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 | |
State | Published - Aug 2014 |
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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 -