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 BakerAaron 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

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

421 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 (US)
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

Bibliographical 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].

Keywords

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

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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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

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

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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.",

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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,

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doi = "10.1093/jhered/esp086",

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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

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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.

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KW - Comparative genomics

KW - G10K

KW - Molecular evolution

KW - Species conservation

KW - Vertebrate biology

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

Abstract

Bibliographical note

Keywords

UN SDGs

Access

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