The common marmoset genome provides insight into primate biology and evolution

Kim C. Worley; Wesley C. Warren; Jeffrey Rogers; Devin Locke; Donna M. Muzny; Elaine R. Mardis; George M. Weinstock; Suzette D. Tardif; Kjersti M. Aagaard; Nicoletta Archidiacono; Nirmala Arul Rayan; Mark A. Batzer; Kathryn Beal; Brona Brejova; Oronzo Capozzi; Saverio B. Capuano; Claudio Casola; Mimi M. Chandrabose; Andrew Cree; Marvin Diep Dao; Pieter J. De Jong; Ricardo Cruz-Herrera del Rosario; Kim D. Delehaunty; Huyen H. Dinh; Evan E. Eichler; Stephen Fitzgerald; Paul Flicek; Catherine C. Fontenot; R. Gerald Fowler; Catrina Fronick; Lucinda A. Fulton; Robert S. Fulton; Ramatu Ayiesha Gabisi; Daniel Gerlach; Tina A. Graves; Preethi H. Gunaratne; Matthew W. Hahn; David Haig; Yi Han; R. Alan Harris; Javier Herrero; La Deana W. Hillier; Robert Hubley; Jennifer F. Hughes; Jennifer Hume; Shalini N. Jhangiani; Lynn B. Jorde; Vandita Joshi; Emre Karakor; Miriam K. Konkel; Carolin Kosiol; Christie LKovar; Evgenia V. Kriventseva; Sandra L. Lee; Lora R. Lewis; Yih Shin Liu; John Lopez; Carlos Lopez-Otin; Belen Lorente-Galdos; Keith G. Mansfield; Tomas Marques-Bonet; Patrick Minx; Doriana Misceo; J. Scott Moncrieff; Margaret B. Morgan; Lynne V. Nazareth; Irene Newsham; Ngoc Bich Nguyen; Geoffrey O. Okwuonu; Shyam Prabhakar; Lora Perales; Ling Ling Pu; Xose S. Puente; Victor Quesada; Megan C. Ranck; Brian J. Raney; Muthuswamy Raveendran; David Rio Deiros; Mariano Rocchi; David Rodriguez; Corinna Ross; Magali Ruffier; San Juana Ruiz; Saba Sajjadian; Jireh Santibanez; Daniel R. Schrider; Steve Searle; Helen Skaletsky; Benjamin Soibam; Arian F.A. Smit; Jayantha B. Tennakoon; Lubomir Tomaska; Brygg Ullmer; Charles E. Vejnar; Mario Ventura; Albert J. Vilella; Tomas Vinar; Jan Hinnerk Vogel; Jerilyn A. Walker; Qing Wang; Crystal M. Warner; Derek E. Wildman; David J. Witherspoon; Rita A. Wright; Yuanqing Wu; Weimin Xiao; Jinchuan Xing; Evgeny M. Zdobnov; Baoli Zhu; Richard A. Gibbs; Richard K. Wilson

doi:10.1038/ng.3042

The common marmoset genome provides insight into primate biology and evolution

Kim C. Worley, Wesley C. Warren, Jeffrey Rogers, Devin Locke, Donna M. Muzny, Elaine R. Mardis, George M. Weinstock, Suzette D. Tardif, Kjersti M. Aagaard, Nicoletta Archidiacono, Nirmala Arul Rayan, Mark A. Batzer, Kathryn Beal, Brona Brejova, Oronzo Capozzi, Saverio B. Capuano, Claudio Casola, Mimi M. Chandrabose, Andrew Cree, Marvin Diep DaoPieter J. De Jong, Ricardo Cruz-Herrera del Rosario, Kim D. Delehaunty, Huyen H. Dinh, Evan E. Eichler, Stephen Fitzgerald, Paul Flicek, Catherine C. Fontenot, R. Gerald Fowler, Catrina Fronick, Lucinda A. Fulton, Robert S. Fulton, Ramatu Ayiesha Gabisi, Daniel Gerlach, Tina A. Graves, Preethi H. Gunaratne, Matthew W. Hahn, David Haig, Yi Han, R. Alan Harris, Javier Herrero, La Deana W. Hillier, Robert Hubley, Jennifer F. Hughes, Jennifer Hume, Shalini N. Jhangiani, Lynn B. Jorde, Vandita Joshi, Emre Karakor, Miriam K. Konkel, Carolin Kosiol, Christie LKovar, Evgenia V. Kriventseva, Sandra L. Lee, Lora R. Lewis, Yih Shin Liu, John Lopez, Carlos Lopez-Otin, Belen Lorente-Galdos, Keith G. Mansfield, Tomas Marques-Bonet, Patrick Minx, Doriana Misceo, J. Scott Moncrieff, Margaret B. Morgan, Lynne V. Nazareth, Irene Newsham, Ngoc Bich Nguyen, Geoffrey O. Okwuonu, Shyam Prabhakar, Lora Perales, Ling Ling Pu, Xose S. Puente, Victor Quesada, Megan C. Ranck, Brian J. Raney, Muthuswamy Raveendran, David Rio Deiros, Mariano Rocchi, David Rodriguez, Corinna Ross, Magali Ruffier, San Juana Ruiz, Saba Sajjadian, Jireh Santibanez, Daniel R. Schrider, Steve Searle, Helen Skaletsky, Benjamin Soibam, Arian F.A. Smit, Jayantha B. Tennakoon, Lubomir Tomaska, Brygg Ullmer, Charles E. Vejnar, Mario Ventura, Albert J. Vilella, Tomas Vinar, Jan Hinnerk Vogel, Jerilyn A. Walker, Qing Wang, Crystal M. Warner, Derek E. Wildman, David J. Witherspoon, Rita A. Wright, Yuanqing Wu, Weimin Xiao, Jinchuan Xing, Evgeny M. Zdobnov, Baoli Zhu, Richard A. Gibbs, Richard K. Wilson

McDonnell Genome Institute (MGI)

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

154 Scopus citations

Abstract

We report the whole-genome sequence of the common marmoset (Callithrix jacchus). The 2.26-Gb genome of a female marmoset was assembled using Sanger read data (6×) and a whole-genome shotgun strategy. A first analysis has permitted comparison with the genomes of apes and Old World monkeys and the identification of specific features that might contribute to the unique biology of this diminutive primate, including genetic changes that may influence body size, frequent twinning and chimerism. We observed positive selection in growth hormone/insulin-like growth factor genes (growth pathways), respiratory complex I genes (metabolic pathways), and genes encoding immunobiological factors and proteases (reproductive and immunity pathways). In addition, both protein-coding and microRNA genes related to reproduction exhibited evidence of rapid sequence evolution. This genome sequence for a New World monkey enables increased power for comparative analyses among available primate genomes and facilitates biomedical research application.

Original language	English
Pages (from-to)	850-857
Number of pages	8
Journal	Nature Genetics
Volume	46
Issue number	8
DOIs	https://doi.org/10.1038/ng.3042
State	Published - Aug 2014

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10.1038/ng.3042

Cite this

Worley, K. C., Warren, W. C., Rogers, J., Locke, D., Muzny, D. M., Mardis, E. R., Weinstock, G. M., Tardif, S. D., Aagaard, K. M., Archidiacono, N., Arul Rayan, N., Batzer, M. A., Beal, K., Brejova, B., Capozzi, O., Capuano, S. B., Casola, C., Chandrabose, M. M., Cree, A., ... Wilson, R. K. (2014). The common marmoset genome provides insight into primate biology and evolution. Nature Genetics, 46(8), 850-857. https://doi.org/10.1038/ng.3042

Worley, Kim C. ; Warren, Wesley C. ; Rogers, Jeffrey ; Locke, Devin ; Muzny, Donna M. ; Mardis, Elaine R. ; Weinstock, George M. ; Tardif, Suzette D. ; Aagaard, Kjersti M. ; Archidiacono, Nicoletta ; Arul Rayan, Nirmala ; Batzer, Mark A. ; Beal, Kathryn ; Brejova, Brona ; Capozzi, Oronzo ; Capuano, Saverio B. ; Casola, Claudio ; Chandrabose, Mimi M. ; Cree, Andrew ; Diep Dao, Marvin ; De Jong, Pieter J. ; Cruz-Herrera del Rosario, Ricardo ; Delehaunty, Kim D. ; Dinh, Huyen H. ; Eichler, Evan E. ; Fitzgerald, Stephen ; Flicek, Paul ; Fontenot, Catherine C. ; Fowler, R. Gerald ; Fronick, Catrina ; Fulton, Lucinda A. ; Fulton, Robert S. ; Gabisi, Ramatu Ayiesha ; Gerlach, Daniel ; Graves, Tina A. ; Gunaratne, Preethi H. ; Hahn, Matthew W. ; Haig, David ; Han, Yi ; Harris, R. Alan ; Herrero, Javier ; Hillier, La Deana W. ; Hubley, Robert ; Hughes, Jennifer F. ; Hume, Jennifer ; Jhangiani, Shalini N. ; Jorde, Lynn B. ; Joshi, Vandita ; Karakor, Emre ; Konkel, Miriam K. ; Kosiol, Carolin ; LKovar, Christie ; Kriventseva, Evgenia V. ; Lee, Sandra L. ; Lewis, Lora R. ; Liu, Yih Shin ; Lopez, John ; Lopez-Otin, Carlos ; Lorente-Galdos, Belen ; Mansfield, Keith G. ; Marques-Bonet, Tomas ; Minx, Patrick ; Misceo, Doriana ; Moncrieff, J. Scott ; Morgan, Margaret B. ; Nazareth, Lynne V. ; Newsham, Irene ; Nguyen, Ngoc Bich ; Okwuonu, Geoffrey O. ; Prabhakar, Shyam ; Perales, Lora ; Pu, Ling Ling ; Puente, Xose S. ; Quesada, Victor ; Ranck, Megan C. ; Raney, Brian J. ; Raveendran, Muthuswamy ; Deiros, David Rio ; Rocchi, Mariano ; Rodriguez, David ; Ross, Corinna ; Ruffier, Magali ; Ruiz, San Juana ; Sajjadian, Saba ; Santibanez, Jireh ; Schrider, Daniel R. ; Searle, Steve ; Skaletsky, Helen ; Soibam, Benjamin ; Smit, Arian F.A. ; Tennakoon, Jayantha B. ; Tomaska, Lubomir ; Ullmer, Brygg ; Vejnar, Charles E. ; Ventura, Mario ; Vilella, Albert J. ; Vinar, Tomas ; Vogel, Jan Hinnerk ; Walker, Jerilyn A. ; Wang, Qing ; Warner, Crystal M. ; Wildman, Derek E. ; Witherspoon, David J. ; Wright, Rita A. ; Wu, Yuanqing ; Xiao, Weimin ; Xing, Jinchuan ; Zdobnov, Evgeny M. ; Zhu, Baoli ; Gibbs, Richard A. ; Wilson, Richard K. / The common marmoset genome provides insight into primate biology and evolution. In: Nature Genetics. 2014 ; Vol. 46, No. 8. pp. 850-857.

@article{e64b1860b1f44bcaaa1dbf25e21e63bf,

title = "The common marmoset genome provides insight into primate biology and evolution",

abstract = "We report the whole-genome sequence of the common marmoset (Callithrix jacchus). The 2.26-Gb genome of a female marmoset was assembled using Sanger read data (6×) and a whole-genome shotgun strategy. A first analysis has permitted comparison with the genomes of apes and Old World monkeys and the identification of specific features that might contribute to the unique biology of this diminutive primate, including genetic changes that may influence body size, frequent twinning and chimerism. We observed positive selection in growth hormone/insulin-like growth factor genes (growth pathways), respiratory complex I genes (metabolic pathways), and genes encoding immunobiological factors and proteases (reproductive and immunity pathways). In addition, both protein-coding and microRNA genes related to reproduction exhibited evidence of rapid sequence evolution. This genome sequence for a New World monkey enables increased power for comparative analyses among available primate genomes and facilitates biomedical research application.",

author = "Worley, {Kim C.} and Warren, {Wesley C.} and Jeffrey Rogers and Devin Locke and Muzny, {Donna M.} and Mardis, {Elaine R.} and Weinstock, {George M.} and Tardif, {Suzette D.} and Aagaard, {Kjersti M.} and Nicoletta Archidiacono and {Arul Rayan}, Nirmala and Batzer, {Mark A.} and Kathryn Beal and Brona Brejova and Oronzo Capozzi and Capuano, {Saverio B.} and Claudio Casola and Chandrabose, {Mimi M.} and Andrew Cree and {Diep Dao}, Marvin and {De Jong}, {Pieter J.} and {Cruz-Herrera del Rosario}, Ricardo and Delehaunty, {Kim D.} and Dinh, {Huyen H.} and Eichler, {Evan E.} and Stephen Fitzgerald and Paul Flicek and Fontenot, {Catherine C.} and Fowler, {R. Gerald} and Catrina Fronick and Fulton, {Lucinda A.} and Fulton, {Robert S.} and Gabisi, {Ramatu Ayiesha} and Daniel Gerlach and Graves, {Tina A.} and Gunaratne, {Preethi H.} and Hahn, {Matthew W.} and David Haig and Yi Han and Harris, {R. Alan} and Javier Herrero and Hillier, {La Deana W.} and Robert Hubley and Hughes, {Jennifer F.} and Jennifer Hume and Jhangiani, {Shalini N.} and Jorde, {Lynn B.} and Vandita Joshi and Emre Karakor and Konkel, {Miriam K.} and Carolin Kosiol and Christie LKovar and Kriventseva, {Evgenia V.} and Lee, {Sandra L.} and Lewis, {Lora R.} and Liu, {Yih Shin} and John Lopez and Carlos Lopez-Otin and Belen Lorente-Galdos and Mansfield, {Keith G.} and Tomas Marques-Bonet and Patrick Minx and Doriana Misceo and Moncrieff, {J. Scott} and Morgan, {Margaret B.} and Nazareth, {Lynne V.} and Irene Newsham and Nguyen, {Ngoc Bich} and Okwuonu, {Geoffrey O.} and Shyam Prabhakar and Lora Perales and Pu, {Ling Ling} and Puente, {Xose S.} and Victor Quesada and Ranck, {Megan C.} and Raney, {Brian J.} and Muthuswamy Raveendran and Deiros, {David Rio} and Mariano Rocchi and David Rodriguez and Corinna Ross and Magali Ruffier and Ruiz, {San Juana} and Saba Sajjadian and Jireh Santibanez and Schrider, {Daniel R.} and Steve Searle and Helen Skaletsky and Benjamin Soibam and Smit, {Arian F.A.} and Tennakoon, {Jayantha B.} and Lubomir Tomaska and Brygg Ullmer and Vejnar, {Charles E.} and Mario Ventura and Vilella, {Albert J.} and Tomas Vinar and Vogel, {Jan Hinnerk} and Walker, {Jerilyn A.} and Qing Wang and Warner, {Crystal M.} and Wildman, {Derek E.} and Witherspoon, {David J.} and Wright, {Rita A.} and Yuanqing Wu and Weimin Xiao and Jinchuan Xing and Zdobnov, {Evgeny M.} and Baoli Zhu and Gibbs, {Richard A.} and Wilson, {Richard K.}",

note = "Funding Information: The authors acknowledge the contributions of the sequence production staff of the Human Genome Sequencing Center: K. Abraham, C. Adams, C. Allen, U. Anosike, T. Attaway, D. Bandaranaike, A. Bell, S.N. Bell, B. Beltran, C. Bickham, J. Chacko, A. Chavez, H.-S. Chu, M. Coyle, M.L. Davila, L. Davy-Carroll, S. Denson, Y. Ding, S. Dugan, V. Ebong, S. Fernandez, P. Fernando, A. Ferrer, J. Ganer, R. Garcia III, T. Garrett, E. Hawkins, S. Hines, M. Holder, B. Hollins, H. Jiang, B. Johnson, H. Kisamo, L. Lago, M. Lago, C.-Y. Lai, T.-K. Le, F. Legall III, S. Lemon, R. Madu, E. Martinez, I. Mercado, C. Mercado, M. Munidasa, D. Ngo, P. Nguyen, O. Nwaokelemeh, M. Obregon, C. Onwere, A. Parra, H. Paul, A. Perez, Y. Perez, E. Primus, J. Quiroz, B. Schneider, I. Sisson, X.-Z. Song, A. Svatek, T. Taylor, R. Thelus, N. Thomas, R. Thornton, Z. Trejos, K. Usmani, S. Vattathil, D. Villasana, D. Walker, K. Wang, S. Wang, C. White, A. Williams, J. Williams, J. Woodworth and L. Zhang. The Washington University Genome Sequencing Center acknowledges the many people who contributed to the sequencing and analysis in this project who are not named here individually. We thank J. Steitz for mRNA data used to annotate the 3′ UTRs of genes. The miRNA analysis group acknowledges the contributions of D. Rajapakshe, C. Athulathmudali, H. Jiang and A. Moehring. We gratefully acknowledge the assistance of D. Opheim with the figures. The marmoset genome project was funded by the National Human Genome Research Institute (NHGRI), including from grants U54 HG003273 (R.A. Gibbs) and U54 HG003079 (R.K.W.), with additional support from the US National Institutes of Health (NIH), including from grants R01 DK077639 (S.D.T.), R01 GM59290 (L.B.J. and M.A.B.), HG002385 (E.E.E.) and P51-OD011133 (Southwest NPRC), and support from the National Science Foundation (NSF BCS-0751508 to D.E.W.) and the VEGA grant agency: 1/0719/14 (T.V.) and 1/1085/12 (B.B.). C.C.F. and M.C.R. were supported in part by a Howard Hughes Medical Institute grant to Louisiana State University through the Undergraduate Biological Sciences Education program. J.X. was supported by NHGRI grant K99 HG005846. P.H.G. was supported by the Cullen Foundation. T.M.-B. was supported by European Research Council Starting Grant (260372) and MICINN (Spain) grant BFU2011-28549. B.L.-G. was supported by the Spanish National Institute of Bioinformatics (see URLs). E.E.E. is an investigator of the Howard Hughes Medical Institute.",

year = "2014",

month = aug,

doi = "10.1038/ng.3042",

language = "English",

volume = "46",

pages = "850--857",

journal = "Nature Genetics",

issn = "1061-4036",

number = "8",

}

Worley, KC, Warren, WC, Rogers, J, Locke, D, Muzny, DM, Mardis, ER, Weinstock, GM, Tardif, SD, Aagaard, KM, Archidiacono, N, Arul Rayan, N, Batzer, MA, Beal, K, Brejova, B, Capozzi, O, Capuano, SB, Casola, C, Chandrabose, MM, Cree, A, Diep Dao, M, De Jong, PJ, Cruz-Herrera del Rosario, R, Delehaunty, KD, Dinh, HH, Eichler, EE, Fitzgerald, S, Flicek, P, Fontenot, CC, Fowler, RG, Fronick, C, Fulton, LA , Fulton, RS, Gabisi, RA, Gerlach, D, Graves, TA, Gunaratne, PH, Hahn, MW, Haig, D, Han, Y, Harris, RA, Herrero, J, Hillier, LDW, Hubley, R, Hughes, JF, Hume, J, Jhangiani, SN, Jorde, LB, Joshi, V, Karakor, E, Konkel, MK, Kosiol, C, LKovar, C, Kriventseva, EV, Lee, SL, Lewis, LR, Liu, YS, Lopez, J, Lopez-Otin, C, Lorente-Galdos, B, Mansfield, KG, Marques-Bonet, T, Minx, P, Misceo, D, Moncrieff, JS, Morgan, MB, Nazareth, LV, Newsham, I, Nguyen, NB, Okwuonu, GO, Prabhakar, S, Perales, L, Pu, LL, Puente, XS, Quesada, V, Ranck, MC, Raney, BJ, Raveendran, M, Deiros, DR, Rocchi, M, Rodriguez, D, Ross, C, Ruffier, M, Ruiz, SJ, Sajjadian, S, Santibanez, J, Schrider, DR, Searle, S, Skaletsky, H, Soibam, B, Smit, AFA, Tennakoon, JB, Tomaska, L, Ullmer, B, Vejnar, CE, Ventura, M, Vilella, AJ, Vinar, T, Vogel, JH, Walker, JA, Wang, Q, Warner, CM, Wildman, DE, Witherspoon, DJ, Wright, RA, Wu, Y, Xiao, W, Xing, J, Zdobnov, EM, Zhu, B, Gibbs, RA & Wilson, RK 2014, 'The common marmoset genome provides insight into primate biology and evolution', Nature Genetics, vol. 46, no. 8, pp. 850-857. https://doi.org/10.1038/ng.3042

The common marmoset genome provides insight into primate biology and evolution. / Worley, Kim C.; Warren, Wesley C.; Rogers, Jeffrey; Locke, Devin; Muzny, Donna M.; Mardis, Elaine R.; Weinstock, George M.; Tardif, Suzette D.; Aagaard, Kjersti M.; Archidiacono, Nicoletta; Arul Rayan, Nirmala; Batzer, Mark A.; Beal, Kathryn; Brejova, Brona; Capozzi, Oronzo; Capuano, Saverio B.; Casola, Claudio; Chandrabose, Mimi M.; Cree, Andrew; Diep Dao, Marvin; De Jong, Pieter J.; Cruz-Herrera del Rosario, Ricardo; Delehaunty, Kim D.; Dinh, Huyen H.; Eichler, Evan E.; Fitzgerald, Stephen; Flicek, Paul; Fontenot, Catherine C.; Fowler, R. Gerald; Fronick, Catrina; Fulton, Lucinda A.; Fulton, Robert S.; Gabisi, Ramatu Ayiesha; Gerlach, Daniel; Graves, Tina A.; Gunaratne, Preethi H.; Hahn, Matthew W.; Haig, David; Han, Yi; Harris, R. Alan; Herrero, Javier; Hillier, La Deana W.; Hubley, Robert; Hughes, Jennifer F.; Hume, Jennifer; Jhangiani, Shalini N.; Jorde, Lynn B.; Joshi, Vandita; Karakor, Emre; Konkel, Miriam K.; Kosiol, Carolin; LKovar, Christie; Kriventseva, Evgenia V.; Lee, Sandra L.; Lewis, Lora R.; Liu, Yih Shin; Lopez, John; Lopez-Otin, Carlos; Lorente-Galdos, Belen; Mansfield, Keith G.; Marques-Bonet, Tomas; Minx, Patrick; Misceo, Doriana; Moncrieff, J. Scott; Morgan, Margaret B.; Nazareth, Lynne V.; Newsham, Irene; Nguyen, Ngoc Bich; Okwuonu, Geoffrey O.; Prabhakar, Shyam; Perales, Lora; Pu, Ling Ling; Puente, Xose S.; Quesada, Victor; Ranck, Megan C.; Raney, Brian J.; Raveendran, Muthuswamy; Deiros, David Rio; Rocchi, Mariano; Rodriguez, David; Ross, Corinna; Ruffier, Magali; Ruiz, San Juana; Sajjadian, Saba; Santibanez, Jireh; Schrider, Daniel R.; Searle, Steve; Skaletsky, Helen; Soibam, Benjamin; Smit, Arian F.A.; Tennakoon, Jayantha B.; Tomaska, Lubomir; Ullmer, Brygg; Vejnar, Charles E.; Ventura, Mario; Vilella, Albert J.; Vinar, Tomas; Vogel, Jan Hinnerk; Walker, Jerilyn A.; Wang, Qing; Warner, Crystal M.; Wildman, Derek E.; Witherspoon, David J.; Wright, Rita A.; Wu, Yuanqing; Xiao, Weimin; Xing, Jinchuan; Zdobnov, Evgeny M.; Zhu, Baoli; Gibbs, Richard A.; Wilson, Richard K.

In: Nature Genetics, Vol. 46, No. 8, 08.2014, p. 850-857.

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

TY - JOUR

T1 - The common marmoset genome provides insight into primate biology and evolution

AU - Worley, Kim C.

AU - Warren, Wesley C.

AU - Rogers, Jeffrey

AU - Locke, Devin

AU - Muzny, Donna M.

AU - Mardis, Elaine R.

AU - Weinstock, George M.

AU - Tardif, Suzette D.

AU - Aagaard, Kjersti M.

AU - Archidiacono, Nicoletta

AU - Arul Rayan, Nirmala

AU - Batzer, Mark A.

AU - Beal, Kathryn

AU - Brejova, Brona

AU - Capozzi, Oronzo

AU - Capuano, Saverio B.

AU - Casola, Claudio

AU - Chandrabose, Mimi M.

AU - Cree, Andrew

AU - Diep Dao, Marvin

AU - De Jong, Pieter J.

AU - Cruz-Herrera del Rosario, Ricardo

AU - Delehaunty, Kim D.

AU - Dinh, Huyen H.

AU - Eichler, Evan E.

AU - Fitzgerald, Stephen

AU - Flicek, Paul

AU - Fontenot, Catherine C.

AU - Fowler, R. Gerald

AU - Fronick, Catrina

AU - Fulton, Lucinda A.

AU - Fulton, Robert S.

AU - Gabisi, Ramatu Ayiesha

AU - Gerlach, Daniel

AU - Graves, Tina A.

AU - Gunaratne, Preethi H.

AU - Hahn, Matthew W.

AU - Haig, David

AU - Han, Yi

AU - Harris, R. Alan

AU - Herrero, Javier

AU - Hillier, La Deana W.

AU - Hubley, Robert

AU - Hughes, Jennifer F.

AU - Hume, Jennifer

AU - Jhangiani, Shalini N.

AU - Jorde, Lynn B.

AU - Joshi, Vandita

AU - Karakor, Emre

AU - Konkel, Miriam K.

AU - Kosiol, Carolin

AU - LKovar, Christie

AU - Kriventseva, Evgenia V.

AU - Lee, Sandra L.

AU - Lewis, Lora R.

AU - Liu, Yih Shin

AU - Lopez, John

AU - Lopez-Otin, Carlos

AU - Lorente-Galdos, Belen

AU - Mansfield, Keith G.

AU - Marques-Bonet, Tomas

AU - Minx, Patrick

AU - Misceo, Doriana

AU - Moncrieff, J. Scott

AU - Morgan, Margaret B.

AU - Nazareth, Lynne V.

AU - Newsham, Irene

AU - Nguyen, Ngoc Bich

AU - Okwuonu, Geoffrey O.

AU - Prabhakar, Shyam

AU - Perales, Lora

AU - Pu, Ling Ling

AU - Puente, Xose S.

AU - Quesada, Victor

AU - Ranck, Megan C.

AU - Raney, Brian J.

AU - Raveendran, Muthuswamy

AU - Deiros, David Rio

AU - Rocchi, Mariano

AU - Rodriguez, David

AU - Ross, Corinna

AU - Ruffier, Magali

AU - Ruiz, San Juana

AU - Sajjadian, Saba

AU - Santibanez, Jireh

AU - Schrider, Daniel R.

AU - Searle, Steve

AU - Skaletsky, Helen

AU - Soibam, Benjamin

AU - Smit, Arian F.A.

AU - Tennakoon, Jayantha B.

AU - Tomaska, Lubomir

AU - Ullmer, Brygg

AU - Vejnar, Charles E.

AU - Ventura, Mario

AU - Vilella, Albert J.

AU - Vinar, Tomas

AU - Vogel, Jan Hinnerk

AU - Walker, Jerilyn A.

AU - Wang, Qing

AU - Warner, Crystal M.

AU - Wildman, Derek E.

AU - Witherspoon, David J.

AU - Wright, Rita A.

AU - Wu, Yuanqing

AU - Xiao, Weimin

AU - Xing, Jinchuan

AU - Zdobnov, Evgeny M.

AU - Zhu, Baoli

AU - Gibbs, Richard A.

AU - Wilson, Richard K.

N1 - Funding Information: The authors acknowledge the contributions of the sequence production staff of the Human Genome Sequencing Center: K. Abraham, C. Adams, C. Allen, U. Anosike, T. Attaway, D. Bandaranaike, A. Bell, S.N. Bell, B. Beltran, C. Bickham, J. Chacko, A. Chavez, H.-S. Chu, M. Coyle, M.L. Davila, L. Davy-Carroll, S. Denson, Y. Ding, S. Dugan, V. Ebong, S. Fernandez, P. Fernando, A. Ferrer, J. Ganer, R. Garcia III, T. Garrett, E. Hawkins, S. Hines, M. Holder, B. Hollins, H. Jiang, B. Johnson, H. Kisamo, L. Lago, M. Lago, C.-Y. Lai, T.-K. Le, F. Legall III, S. Lemon, R. Madu, E. Martinez, I. Mercado, C. Mercado, M. Munidasa, D. Ngo, P. Nguyen, O. Nwaokelemeh, M. Obregon, C. Onwere, A. Parra, H. Paul, A. Perez, Y. Perez, E. Primus, J. Quiroz, B. Schneider, I. Sisson, X.-Z. Song, A. Svatek, T. Taylor, R. Thelus, N. Thomas, R. Thornton, Z. Trejos, K. Usmani, S. Vattathil, D. Villasana, D. Walker, K. Wang, S. Wang, C. White, A. Williams, J. Williams, J. Woodworth and L. Zhang. The Washington University Genome Sequencing Center acknowledges the many people who contributed to the sequencing and analysis in this project who are not named here individually. We thank J. Steitz for mRNA data used to annotate the 3′ UTRs of genes. The miRNA analysis group acknowledges the contributions of D. Rajapakshe, C. Athulathmudali, H. Jiang and A. Moehring. We gratefully acknowledge the assistance of D. Opheim with the figures. The marmoset genome project was funded by the National Human Genome Research Institute (NHGRI), including from grants U54 HG003273 (R.A. Gibbs) and U54 HG003079 (R.K.W.), with additional support from the US National Institutes of Health (NIH), including from grants R01 DK077639 (S.D.T.), R01 GM59290 (L.B.J. and M.A.B.), HG002385 (E.E.E.) and P51-OD011133 (Southwest NPRC), and support from the National Science Foundation (NSF BCS-0751508 to D.E.W.) and the VEGA grant agency: 1/0719/14 (T.V.) and 1/1085/12 (B.B.). C.C.F. and M.C.R. were supported in part by a Howard Hughes Medical Institute grant to Louisiana State University through the Undergraduate Biological Sciences Education program. J.X. was supported by NHGRI grant K99 HG005846. P.H.G. was supported by the Cullen Foundation. T.M.-B. was supported by European Research Council Starting Grant (260372) and MICINN (Spain) grant BFU2011-28549. B.L.-G. was supported by the Spanish National Institute of Bioinformatics (see URLs). E.E.E. is an investigator of the Howard Hughes Medical Institute.

PY - 2014/8

Y1 - 2014/8

N2 - We report the whole-genome sequence of the common marmoset (Callithrix jacchus). The 2.26-Gb genome of a female marmoset was assembled using Sanger read data (6×) and a whole-genome shotgun strategy. A first analysis has permitted comparison with the genomes of apes and Old World monkeys and the identification of specific features that might contribute to the unique biology of this diminutive primate, including genetic changes that may influence body size, frequent twinning and chimerism. We observed positive selection in growth hormone/insulin-like growth factor genes (growth pathways), respiratory complex I genes (metabolic pathways), and genes encoding immunobiological factors and proteases (reproductive and immunity pathways). In addition, both protein-coding and microRNA genes related to reproduction exhibited evidence of rapid sequence evolution. This genome sequence for a New World monkey enables increased power for comparative analyses among available primate genomes and facilitates biomedical research application.

AB - We report the whole-genome sequence of the common marmoset (Callithrix jacchus). The 2.26-Gb genome of a female marmoset was assembled using Sanger read data (6×) and a whole-genome shotgun strategy. A first analysis has permitted comparison with the genomes of apes and Old World monkeys and the identification of specific features that might contribute to the unique biology of this diminutive primate, including genetic changes that may influence body size, frequent twinning and chimerism. We observed positive selection in growth hormone/insulin-like growth factor genes (growth pathways), respiratory complex I genes (metabolic pathways), and genes encoding immunobiological factors and proteases (reproductive and immunity pathways). In addition, both protein-coding and microRNA genes related to reproduction exhibited evidence of rapid sequence evolution. This genome sequence for a New World monkey enables increased power for comparative analyses among available primate genomes and facilitates biomedical research application.

UR - http://www.scopus.com/inward/record.url?scp=84905588751&partnerID=8YFLogxK

U2 - 10.1038/ng.3042

DO - 10.1038/ng.3042

M3 - Article

C2 - 25038751

AN - SCOPUS:84905588751

VL - 46

SP - 850

EP - 857

JO - Nature Genetics

JF - Nature Genetics

SN - 1061-4036

IS - 8

ER -

The common marmoset genome provides insight into primate biology and evolution

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