ze Cheng and Janine DEAKIN and Amber Alsop and Katherine Thompson and Patrick Kirby and Anthony Papenfuss and Matthew Wakefield and Tsviya Olender and Doron Lancet and Gavin Huttley and Arian Smit and Andrew Pask and Peter Temple-Smith and Mark Batzer and Jerilyn Walker and Konkel, {Miriam K.} and Robert, {Harris S.} and Camilla Whittington and Emily Wong and Neil Gemmell and Emmanuel Buschiazzo and Iris Jentzsch and Angelika Merkel and Juergen Schmitz and Anja Zemann and Gennady Churakov and Jan Kriegs and Juergen Brosius and Elizabeth Murchison and Ravi Sachidanandam and Carly Smith and Gregory Hannon and Enkhjargal Tsend-Ayush and Daniel McMillan and Rosalind Attenborough and Willem Rens and Malcolm Ferguson-Smith and Christophe Lefevre and Julie Sharp and Nicholas, {Kevin R.} and Ray, {David A.} and Michael Kube and reinhardt Reinhardt and Thomas Pringle and James Taylor and Russell Jones and Brett Nixon and Jean-Louis Dacheux and Hitoshi Niwa and Yoko Sekita and Xiaoqiu Huang and Alexander Stark and Pouya Kheradpour and Manolis Kellis and Paul Flicek and Yuan Chen and Caleb Webber and Ross Hardison and Joanne Nelson and Kym Hallsworth-Pepin and Kim Delehaunty and Chris Markovic and Pat Minx and Yucheng Feng and Colin Kremitzki and Makedonka Mitreva and Jarret Glasscock and Todd Wylie and Patricia Wohldmann and Prathapan Thiru and Michael Nhan and Craig Pohl and Smith, {Scott M.} and Shunfeng Hou and Renfree, {M. B.} and Elaine Mardis and Richard Wilson",

year = "2008",

doi = "10.1038/nature06936",

language = "English",

volume = "453",

pages = "175--256",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Publishing Group",

}

Warren, W, Hillier, L, Marshall Graves, J, Birney, E, Ponting, C, Grutzner, F, Belov, K, Miller, W, Clarke, L, Chinwalla, A, Yang, S-P, Heger, A, Locke, D, Miethke, P, Waters, P, Veyrunes, F, Fulton, L, Fulton, B, Graves, T, Wallis, J, Puente, X, Lopez-Otin, C, Ordonez, G, Eichler, E, Chen, L, Cheng, Z, DEAKIN, J, Alsop, A, Thompson, K, Kirby, P, Papenfuss, A, Wakefield, M, Olender, T, Lancet, D, Huttley, G, Smit, A, Pask, A, Temple-Smith, P, Batzer, M, Walker, J, Konkel, MK, Robert, HS, Whittington, C, Wong, E, Gemmell, N, Buschiazzo, E, Jentzsch, I, Merkel, A, Schmitz, J, Zemann, A, Churakov, G, Kriegs, J, Brosius, J, Murchison, E, Sachidanandam, R, Smith, C, Hannon, G, Tsend-Ayush, E, McMillan, D, Attenborough, R, Rens, W, Ferguson-Smith, M, Lefevre, C, Sharp, J, Nicholas, KR, Ray, DA, Kube, M, Reinhardt, R, Pringle, T, Taylor, J, Jones, R, Nixon, B, Dacheux, J-L, Niwa, H, Sekita, Y, Huang, X, Stark, A, Kheradpour, P, Kellis, M, Flicek, P, Chen, Y, Webber, C, Hardison, R, Nelson, J, Hallsworth-Pepin, K, Delehaunty, K, Markovic, C, Minx, P, Feng, Y, Kremitzki, C, Mitreva, M, Glasscock, J, Wylie, T, Wohldmann, P, Thiru, P, Nhan, M, Pohl, C, Smith, SM, Hou, S, Renfree, MB, Mardis, E & Wilson, R 2008, 'Genome analysis of the platypus reveals unique signatures of evolution', Nature, vol. 453, pp. 175-256. https://doi.org/10.1038/nature06936

TY - JOUR

T1 - Genome analysis of the platypus reveals unique signatures of evolution

AU - Warren, Wesley

AU - Hillier, LaDeana

AU - Marshall Graves, Jenny

AU - Birney, Ewan

AU - Ponting, Chris

AU - Grutzner, Frank

AU - Belov, Katherine

AU - Miller, Webb

AU - Clarke, Laura

AU - Chinwalla, Asif

AU - Yang, Shiaw-Pyng

AU - Heger, Andreas

AU - Locke, Devin

AU - Miethke, Pat

AU - Waters, Paul

AU - Veyrunes, Frederick

AU - Fulton, Lucinda

AU - Fulton, Bob

AU - Graves, Tina

AU - Wallis, John

AU - Puente, Xose

AU - Lopez-Otin, Carlos

AU - Ordonez, Gonzalo

AU - Eichler, Evan

AU - Chen, L

AU - Cheng, Ze

AU - DEAKIN, Janine

AU - Alsop, Amber

AU - Thompson, Katherine

AU - Kirby, Patrick

AU - Papenfuss, Anthony

AU - Wakefield, Matthew

AU - Olender, Tsviya

AU - Lancet, Doron

AU - Huttley, Gavin

AU - Smit, Arian

AU - Pask, Andrew

AU - Temple-Smith, Peter

AU - Batzer, Mark

AU - Walker, Jerilyn

AU - Konkel, Miriam K.

AU - Robert, Harris S.

AU - Whittington, Camilla

AU - Wong, Emily

AU - Gemmell, Neil

AU - Buschiazzo, Emmanuel

AU - Jentzsch, Iris

AU - Merkel, Angelika

AU - Schmitz, Juergen

AU - Zemann, Anja

AU - Churakov, Gennady

AU - Kriegs, Jan

AU - Brosius, Juergen

AU - Murchison, Elizabeth

AU - Sachidanandam, Ravi

AU - Smith, Carly

AU - Hannon, Gregory

AU - Tsend-Ayush, Enkhjargal

AU - McMillan, Daniel

AU - Attenborough, Rosalind

AU - Rens, Willem

AU - Ferguson-Smith, Malcolm

AU - Lefevre, Christophe

AU - Sharp, Julie

AU - Nicholas, Kevin R.

AU - Ray, David A.

AU - Kube, Michael

AU - Reinhardt, reinhardt

AU - Pringle, Thomas

AU - Taylor, James

AU - Jones, Russell

AU - Nixon, Brett

AU - Dacheux, Jean-Louis

AU - Niwa, Hitoshi

AU - Sekita, Yoko

AU - Huang, Xiaoqiu

AU - Stark, Alexander

AU - Kheradpour, Pouya

AU - Kellis, Manolis

AU - Flicek, Paul

AU - Chen, Yuan

AU - Webber, Caleb

AU - Hardison, Ross

AU - Nelson, Joanne

AU - Hallsworth-Pepin, Kym

AU - Delehaunty, Kim

AU - Markovic, Chris

AU - Minx, Pat

AU - Feng, Yucheng

AU - Kremitzki, Colin

AU - Mitreva, Makedonka

AU - Glasscock, Jarret

AU - Wylie, Todd

AU - Wohldmann, Patricia

AU - Thiru, Prathapan

AU - Nhan, Michael

AU - Pohl, Craig

AU - Smith, Scott M.

AU - Hou, Shunfeng

AU - Renfree, M. B.

AU - Mardis, Elaine

AU - Wilson, Richard

PY - 2008

Y1 - 2008

N2 - We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venomsimilar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation.

AB - We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venomsimilar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation.

UR - http://dx.doi.org/10.1038/nature07253

U2 - 10.1038/nature06936

DO - 10.1038/nature06936

M3 - Article

SN - 0028-0836

VL - 453

SP - 175

EP - 256

JO - Nature

JF - Nature

ER -

Genome analysis of the platypus reveals unique signatures of evolution

Abstract

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