High-resolution comparative analysis of great ape genomes

Zev N. Kronenberg; Ian T. Fiddes; David Gordon; Shwetha Murali; Stuart Cantsilieris; Olivia S. Meyerson; Jason G. Underwood; Bradley J. Nelson; Mark J.P. Chaisson; Max L. Dougherty; Katherine M. Munson; Alex R. Hastie; Mark Diekhans; Fereydoun Hormozdiari; Nicola Lorusso; Kendra Hoekzema; Ruolan Qiu; Karen Clark; Archana Raja; Anne Marie E. Welch; Melanie Sorensen; Carl Baker; Robert S. Fulton; Joel Armstrong; Tina A. Graves-Lindsay; Ahmet M. Denli; Emma R. Hoppe; Ping Hsun Hsieh; Christopher M. Hill; Andy Wing Chun Pang; Joyce Lee; Ernest T. Lam; Susan K. Dutcher; Fred H. Gage; Wesley C. Warren; Jay Shendure; David Haussler; Valerie A. Schneider; Han Cao; Mario Ventura; Richard K. Wilson; Benedict Paten; Alex Pollen; Evan E. Eichler

doi:10.1126/science.aar6343

High-resolution comparative analysis of great ape genomes

Zev N. Kronenberg, Ian T. Fiddes, David Gordon, Shwetha Murali, Stuart Cantsilieris, Olivia S. Meyerson, Jason G. Underwood, Bradley J. Nelson, Mark J.P. Chaisson, Max L. Dougherty, Katherine M. Munson, Alex R. Hastie, Mark Diekhans, Fereydoun Hormozdiari, Nicola Lorusso, Kendra Hoekzema, Ruolan Qiu, Karen Clark, Archana Raja, Anne Marie E. WelchMelanie Sorensen, Carl Baker, Robert S. Fulton, Joel Armstrong, Tina A. Graves-Lindsay, Ahmet M. Denli, Emma R. Hoppe, Ping Hsun Hsieh, Christopher M. Hill, Andy Wing Chun Pang, Joyce Lee, Ernest T. Lam, Susan K. Dutcher, Fred H. Gage, Wesley C. Warren, Jay Shendure, David Haussler, Valerie A. Schneider, Han Cao, Mario Ventura, Richard K. Wilson, Benedict Paten, Alex Pollen, Evan E. Eichler

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243 Scopus citations

Abstract

Genetic studies of human evolution require high-quality contiguous ape genome assemblies that are not guided by the human reference. We coupled long-read sequence assembly and full-length complementary DNA sequencing with a multiplatform scaffolding approach to produce ab initio chimpanzee and orangutan genome assemblies. By comparing these with two long-read de novo human genome assemblies and a gorilla genome assembly, we characterized lineage-specific and shared great ape genetic variation ranging from single- to mega-base pair-sized variants. We identified ∼17,000 fixed human-specific structural variants identifying genic and putative regulatory changes that have emerged in humans since divergence from nonhuman apes. Interestingly, these variants are enriched near genes that are down-regulated in human compared to chimpanzee cerebral organoids, particularly in cells analogous to radial glial neural progenitors.

Original language	English
Article number	eaar6343
Journal	Science
Volume	360
Issue number	6393
DOIs	https://doi.org/10.1126/science.aar6343
State	Published - Jun 8 2018

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Kronenberg, Z. N., Fiddes, I. T., Gordon, D., Murali, S., Cantsilieris, S., Meyerson, O. S., Underwood, J. G., Nelson, B. J., Chaisson, M. J. P., Dougherty, M. L., Munson, K. M., Hastie, A. R., Diekhans, M., Hormozdiari, F., Lorusso, N., Hoekzema, K., Qiu, R., Clark, K., Raja, A., ... Eichler, E. E. (2018). High-resolution comparative analysis of great ape genomes. Science, 360(6393), Article eaar6343. https://doi.org/10.1126/science.aar6343

@article{43336acb89fe4d82a068f93295d8894c,

title = "High-resolution comparative analysis of great ape genomes",

abstract = "Genetic studies of human evolution require high-quality contiguous ape genome assemblies that are not guided by the human reference. We coupled long-read sequence assembly and full-length complementary DNA sequencing with a multiplatform scaffolding approach to produce ab initio chimpanzee and orangutan genome assemblies. By comparing these with two long-read de novo human genome assemblies and a gorilla genome assembly, we characterized lineage-specific and shared great ape genetic variation ranging from single- to mega-base pair-sized variants. We identified ∼17,000 fixed human-specific structural variants identifying genic and putative regulatory changes that have emerged in humans since divergence from nonhuman apes. Interestingly, these variants are enriched near genes that are down-regulated in human compared to chimpanzee cerebral organoids, particularly in cells analogous to radial glial neural progenitors.",

author = "Kronenberg, {Zev N.} and Fiddes, {Ian T.} and David Gordon and Shwetha Murali and Stuart Cantsilieris and Meyerson, {Olivia S.} and Underwood, {Jason G.} and Nelson, {Bradley J.} and Chaisson, {Mark J.P.} and Dougherty, {Max L.} and Munson, {Katherine M.} and Hastie, {Alex R.} and Mark Diekhans and Fereydoun Hormozdiari and Nicola Lorusso and Kendra Hoekzema and Ruolan Qiu and Karen Clark and Archana Raja and Welch, {Anne Marie E.} and Melanie Sorensen and Carl Baker and Fulton, {Robert S.} and Joel Armstrong and Graves-Lindsay, {Tina A.} and Denli, {Ahmet M.} and Hoppe, {Emma R.} and Hsieh, {Ping Hsun} and Hill, {Christopher M.} and Pang, {Andy Wing Chun} and Joyce Lee and Lam, {Ernest T.} and Dutcher, {Susan K.} and Gage, {Fred H.} and Warren, {Wesley C.} and Jay Shendure and David Haussler and Schneider, {Valerie A.} and Han Cao and Mario Ventura and Wilson, {Richard K.} and Benedict Paten and Alex Pollen and Eichler, {Evan E.}",

year = "2018",

month = jun,

day = "8",

doi = "10.1126/science.aar6343",

language = "English",

volume = "360",

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Kronenberg, ZN, Fiddes, IT, Gordon, D, Murali, S, Cantsilieris, S, Meyerson, OS, Underwood, JG, Nelson, BJ, Chaisson, MJP, Dougherty, ML, Munson, KM, Hastie, AR, Diekhans, M, Hormozdiari, F, Lorusso, N, Hoekzema, K, Qiu, R, Clark, K, Raja, A, Welch, AME, Sorensen, M, Baker, C, Fulton, RS, Armstrong, J, Graves-Lindsay, TA, Denli, AM, Hoppe, ER, Hsieh, PH, Hill, CM, Pang, AWC, Lee, J, Lam, ET, Dutcher, SK, Gage, FH, Warren, WC, Shendure, J, Haussler, D, Schneider, VA, Cao, H, Ventura, M, Wilson, RK, Paten, B, Pollen, A & Eichler, EE 2018, 'High-resolution comparative analysis of great ape genomes', Science, vol. 360, no. 6393, eaar6343. https://doi.org/10.1126/science.aar6343

TY - JOUR

T1 - High-resolution comparative analysis of great ape genomes

AU - Kronenberg, Zev N.

AU - Fiddes, Ian T.

AU - Gordon, David

AU - Murali, Shwetha

AU - Cantsilieris, Stuart

AU - Meyerson, Olivia S.

AU - Underwood, Jason G.

AU - Nelson, Bradley J.

AU - Chaisson, Mark J.P.

AU - Dougherty, Max L.

AU - Munson, Katherine M.

AU - Hastie, Alex R.

AU - Diekhans, Mark

AU - Hormozdiari, Fereydoun

AU - Lorusso, Nicola

AU - Hoekzema, Kendra

AU - Qiu, Ruolan

AU - Clark, Karen

AU - Raja, Archana

AU - Welch, Anne Marie E.

AU - Sorensen, Melanie

AU - Baker, Carl

AU - Fulton, Robert S.

AU - Armstrong, Joel

AU - Graves-Lindsay, Tina A.

AU - Denli, Ahmet M.

AU - Hoppe, Emma R.

AU - Hsieh, Ping Hsun

AU - Hill, Christopher M.

AU - Pang, Andy Wing Chun

AU - Lee, Joyce

AU - Lam, Ernest T.

AU - Dutcher, Susan K.

AU - Gage, Fred H.

AU - Warren, Wesley C.

AU - Shendure, Jay

AU - Haussler, David

AU - Schneider, Valerie A.

AU - Cao, Han

AU - Ventura, Mario

AU - Wilson, Richard K.

AU - Paten, Benedict

AU - Pollen, Alex

AU - Eichler, Evan E.

PY - 2018/6/8

Y1 - 2018/6/8

N2 - Genetic studies of human evolution require high-quality contiguous ape genome assemblies that are not guided by the human reference. We coupled long-read sequence assembly and full-length complementary DNA sequencing with a multiplatform scaffolding approach to produce ab initio chimpanzee and orangutan genome assemblies. By comparing these with two long-read de novo human genome assemblies and a gorilla genome assembly, we characterized lineage-specific and shared great ape genetic variation ranging from single- to mega-base pair-sized variants. We identified ∼17,000 fixed human-specific structural variants identifying genic and putative regulatory changes that have emerged in humans since divergence from nonhuman apes. Interestingly, these variants are enriched near genes that are down-regulated in human compared to chimpanzee cerebral organoids, particularly in cells analogous to radial glial neural progenitors.

AB - Genetic studies of human evolution require high-quality contiguous ape genome assemblies that are not guided by the human reference. We coupled long-read sequence assembly and full-length complementary DNA sequencing with a multiplatform scaffolding approach to produce ab initio chimpanzee and orangutan genome assemblies. By comparing these with two long-read de novo human genome assemblies and a gorilla genome assembly, we characterized lineage-specific and shared great ape genetic variation ranging from single- to mega-base pair-sized variants. We identified ∼17,000 fixed human-specific structural variants identifying genic and putative regulatory changes that have emerged in humans since divergence from nonhuman apes. Interestingly, these variants are enriched near genes that are down-regulated in human compared to chimpanzee cerebral organoids, particularly in cells analogous to radial glial neural progenitors.

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U2 - 10.1126/science.aar6343

DO - 10.1126/science.aar6343

M3 - Article

C2 - 29880660

AN - SCOPUS:85048568612

SN - 0036-8075

VL - 360

JO - Science

JF - Science

IS - 6393

M1 - eaar6343

ER -

High-resolution comparative analysis of great ape genomes

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