Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility

Wesley C. Warren; R. Alan Harris; Marina Haukness; Ian T. Fiddes; Shwetha C. Murali; Jason Fernandes; Philip C. Dishuck; Jessica M. Storer; Muthuswamy Raveendran; La Deana W. Hillier; David Porubsky; Yafei Mao; David Gordon; Mitchell R. Vollger; Alexandra P. Lewis; Katherine M. Munson; Elizabeth Devogelaere; Joel Armstrong; Mark Diekhans; Jerilyn A. Walker; Chad Tomlinson; Tina A. Graves-Lindsay; Milinn Kremitzki; Sofie R. Salama; Peter A. Audano; Merly Escalona9; Nicholas W. Maurer; Francesca Antonacci; Ludovica Mercuri; Flavia A.M. Maggiolini; Claudia Rita Catacchio; Jason G. Underwood; David H. O'Connor; Ashley D. Sanders; Jan O. Korbel; Betsy Ferguson; H. Michael Kubisch; Louis Picker; Ned H. Kalin; Douglas Rosene; Jon Levine; David H. Abbott; Stanton B. Gray25; Mar M. Sanchez; Zsofia A. Kovacs-Balint; Joseph W. Kemnitz; Sara M. Thomasy; Jeffrey A. Roberts; Erin L. Kinnally; John P. Capitanio; J. H.Pate Skene; Michael Platt; Shelley A. Cole; Richard E. Green; Mario Ventura; Roger W. Wiseman; Benedict Paten; Mark A. Batzer; Jeffrey Rogers; Evan E. Eichler

doi:10.1126/science.abc6617

Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility

Wesley C. Warren, R. Alan Harris, Marina Haukness, Ian T. Fiddes, Shwetha C. Murali, Jason Fernandes, Philip C. Dishuck, Jessica M. Storer, Muthuswamy Raveendran, La Deana W. Hillier, David Porubsky, Yafei Mao, David Gordon, Mitchell R. Vollger, Alexandra P. Lewis, Katherine M. Munson, Elizabeth Devogelaere, Joel Armstrong, Mark Diekhans, Jerilyn A. WalkerChad Tomlinson, Tina A. Graves-Lindsay, Milinn Kremitzki, Sofie R. Salama, Peter A. Audano, Merly Escalona9, Nicholas W. Maurer, Francesca Antonacci, Ludovica Mercuri, Flavia A.M. Maggiolini, Claudia Rita Catacchio, Jason G. Underwood, David H. O'Connor, Ashley D. Sanders, Jan O. Korbel, Betsy Ferguson, H. Michael Kubisch, Louis Picker, Ned H. Kalin, Douglas Rosene, Jon Levine, David H. Abbott, Stanton B. Gray25, Mar M. Sanchez, Zsofia A. Kovacs-Balint, Joseph W. Kemnitz, Sara M. Thomasy, Jeffrey A. Roberts, Erin L. Kinnally, John P. Capitanio, J. H.Pate Skene, Michael Platt, Shelley A. Cole, Richard E. Green, Mario Ventura, Roger W. Wiseman, Benedict Paten, Mark A. Batzer, Jeffrey Rogers, Evan E. Eichler

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Abstract

The rhesus macaque (Macaca mulatta) is the most widely studied nonhuman primate (NHP) in biomedical research. We present an updated reference genome assembly (Mmul_10, contig N50 = 46 Mbp) that increases the sequence contiguity 120-fold and annotate it using 6.5 million full-length transcripts, thus improving our understanding of gene content, isoform diversity, and repeat organization. With the improved assembly of segmental duplications, we discovered new lineage-specific genes and expanded gene families that are potentially informative in studies of evolution and disease susceptibility. Wholegenome sequencing (WGS) data from 853 rhesus macaques identified 85.7 million single-nucleotide variants (SNVs) and 10.5 million indel variants, including potentially damaging variants in genes associated with human autism and developmental delay, providing a framework for developing noninvasive NHP models of human disease.

Original language	English (US)
Article number	eabc6617
Journal	Science
Volume	370
Issue number	6523
DOIs	https://doi.org/10.1126/science.abc6617
State	Published - Dec 18 2020

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Warren, W. C., Harris, R. A., Haukness, M., Fiddes, I. T., Murali, S. C., Fernandes, J., Dishuck, P. C., Storer, J. M., Raveendran, M., Hillier, L. D. W., Porubsky, D., Mao, Y., Gordon, D., Vollger, M. R., Lewis, A. P., Munson, K. M., Devogelaere, E., Armstrong, J., Diekhans, M., ... Eichler, E. E. (2020). Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility. Science, 370(6523), Article eabc6617. https://doi.org/10.1126/science.abc6617

Warren, WC, Harris, RA, Haukness, M, Fiddes, IT, Murali, SC, Fernandes, J, Dishuck, PC, Storer, JM, Raveendran, M, Hillier, LDW, Porubsky, D, Mao, Y, Gordon, D, Vollger, MR, Lewis, AP, Munson, KM, Devogelaere, E, Armstrong, J, Diekhans, M, Walker, JA, Tomlinson, C, Graves-Lindsay, TA, Kremitzki, M, Salama, SR, Audano, PA, Escalona9, M, Maurer, NW, Antonacci, F, Mercuri, L, Maggiolini, FAM, Catacchio, CR, Underwood, JG, O'Connor, DH, Sanders, AD, Korbel, JO, Ferguson, B, Kubisch, HM, Picker, L, Kalin, NH, Rosene, D, Levine, J, Abbott, DH, Gray25, SB, Sanchez, MM, Kovacs-Balint, ZA, Kemnitz, JW, Thomasy, SM, Roberts, JA, Kinnally, EL, Capitanio, JP, Skene, JHP, Platt, M, Cole, SA, Green, RE, Ventura, M, Wiseman, RW, Paten, B, Batzer, MA, Rogers, J & Eichler, EE 2020, 'Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility', Science, vol. 370, no. 6523, eabc6617. https://doi.org/10.1126/science.abc6617

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title = "Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility",

abstract = "The rhesus macaque (Macaca mulatta) is the most widely studied nonhuman primate (NHP) in biomedical research. We present an updated reference genome assembly (Mmul_10, contig N50 = 46 Mbp) that increases the sequence contiguity 120-fold and annotate it using 6.5 million full-length transcripts, thus improving our understanding of gene content, isoform diversity, and repeat organization. With the improved assembly of segmental duplications, we discovered new lineage-specific genes and expanded gene families that are potentially informative in studies of evolution and disease susceptibility. Wholegenome sequencing (WGS) data from 853 rhesus macaques identified 85.7 million single-nucleotide variants (SNVs) and 10.5 million indel variants, including potentially damaging variants in genes associated with human autism and developmental delay, providing a framework for developing noninvasive NHP models of human disease.",

author = "Warren, {Wesley C.} and Harris, {R. Alan} and Marina Haukness and Fiddes, {Ian T.} and Murali, {Shwetha C.} and Jason Fernandes and Dishuck, {Philip C.} and Storer, {Jessica M.} and Muthuswamy Raveendran and Hillier, {La Deana W.} and David Porubsky and Yafei Mao and David Gordon and Vollger, {Mitchell R.} and Lewis, {Alexandra P.} and Munson, {Katherine M.} and Elizabeth Devogelaere and Joel Armstrong and Mark Diekhans and Walker, {Jerilyn A.} and Chad Tomlinson and Graves-Lindsay, {Tina A.} and Milinn Kremitzki and Salama, {Sofie R.} and Audano, {Peter A.} and Merly Escalona9 and Maurer, {Nicholas W.} and Francesca Antonacci and Ludovica Mercuri and Maggiolini, {Flavia A.M.} and Catacchio, {Claudia Rita} and Underwood, {Jason G.} and O'Connor, {David H.} and Sanders, {Ashley D.} and Korbel, {Jan O.} and Betsy Ferguson and Kubisch, {H. Michael} and Louis Picker and Kalin, {Ned H.} and Douglas Rosene and Jon Levine and Abbott, {David H.} and Gray25, {Stanton B.} and Sanchez, {Mar M.} and Kovacs-Balint, {Zsofia A.} and Kemnitz, {Joseph W.} and Thomasy, {Sara M.} and Roberts, {Jeffrey A.} and Kinnally, {Erin L.} and Capitanio, {John P.} and Skene, {J. H.Pate} and Michael Platt and Cole, {Shelley A.} and Green, {Richard E.} and Mario Ventura and Wiseman, {Roger W.} and Benedict Paten and Batzer, {Mark A.} and Jeffrey Rogers and Eichler, {Evan E.}",

year = "2020",

month = dec,

day = "18",

doi = "10.1126/science.abc6617",

language = "English (US)",

volume = "370",

journal = "Science",

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T1 - Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility

AU - Warren, Wesley C.

AU - Harris, R. Alan

AU - Haukness, Marina

AU - Fiddes, Ian T.

AU - Murali, Shwetha C.

AU - Fernandes, Jason

AU - Dishuck, Philip C.

AU - Storer, Jessica M.

AU - Raveendran, Muthuswamy

AU - Hillier, La Deana W.

AU - Porubsky, David

AU - Mao, Yafei

AU - Gordon, David

AU - Vollger, Mitchell R.

AU - Lewis, Alexandra P.

AU - Munson, Katherine M.

AU - Devogelaere, Elizabeth

AU - Armstrong, Joel

AU - Diekhans, Mark

AU - Walker, Jerilyn A.

AU - Tomlinson, Chad

AU - Graves-Lindsay, Tina A.

AU - Kremitzki, Milinn

AU - Salama, Sofie R.

AU - Audano, Peter A.

AU - Escalona9, Merly

AU - Maurer, Nicholas W.

AU - Antonacci, Francesca

AU - Mercuri, Ludovica

AU - Maggiolini, Flavia A.M.

AU - Catacchio, Claudia Rita

AU - Underwood, Jason G.

AU - O'Connor, David H.

AU - Sanders, Ashley D.

AU - Korbel, Jan O.

AU - Ferguson, Betsy

AU - Kubisch, H. Michael

AU - Picker, Louis

AU - Kalin, Ned H.

AU - Rosene, Douglas

AU - Levine, Jon

AU - Abbott, David H.

AU - Gray25, Stanton B.

AU - Sanchez, Mar M.

AU - Kovacs-Balint, Zsofia A.

AU - Kemnitz, Joseph W.

AU - Thomasy, Sara M.

AU - Roberts, Jeffrey A.

AU - Kinnally, Erin L.

AU - Capitanio, John P.

AU - Skene, J. H.Pate

AU - Platt, Michael

AU - Cole, Shelley A.

AU - Green, Richard E.

AU - Ventura, Mario

AU - Wiseman, Roger W.

AU - Paten, Benedict

AU - Batzer, Mark A.

AU - Rogers, Jeffrey

AU - Eichler, Evan E.

PY - 2020/12/18

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Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility

Abstract

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