Genome analysis of the platypus reveals unique signatures of evolution

Welsey C Warren; LaDeana W Hillier; Jennifer A Marshall-Graves; Ewan Birney; Chris P Ponting; Frank Grutzner; Katherine Belov; Webb Miller; Laura Clarke; Asif T Chinwalla; S-P Yang; Andreas Heger; Devin P Locke; Pat Miethke; Paul D Waters; Frederick Veyrunes; Lucinda Fulton; Bob Fulton; Tina Graves; John Wallis; Xose S Puente; Carlos Lopez-Otin; Gonzalo R Ordonez; Evan E Eichler; Lin Chen; Ze Cheng; Janine E Deakin; Amber Alsop; Katherine Thompson; Patrick Kirby; Anthony T Papenfuss; Matthew J Wakefield; Tsviya Olender; Doron Lancet; Gavin A Huttley; Arian FA Smit; Andrew Pask; Peter Derek Mcneill Temple-Smith; Mark A Batzer; Jerilyn A Walker; Mariam K Konkel; Robert S Harris; Camilla M Whittington; Emily SW Wong; Neil J Gemmell; Emmanuel Buschiazzo; Iris M Vargas Jentzsch; Angelika Merkel; Juergen Schmitz; Anja Zemann; Gennady Churakov; Jan Ole Kriegs; Juergen Brosius; Elizabeth P Murchison; Ravi Sachidanandam; Carly Smith; Gregory J Hannon; Enkhjargal Tsend-Ayush; Daniel McMillan; Rosalind Attenborough; Willem Rens; Malcolm Ferguson-Smith; Christophe Marc Lefevre; Julie A Sharp; Kevin R Nicholas; David A Ray; Michael Kube; Richard Reinhardt; Thomas H Pringle; James Taylor; Russell C 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 N Nhan; Craig S Pohl; Scott M Smith; Shunfeng Hou; Marilyn Renfree; Elaine R Mardis; Richard K Wilson

doi:10.1038/nature06936

Genome analysis of the platypus reveals unique signatures of evolution

Welsey C Warren, LaDeana W Hillier, Jennifer A Marshall-Graves, Ewan Birney, Chris P Ponting, Frank Grutzner, Katherine Belov, Webb Miller, Laura Clarke, Asif T Chinwalla, S-P Yang, Andreas Heger, Devin P Locke, Pat Miethke, Paul D Waters, Frederick Veyrunes, Lucinda Fulton, Bob Fulton, Tina Graves, John WallisXose S Puente, Carlos Lopez-Otin, Gonzalo R Ordonez, Evan E Eichler, Lin Chen, Ze Cheng, Janine E Deakin, Amber Alsop, Katherine Thompson, Patrick Kirby, Anthony T Papenfuss, Matthew J Wakefield, Tsviya Olender, Doron Lancet, Gavin A Huttley, Arian FA Smit, Andrew Pask, Peter Derek Mcneill Temple-Smith, Mark A Batzer, Jerilyn A Walker, Mariam K Konkel, Robert S Harris, Camilla M Whittington, Emily SW Wong, Neil J Gemmell, Emmanuel Buschiazzo, Iris M Vargas Jentzsch, Angelika Merkel, Juergen Schmitz, Anja Zemann, Gennady Churakov, Jan Ole Kriegs, Juergen Brosius, Elizabeth P Murchison, Ravi Sachidanandam, Carly Smith, Gregory J Hannon, Enkhjargal Tsend-Ayush, Daniel McMillan, Rosalind Attenborough, Willem Rens, Malcolm Ferguson-Smith, Christophe Marc Lefevre, Julie A Sharp, Kevin R Nicholas, David A Ray, Michael Kube, Richard Reinhardt, Thomas H Pringle, James Taylor, Russell C 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 N Nhan, Craig S Pohl, Scott M Smith, Shunfeng Hou, Marilyn Renfree, Elaine R Mardis, Richard K Wilson

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

501 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 venom similar 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 - 183
Number of pages	9
Journal	Nature
Volume	453
Issue number	7192
DOIs	https://doi.org/10.1038/nature06936
Publication status	Published - 2008

Access to Document

10.1038/nature06936

RM sElocation

Cite this

Warren, W. C., Hillier, L. W., Marshall-Graves, J. A., Birney, E., Ponting, C. P., Grutzner, F., Belov, K., Miller, W., Clarke, L., Chinwalla, A. T., Yang, S-P., Heger, A., Locke, D. P., Miethke, P., Waters, P. D., Veyrunes, F., Fulton, L., Fulton, B., Graves, T., ... Wilson, R. K. (2008). Genome analysis of the platypus reveals unique signatures of evolution. Nature, 453(7192), 175 - 183. https://doi.org/10.1038/nature06936

Warren, Welsey C ; Hillier, LaDeana W ; Marshall-Graves, Jennifer A ; Birney, Ewan ; Ponting, Chris P ; Grutzner, Frank ; Belov, Katherine ; Miller, Webb ; Clarke, Laura ; Chinwalla, Asif T ; Yang, S-P ; Heger, Andreas ; Locke, Devin P ; Miethke, Pat ; Waters, Paul D ; Veyrunes, Frederick ; Fulton, Lucinda ; Fulton, Bob ; Graves, Tina ; Wallis, John ; Puente, Xose S ; Lopez-Otin, Carlos ; Ordonez, Gonzalo R ; Eichler, Evan E ; Chen, Lin ; Cheng, Ze ; Deakin, Janine E ; Alsop, Amber ; Thompson, Katherine ; Kirby, Patrick ; Papenfuss, Anthony T ; Wakefield, Matthew J ; Olender, Tsviya ; Lancet, Doron ; Huttley, Gavin A ; Smit, Arian FA ; Pask, Andrew ; Temple-Smith, Peter Derek Mcneill ; Batzer, Mark A ; Walker, Jerilyn A ; Konkel, Mariam K ; Harris, Robert S ; Whittington, Camilla M ; Wong, Emily SW ; Gemmell, Neil J ; Buschiazzo, Emmanuel ; Vargas Jentzsch, Iris M ; Merkel, Angelika ; Schmitz, Juergen ; Zemann, Anja ; Churakov, Gennady ; Kriegs, Jan Ole ; Brosius, Juergen ; Murchison, Elizabeth P ; Sachidanandam, Ravi ; Smith, Carly ; Hannon, Gregory J ; Tsend-Ayush, Enkhjargal ; McMillan, Daniel ; Attenborough, Rosalind ; Rens, Willem ; Ferguson-Smith, Malcolm ; Lefevre, Christophe Marc ; Sharp, Julie A ; Nicholas, Kevin R ; Ray, David A ; Kube, Michael ; Reinhardt, Richard ; Pringle, Thomas H ; Taylor, James ; Jones, Russell C ; Nixon, Brett ; Dacheux, Jean-Louis ; Niwa, Hitoshi ; Sekita, Yoko ; Huang, Xiaoqiu ; Stark, Alexander ; Kheradpour, Pouya ; Kellis, Manolis ; Flicek, Paul ; Chen, Yuan ; Webber, Caleb ; Hardison, Ross ; Nelson, Joanne ; Hallsworth-Pepin, Kym ; Delehaunty, Kim ; Markovic, Chris ; Minx, Pat ; Feng, Yucheng ; Kremitzki, Colin ; Mitreva, Makedonka ; Glasscock, Jarret ; Wylie, Todd ; Wohldmann, Patricia ; Thiru, Prathapan ; Nhan, Michael N ; Pohl, Craig S ; Smith, Scott M ; Hou, Shunfeng ; Renfree, Marilyn ; Mardis, Elaine R ; Wilson, Richard K. / Genome analysis of the platypus reveals unique signatures of evolution. In: Nature. 2008 ; Vol. 453, No. 7192. pp. 175 - 183.

@article{192af2920fe441919946a9e1f2b31d3c,

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 venom similar 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 = "Warren, {Welsey C} and Hillier, {LaDeana W} and Marshall-Graves, {Jennifer A} and Ewan Birney and Ponting, {Chris P} and Frank Grutzner and Katherine Belov and Webb Miller and Laura Clarke and Chinwalla, {Asif T} and S-P Yang and Andreas Heger and Locke, {Devin P} and Pat Miethke and Waters, {Paul D} and Frederick Veyrunes and Lucinda Fulton and Bob Fulton and Tina Graves and John Wallis and Puente, {Xose S} and Carlos Lopez-Otin and Ordonez, {Gonzalo R} and Eichler, {Evan E} and Lin Chen and Ze Cheng and Deakin, {Janine E} and Amber Alsop and Katherine Thompson and Patrick Kirby and Papenfuss, {Anthony T} and Wakefield, {Matthew J} and Tsviya Olender and Doron Lancet and Huttley, {Gavin A} and Smit, {Arian FA} and Andrew Pask and Temple-Smith, {Peter Derek Mcneill} and Batzer, {Mark A} and Walker, {Jerilyn A} and Konkel, {Mariam K} and Harris, {Robert S} and Whittington, {Camilla M} and Wong, {Emily SW} and Gemmell, {Neil J} and Emmanuel Buschiazzo and {Vargas Jentzsch}, {Iris M} and Angelika Merkel and Juergen Schmitz and Anja Zemann and Gennady Churakov and Kriegs, {Jan Ole} and Juergen Brosius and Murchison, {Elizabeth P} and Ravi Sachidanandam and Carly Smith and Hannon, {Gregory J} and Enkhjargal Tsend-Ayush and Daniel McMillan and Rosalind Attenborough and Willem Rens and Malcolm Ferguson-Smith and Lefevre, {Christophe Marc} and Sharp, {Julie A} and Nicholas, {Kevin R} and Ray, {David A} and Michael Kube and Richard Reinhardt and Pringle, {Thomas H} and James Taylor and Jones, {Russell C} 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 Nhan, {Michael N} and Pohl, {Craig S} and Smith, {Scott M} and Shunfeng Hou and Marilyn Renfree and Mardis, {Elaine R} and Wilson, {Richard K}",

year = "2008",

doi = "10.1038/nature06936",

language = "English",

volume = "453",

pages = "175 -- 183",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Publishing Group",

number = "7192",

}

Warren, WC, Hillier, LW, Marshall-Graves, JA, Birney, E, Ponting, CP, Grutzner, F, Belov, K, Miller, W, Clarke, L, Chinwalla, AT, Yang, S-P, Heger, A, Locke, DP, Miethke, P, Waters, PD, Veyrunes, F, Fulton, L, Fulton, B, Graves, T, Wallis, J, Puente, XS, Lopez-Otin, C, Ordonez, GR, Eichler, EE, Chen, L, Cheng, Z, Deakin, JE, Alsop, A, Thompson, K, Kirby, P, Papenfuss, AT, Wakefield, MJ, Olender, T, Lancet, D, Huttley, GA, Smit, AFA, Pask, A, Temple-Smith, PDM, Batzer, MA, Walker, JA, Konkel, MK, Harris, RS, Whittington, CM, Wong, ESW, Gemmell, NJ, Buschiazzo, E, Vargas Jentzsch, IM, Merkel, A, Schmitz, J, Zemann, A, Churakov, G, Kriegs, JO, Brosius, J, Murchison, EP, Sachidanandam, R, Smith, C, Hannon, GJ, Tsend-Ayush, E, McMillan, D, Attenborough, R, Rens, W, Ferguson-Smith, M, Lefevre, CM, Sharp, JA, Nicholas, KR, Ray, DA, Kube, M, Reinhardt, R, Pringle, TH, Taylor, J, Jones, RC, 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, MN, Pohl, CS, Smith, SM, Hou, S, Renfree, M, Mardis, ER & Wilson, RK 2008, 'Genome analysis of the platypus reveals unique signatures of evolution', Nature, vol. 453, no. 7192, pp. 175 - 183. https://doi.org/10.1038/nature06936

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

In: Nature, Vol. 453, No. 7192, 2008, p. 175 - 183.

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

TY - JOUR

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

AU - Warren, Welsey C

AU - Hillier, LaDeana W

AU - Marshall-Graves, Jennifer A

AU - Birney, Ewan

AU - Ponting, Chris P

AU - Grutzner, Frank

AU - Belov, Katherine

AU - Miller, Webb

AU - Clarke, Laura

AU - Chinwalla, Asif T

AU - Yang, S-P

AU - Heger, Andreas

AU - Locke, Devin P

AU - Miethke, Pat

AU - Waters, Paul D

AU - Veyrunes, Frederick

AU - Fulton, Lucinda

AU - Fulton, Bob

AU - Graves, Tina

AU - Wallis, John

AU - Puente, Xose S

AU - Lopez-Otin, Carlos

AU - Ordonez, Gonzalo R

AU - Eichler, Evan E

AU - Chen, Lin

AU - Cheng, Ze

AU - Deakin, Janine E

AU - Alsop, Amber

AU - Thompson, Katherine

AU - Kirby, Patrick

AU - Papenfuss, Anthony T

AU - Wakefield, Matthew J

AU - Olender, Tsviya

AU - Lancet, Doron

AU - Huttley, Gavin A

AU - Smit, Arian FA

AU - Pask, Andrew

AU - Temple-Smith, Peter Derek Mcneill

AU - Batzer, Mark A

AU - Walker, Jerilyn A

AU - Konkel, Mariam K

AU - Harris, Robert S

AU - Whittington, Camilla M

AU - Wong, Emily SW

AU - Gemmell, Neil J

AU - Buschiazzo, Emmanuel

AU - Vargas Jentzsch, Iris M

AU - Merkel, Angelika

AU - Schmitz, Juergen

AU - Zemann, Anja

AU - Churakov, Gennady

AU - Kriegs, Jan Ole

AU - Brosius, Juergen

AU - Murchison, Elizabeth P

AU - Sachidanandam, Ravi

AU - Smith, Carly

AU - Hannon, Gregory J

AU - Tsend-Ayush, Enkhjargal

AU - McMillan, Daniel

AU - Attenborough, Rosalind

AU - Rens, Willem

AU - Ferguson-Smith, Malcolm

AU - Lefevre, Christophe Marc

AU - Sharp, Julie A

AU - Nicholas, Kevin R

AU - Ray, David A

AU - Kube, Michael

AU - Reinhardt, Richard

AU - Pringle, Thomas H

AU - Taylor, James

AU - Jones, Russell C

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 N

AU - Pohl, Craig S

AU - Smith, Scott M

AU - Hou, Shunfeng

AU - Renfree, Marilyn

AU - Mardis, Elaine R

AU - Wilson, Richard K

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 venom similar 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 venom similar 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://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18464734

U2 - 10.1038/nature06936

DO - 10.1038/nature06936

M3 - Article

VL - 453

SP - 175

EP - 183

JO - Nature

JF - Nature

SN - 0028-0836

IS - 7192

ER -