Genome 10K: A proposal to obtain whole-genome sequence for 10000 vertebrate species

David Haussler; Stephen J. O'Brien; Oliver A. Ryder; F. Keith Barker; Michele Clamp; Andrew J. Crawford; Robert Hanner; Olivier Hanotte; Warren E. Johnson; Jimmy A. McGuire; Webb Miller; Robert W. Murphy; William J. Murphy; Frederick H. Sheldon; Barry Sinervo; Byrappa Venkatesh; Edward O. Wiley; Fred W. Allendorf; George Amato; C. Scott Baker; Aaron Bauer; Albano Beja-Pereira; Eldredge Bermingham; Giacomo Bernardi; Cibele R. Bonvicino; Sydney Brenner; Terry Burke; Joel Cracraft; Mark Diekhans; Scott Edwards; Per G.P. Ericson; James Estes; Jon Fjelsda; Nate Flesness; Tony Gamble; Philippe Gaubert; Alexander S. Graphodatsky; Jennifer A. Marshall Graves; Eric D. Green; Richard E. Green; Shannon Hackett; Paul Hebert; Kristofer M. Helgen; Leo Joseph; Bailey Kessing; David M. Kingsley; Harris A. Lewin; Gordon Luikart; Paolo Martelli; Miguel A.M. Moreira; Ngan Nguyen; Guillermo Ortí; Brian L. Pike; David Michael Rawson; Stephan C. Schuster; Héctor N. Seuánez; H. Bradley Shaffer; Mark S. Springer; Joshua Michael Stuart; Joanna Sumner; Emma Teeling; Robert C. Vrijenhoek; Robert D. Ward; Wesley C. Warren; Robert Wayne; Terrie M. Williams; Nathan D. Wolfe; Ya Ping Zhang; Jennifer Graves; Mark Springer; Terrie Williams; Nathan Wolfe; Scott V. Edwards; Guillermo Orti; David M. Rawson; Adam Felsenfeld; Hector N. Seuanez; Joshua M. Stuart; Steve Turner

doi:10.1093/jhered/esp086

Genome 10K: A proposal to obtain whole-genome sequence for 10000 vertebrate species

David Haussler
, Stephen J. O'Brien
, Oliver A. Ryder
, F. Keith Barker
, Michele Clamp
, Andrew J. Crawford
, Robert Hanner
, Olivier Hanotte
, Warren E. Johnson
, Jimmy A. McGuire
, Webb Miller
, Robert W. Murphy
, William J. Murphy
, Frederick H. Sheldon
, Barry Sinervo
, Byrappa Venkatesh
, Edward O. Wiley
, Fred W. Allendorf
, George Amato
, C. Scott Baker

Aaron Bauer, Albano Beja-Pereira, Eldredge Bermingham, Giacomo Bernardi, Cibele R. Bonvicino, Sydney Brenner, Terry Burke, Joel Cracraft, Mark Diekhans, Scott Edwards, Per G.P. Ericson, James Estes, Jon Fjelsda, Nate Flesness, Tony Gamble, Philippe Gaubert, Alexander S. Graphodatsky, Jennifer A. Marshall Graves, Eric D. Green, Richard E. Green, Shannon Hackett, Paul Hebert, Kristofer M. Helgen, Leo Joseph, Bailey Kessing, David M. Kingsley, Harris A. Lewin, Gordon Luikart, Paolo Martelli, Miguel A.M. Moreira, Ngan Nguyen, Guillermo Ortí, Brian L. Pike, David Michael Rawson, Stephan C. Schuster, Héctor N. Seuánez, H. Bradley Shaffer, Mark S. Springer, Joshua Michael Stuart, Joanna Sumner, Emma Teeling, Robert C. Vrijenhoek, Robert D. Ward, Wesley C. Warren, Robert Wayne, Terrie M. Williams, Nathan D. Wolfe, Ya Ping Zhang, Jennifer Graves, Mark Springer, Terrie Williams, Nathan Wolfe, Scott V. Edwards, Guillermo Orti, David M. Rawson, Adam Felsenfeld, Hector N. Seuanez, Joshua M. Stuart, Steve Turner

Flathead Lake Biological Station

University of California at Santa Cruz
National Institutes of Health
Zoological Society of San Diego
University of Minnesota Twin Cities
Broad Institute
Universidad de los Andes Colombia
University of Guelph
University of Nottingham
University of California at Berkeley
Pennsylvania State University
Royal Ontario Museum
Texas A&M University
Louisiana State University
Agency for Science, Technology and Research, Singapore
University of Kansas
University of Montana
American Museum of Natural History
Oregon State University
Villanova University
University of Porto
Smithsonian Institution
Instituto Nacional de Câncer
Fundação Oswaldo Cruz
Salk Institute for Biological Studies
Okinawa Institute of Science and Technology Graduate University
University of Sheffield
Harvard University
Swedish Museum of Natural History
University of Copenhagen
International Species Information System
Muséum national d'histoire naturelle
RAS - Institute of Chemical Biology and Fundamental Medicine, Siberian Branch
Australian National University
Max Planck Institute for Evolutionary Anthropology
Field Museum of Natural History
CSIRO
SAIC
Stanford University
University of Illinois at Urbana-Champaign
Ocean Park
George Washington University
Global Viral Forecasting Initiative
University of Bedfordshire
Universidade Federal do Rio de Janeiro
University of California at Davis
University of California at Riverside
Museums Victoria
University College Dublin
Monterey Bay Aquarium Research Institute
Washington University St. Louis
University of California at Los Angeles
CAS - Kunming Institute of Zoology

Research output: Contribution to journal › Review article › peer-review

444 Scopus citations

Abstract

The human genome project has been recently complemented by whole-genome assessment sequence of 32 mammals and 24 nonmammalian vertebrate species suitable for comparative genomic analyses. Here we anticipate a precipitous drop in costs and increase in sequencing efficiency, with concomitant development of improved annotation technology and, therefore, propose to create a collection of tissue and DNA specimens for 10000 vertebrate species specifically designated for whole-genome sequencing in the very near future. For this purpose, we, the Genome 10K Community of Scientists (G10KCOS), will assemble and allocate a biospecimen collection of some 16203 representative vertebrate species spanning evolutionary diversity across living mammals, birds, nonavian reptiles, amphibians, and fishes (ca. 60000 living species). In this proposal, we present precise counts for these 16203 individual species with specimens presently tagged and stipulated for DNA sequencing by the G10KCOS. DNA sequencing has ushered in a new era of investigation in the biological sciences, allowing us to embark for the first time on a truly comprehensive study of vertebrate evolution, the results of which will touch nearly every aspect of vertebrate biological enquiry.

Original language	English
Pages (from-to)	659-674
Number of pages	16
Journal	Journal of Heredity
Volume	100
Issue number	6
DOIs	https://doi.org/10.1093/jhered/esp086
State	Published - Nov 1 2009

Funding

American Genetic Association, Gordon and Betty Moore Foundation, NHGRI Intramural Sequencing Center, and UCSC Alumni Association to cost of the Genome 10K workshop; Howard Hughes Medical Institute to D.H.; Gordon and Betty Moore Foundation to S.C.S.; Assembling the Euteleost Tree of Life to E.W.; National Science Foundation (0732819 to E.W., DEB-0640967 and 0543556 to J.A.M., 0817042 to H.B.S., EF0629849 to W.J.M., DEB-0443470 to G.O.); The Global Viral Forecasting Initiative to N.W., B.P., and M.L.; Biomedical Research Council of A*STAR, Singapore to B.V.; Natural Sciences and Engineering Research Council Discovery Grant to R.W.M.; National Basic Research Program of China (973 Program, 2007CB411600), the National Natural Science Foundation of China (30621092), and Bureau of Science and Technology of Yunnan Province to Y.Z.; MCB and SB RAS Programs (A.S.G.); Portuguese-American Foundation for Development, CIBIO, UP, University of Montana [G.L.] and Portuguese Science Foundation [PTDC/ CVT/69438/2006; PTDC/BIA-BDE/65625/2006 to G.L].

Funders	Funder number
0732819, 0543556, DEB-0640967, 0817042, DEB-0443470, EF0629849
University of California at Santa Cruz
Agency for Science, Technology and Research, Singapore
National Natural Science Foundation of China	30621092
PTDC/ CVT/69438/2006, PTDC/BIA-BDE/65625/2006
2007CB411600

Keywords

Ancestral state reconstruction
Comparative genomics
G10K
Molecular evolution
Species conservation
Vertebrate biology

Access to Document

10.1093/jhered/esp086

Cite this

Haussler, D., O'Brien, S. J., Ryder, O. A., Keith Barker, F., Clamp, M., Crawford, A. J., Hanner, R., Hanotte, O., Johnson, W. E., McGuire, J. A., Miller, W., Murphy, R. W., Murphy, W. J., Sheldon, F. H., Sinervo, B., Venkatesh, B., Wiley, E. O., Allendorf, F. W., Amato, G., ... Turner, S. (2009). Genome 10K: A proposal to obtain whole-genome sequence for 10000 vertebrate species. Journal of Heredity, 100(6), 659-674. https://doi.org/10.1093/jhered/esp086

@article{6f50e02e4b8a4fba932ad870f4fc0725,

title = "Genome 10K: A proposal to obtain whole-genome sequence for 10000 vertebrate species",

abstract = "The human genome project has been recently complemented by whole-genome assessment sequence of 32 mammals and 24 nonmammalian vertebrate species suitable for comparative genomic analyses. Here we anticipate a precipitous drop in costs and increase in sequencing efficiency, with concomitant development of improved annotation technology and, therefore, propose to create a collection of tissue and DNA specimens for 10000 vertebrate species specifically designated for whole-genome sequencing in the very near future. For this purpose, we, the Genome 10K Community of Scientists (G10KCOS), will assemble and allocate a biospecimen collection of some 16203 representative vertebrate species spanning evolutionary diversity across living mammals, birds, nonavian reptiles, amphibians, and fishes (ca. 60000 living species). In this proposal, we present precise counts for these 16203 individual species with specimens presently tagged and stipulated for DNA sequencing by the G10KCOS. DNA sequencing has ushered in a new era of investigation in the biological sciences, allowing us to embark for the first time on a truly comprehensive study of vertebrate evolution, the results of which will touch nearly every aspect of vertebrate biological enquiry.",

keywords = "Ancestral state reconstruction, Comparative genomics, G10K, Molecular evolution, Species conservation, Vertebrate biology",

author = "David Haussler and O'Brien, \{Stephen J.\} and Ryder, \{Oliver A.\} and \{Keith Barker\}, F. and Michele Clamp and Crawford, \{Andrew J.\} and Robert Hanner and Olivier Hanotte and Johnson, \{Warren E.\} and McGuire, \{Jimmy A.\} and Webb Miller and Murphy, \{Robert W.\} and Murphy, \{William J.\} and Sheldon, \{Frederick H.\} and Barry Sinervo and Byrappa Venkatesh and Wiley, \{Edward O.\} and Allendorf, \{Fred W.\} and George Amato and \{Scott Baker\}, C. and Aaron Bauer and Albano Beja-Pereira and Eldredge Bermingham and Giacomo Bernardi and Bonvicino, \{Cibele R.\} and Sydney Brenner and Terry Burke and Joel Cracraft and Mark Diekhans and Scott Edwards and Ericson, \{Per G.P.\} and James Estes and Jon Fjelsda and Nate Flesness and Tony Gamble and Philippe Gaubert and Graphodatsky, \{Alexander S.\} and \{Marshall Graves\}, \{Jennifer A.\} and Green, \{Eric D.\} and Green, \{Richard E.\} and Shannon Hackett and Paul Hebert and Helgen, \{Kristofer M.\} and Leo Joseph and Bailey Kessing and Kingsley, \{David M.\} and Lewin, \{Harris A.\} and Gordon Luikart and Paolo Martelli and Moreira, \{Miguel A.M.\} and Ngan Nguyen and Guillermo Ort{\'i} and Pike, \{Brian L.\} and Rawson, \{David Michael\} and Schuster, \{Stephan C.\} and Seu{\'a}nez, \{H{\'e}ctor N.\} and \{Bradley Shaffer\}, H. and Springer, \{Mark S.\} and Stuart, \{Joshua Michael\} and Joanna Sumner and Emma Teeling and Vrijenhoek, \{Robert C.\} and Ward, \{Robert D.\} and Warren, \{Wesley C.\} and Robert Wayne and Williams, \{Terrie M.\} and Wolfe, \{Nathan D.\} and Zhang, \{Ya Ping\} and Jennifer Graves and Mark Springer and Terrie Williams and Nathan Wolfe and Edwards, \{Scott V.\} and Guillermo Orti and Rawson, \{David M.\} and Adam Felsenfeld and Seuanez, \{Hector N.\} and Stuart, \{Joshua M.\} and Steve Turner",

note = "Funding Information: American Genetic Association, Gordon and Betty Moore Foundation, NHGRI Intramural Sequencing Center, and UCSC Alumni Association to cost of the Genome 10K workshop; Howard Hughes Medical Institute to D.H.; Gordon and Betty Moore Foundation to S.C.S.; Assembling the Euteleost Tree of Life to E.W.; National Science Foundation (0732819 to E.W., DEB-0640967 and 0543556 to J.A.M., 0817042 to H.B.S., EF0629849 to W.J.M., DEB-0443470 to G.O.); The Global Viral Forecasting Initiative to N.W., B.P., and M.L.; Biomedical Research Council of A*STAR, Singapore to B.V.; Natural Sciences and Engineering Research Council Discovery Grant to R.W.M.; National Basic Research Program of China (973 Program, 2007CB411600), the National Natural Science Foundation of China (30621092), and Bureau of Science and Technology of Yunnan Province to Y.Z.; MCB and SB RAS Programs (A.S.G.); Portuguese-American Foundation for Development, CIBIO, UP, University of Montana [G.L.] and Portuguese Science Foundation [PTDC/ CVT/69438/2006; PTDC/BIA-BDE/65625/2006 to G.L].",

year = "2009",

month = nov,

day = "1",

doi = "10.1093/jhered/esp086",

language = "English",

volume = "100",

pages = "659--674",

journal = "Journal of Heredity",

issn = "0022-1503",

publisher = "Oxford University Press",

number = "6",

}

Haussler, D, O'Brien, SJ, Ryder, OA, Keith Barker, F, Clamp, M, Crawford, AJ, Hanner, R, Hanotte, O, Johnson, WE, McGuire, JA, Miller, W, Murphy, RW, Murphy, WJ, Sheldon, FH, Sinervo, B, Venkatesh, B, Wiley, EO, Allendorf, FW, Amato, G, Scott Baker, C, Bauer, A, Beja-Pereira, A, Bermingham, E, Bernardi, G, Bonvicino, CR, Brenner, S, Burke, T, Cracraft, J, Diekhans, M, Edwards, S, Ericson, PGP, Estes, J, Fjelsda, J, Flesness, N, Gamble, T, Gaubert, P, Graphodatsky, AS, Marshall Graves, JA, Green, ED, Green, RE, Hackett, S, Hebert, P, Helgen, KM, Joseph, L, Kessing, B, Kingsley, DM, Lewin, HA, Luikart, G, Martelli, P, Moreira, MAM, Nguyen, N, Ortí, G, Pike, BL, Rawson, DM, Schuster, SC, Seuánez, HN, Bradley Shaffer, H, Springer, MS, Stuart, JM, Sumner, J, Teeling, E, Vrijenhoek, RC, Ward, RD, Warren, WC, Wayne, R, Williams, TM, Wolfe, ND, Zhang, YP, Graves, J, Springer, M, Williams, T, Wolfe, N, Edwards, SV, Orti, G, Rawson, DM, Felsenfeld, A, Seuanez, HN, Stuart, JM & Turner, S 2009, 'Genome 10K: A proposal to obtain whole-genome sequence for 10000 vertebrate species', Journal of Heredity, vol. 100, no. 6, pp. 659-674. https://doi.org/10.1093/jhered/esp086

TY - JOUR

T1 - Genome 10K

T2 - A proposal to obtain whole-genome sequence for 10000 vertebrate species

AU - Haussler, David

AU - O'Brien, Stephen J.

AU - Ryder, Oliver A.

AU - Keith Barker, F.

AU - Clamp, Michele

AU - Crawford, Andrew J.

AU - Hanner, Robert

AU - Hanotte, Olivier

AU - Johnson, Warren E.

AU - McGuire, Jimmy A.

AU - Miller, Webb

AU - Murphy, Robert W.

AU - Murphy, William J.

AU - Sheldon, Frederick H.

AU - Sinervo, Barry

AU - Venkatesh, Byrappa

AU - Wiley, Edward O.

AU - Allendorf, Fred W.

AU - Amato, George

AU - Scott Baker, C.

AU - Bauer, Aaron

AU - Beja-Pereira, Albano

AU - Bermingham, Eldredge

AU - Bernardi, Giacomo

AU - Bonvicino, Cibele R.

AU - Brenner, Sydney

AU - Burke, Terry

AU - Cracraft, Joel

AU - Diekhans, Mark

AU - Edwards, Scott

AU - Ericson, Per G.P.

AU - Estes, James

AU - Fjelsda, Jon

AU - Flesness, Nate

AU - Gamble, Tony

AU - Gaubert, Philippe

AU - Graphodatsky, Alexander S.

AU - Marshall Graves, Jennifer A.

AU - Green, Eric D.

AU - Green, Richard E.

AU - Hackett, Shannon

AU - Hebert, Paul

AU - Helgen, Kristofer M.

AU - Joseph, Leo

AU - Kessing, Bailey

AU - Kingsley, David M.

AU - Lewin, Harris A.

AU - Luikart, Gordon

AU - Martelli, Paolo

AU - Moreira, Miguel A.M.

AU - Nguyen, Ngan

AU - Ortí, Guillermo

AU - Pike, Brian L.

AU - Rawson, David Michael

AU - Schuster, Stephan C.

AU - Seuánez, Héctor N.

AU - Bradley Shaffer, H.

AU - Springer, Mark S.

AU - Stuart, Joshua Michael

AU - Sumner, Joanna

AU - Teeling, Emma

AU - Vrijenhoek, Robert C.

AU - Ward, Robert D.

AU - Warren, Wesley C.

AU - Wayne, Robert

AU - Williams, Terrie M.

AU - Wolfe, Nathan D.

AU - Zhang, Ya Ping

AU - Graves, Jennifer

AU - Springer, Mark

AU - Williams, Terrie

AU - Wolfe, Nathan

AU - Edwards, Scott V.

AU - Orti, Guillermo

AU - Rawson, David M.

AU - Felsenfeld, Adam

AU - Seuanez, Hector N.

AU - Stuart, Joshua M.

AU - Turner, Steve

N1 - Funding Information: American Genetic Association, Gordon and Betty Moore Foundation, NHGRI Intramural Sequencing Center, and UCSC Alumni Association to cost of the Genome 10K workshop; Howard Hughes Medical Institute to D.H.; Gordon and Betty Moore Foundation to S.C.S.; Assembling the Euteleost Tree of Life to E.W.; National Science Foundation (0732819 to E.W., DEB-0640967 and 0543556 to J.A.M., 0817042 to H.B.S., EF0629849 to W.J.M., DEB-0443470 to G.O.); The Global Viral Forecasting Initiative to N.W., B.P., and M.L.; Biomedical Research Council of A*STAR, Singapore to B.V.; Natural Sciences and Engineering Research Council Discovery Grant to R.W.M.; National Basic Research Program of China (973 Program, 2007CB411600), the National Natural Science Foundation of China (30621092), and Bureau of Science and Technology of Yunnan Province to Y.Z.; MCB and SB RAS Programs (A.S.G.); Portuguese-American Foundation for Development, CIBIO, UP, University of Montana [G.L.] and Portuguese Science Foundation [PTDC/ CVT/69438/2006; PTDC/BIA-BDE/65625/2006 to G.L].

PY - 2009/11/1

Y1 - 2009/11/1

N2 - The human genome project has been recently complemented by whole-genome assessment sequence of 32 mammals and 24 nonmammalian vertebrate species suitable for comparative genomic analyses. Here we anticipate a precipitous drop in costs and increase in sequencing efficiency, with concomitant development of improved annotation technology and, therefore, propose to create a collection of tissue and DNA specimens for 10000 vertebrate species specifically designated for whole-genome sequencing in the very near future. For this purpose, we, the Genome 10K Community of Scientists (G10KCOS), will assemble and allocate a biospecimen collection of some 16203 representative vertebrate species spanning evolutionary diversity across living mammals, birds, nonavian reptiles, amphibians, and fishes (ca. 60000 living species). In this proposal, we present precise counts for these 16203 individual species with specimens presently tagged and stipulated for DNA sequencing by the G10KCOS. DNA sequencing has ushered in a new era of investigation in the biological sciences, allowing us to embark for the first time on a truly comprehensive study of vertebrate evolution, the results of which will touch nearly every aspect of vertebrate biological enquiry.

AB - The human genome project has been recently complemented by whole-genome assessment sequence of 32 mammals and 24 nonmammalian vertebrate species suitable for comparative genomic analyses. Here we anticipate a precipitous drop in costs and increase in sequencing efficiency, with concomitant development of improved annotation technology and, therefore, propose to create a collection of tissue and DNA specimens for 10000 vertebrate species specifically designated for whole-genome sequencing in the very near future. For this purpose, we, the Genome 10K Community of Scientists (G10KCOS), will assemble and allocate a biospecimen collection of some 16203 representative vertebrate species spanning evolutionary diversity across living mammals, birds, nonavian reptiles, amphibians, and fishes (ca. 60000 living species). In this proposal, we present precise counts for these 16203 individual species with specimens presently tagged and stipulated for DNA sequencing by the G10KCOS. DNA sequencing has ushered in a new era of investigation in the biological sciences, allowing us to embark for the first time on a truly comprehensive study of vertebrate evolution, the results of which will touch nearly every aspect of vertebrate biological enquiry.

KW - Ancestral state reconstruction

KW - Comparative genomics

KW - G10K

KW - Molecular evolution

KW - Species conservation

KW - Vertebrate biology

UR - https://www.scopus.com/pages/publications/71049176982

U2 - 10.1093/jhered/esp086

DO - 10.1093/jhered/esp086

M3 - Review article

C2 - 19892720

AN - SCOPUS:71049176982

SN - 0022-1503

VL - 100

SP - 659

EP - 674

JO - Journal of Heredity

JF - Journal of Heredity

IS - 6

ER -

Genome 10K: A proposal to obtain whole-genome sequence for 10000 vertebrate species

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