Structurally divergent and recurrently mutated regions of primate genomes

被引：24

作者：

Mao, Yafei ^{[1
,2
]}

Harvey, William T. ^{[1
]}

Porubsky, David ^{[1
]}

Munson, Katherine M. ^{[1
]}

Hoekzema, Kendra ^{[1
]}

Lewis, Alexandra P. ^{[1
]}

Audano, Peter A. ^{[1
]}

Rozanski, Allison ^{[1
]}

Yang, Xiangyu ^{[2
]}

Zhang, Shilong ^{[2
]}

Yoo, Dongahn ^{[1
]}

Gordon, David S. ^{[1
,3
]}

Fair, Tyler ^{[4
]}

Wei, Xiaoxi ^{[2
]}

Logsdon, Glennis A. ^{[1
,22
]}

Haukness, Marina ^{[5
]}

Dishuck, Philip C. ^{[1
]}

Jeong, Hyeonsoo ^{[1
]}

del Rosario, Ricardo ^{[6
,7
]}

Bauer, Vanessa L. ^{[8
]}

Fattor, Will T. ^{[8
]}

Wilkerson, Gregory K. ^{[9
,10
]}

Mao, Yuxiang ^{[11
,12
]}

Shi, Yongyong ^{[2
,11
,12
]}

Sun, Qiang ^{[11
,12
]}

Lu, Qing

Paten, Benedict

Bakken, Trygve E. ^{[13
]}

Pollen, Alex A. ^{[14
]}

Feng, Guoping

Sawyer, Sara L.

Warren, Wesley C. ^{[15
,16
,17
]}

Carbone, Lucia ^{[18
,19
,20
,21
]}

Eichler, Evan E. ^{[1
,3
]}

机构：

[1] Univ Washington, Sch Med, Dept Genome Sci, Seattle, WA 98109 USA

[2] Shanghai Jiao Tong Univ, Biox Inst, Key Lab Genet Dev & Neuropsychiat Disorders, Minist Educ, Shanghai, Peoples R China

[3] Univ Washington, Howard Hughes Med Inst, Seattle, WA 98195 USA

[4] Univ Calif San Francisco, Eli & Edythe Broad Ctr Regenerat Med & Stem Cell R, San Francisco, CA 94143 USA

[5] Univ Calif Santa Cruz, UC St Cruz Genom Inst, Santa Cruz, CA USA

[6] MIT, McGovern Inst Brain Res, Dept Brain & Cognit Sci, Cambridge, MA USA

[7] MIT, Stanley Ctr Psychiat Res, Broad Inst, Cambridge, MA USA

[8] Univ Colorado, BioFrontiers Inst, Dept Mol Cellular & Dev Biol, Boulder, CO USA

[9] Univ Texas MD Anderson Canc Ctr, Dept Vet Sci, Michale E Keeling Ctr Comparat Med & Res, Bastrop, TX USA

[10] North Carolina State Univ, Dept Clin Sci, Raleigh, NC USA

[11] Chinese Acad Sci, Ctr Excellence Brain Sci & Intelligence Technol, State Key Lab Neurosci, Inst Neurosci, Shanghai, Peoples R China

[12] Shanghai Ctr Brain Sci & Brain Inspired Technol, Shanghai, Peoples R China

[13] Allen Inst Brain Sci, Seattle, WA USA

[14] Univ Calif San Francisco, Dept Neurol, San Francisco, CA USA

[15] Univ Missouri, Bond Life Sci Ctr, Dept Anim Sci, Columbia, MO USA

[16] Univ Missouri, Sch Med, Dept Surg, Columbia, MO USA

[17] Univ Missouri, Inst Data Sci & Informat, Columbia, MO USA

[18] Oregon Hlth & Sci Univ, Dept Med, Knight Cardiovasc Inst, Portland, OR USA

[19] Oregon Natl Primate Res Ctr, Div Genet, Beaverton, OR USA

[20] Oregon Hlth & Sci Univ, Dept Mol & Med Genet, Portland, OR USA

[21] Oregon Hlth & Sci Univ, Dept Med Informat & Clin Epidemiol, Portland, OR USA

[22] Univ Penn, Perelman Sch Med, Dept Genet, Epigenet Inst, Philadelphia, PA USA

来源：

CELL | 2024年 / 187卷 / 06期

基金：

中国国家自然科学基金; 美国国家卫生研究院;

关键词：

COPY NUMBER VARIATION; SEGMENTAL DUPLICATIONS; ANDROGEN RECEPTOR; SEQUENCE; GENE; DIVERSITY; EVOLUTION; COMPLEX; PROJECT; RECONSTRUCTION;

D O I：

10.1016/j.cell.2024.01.052

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

We sequenced and assembled using multiple long -read sequencing technologies the genomes of chimpanzee, bonobo, gorilla, orangutan, gibbon, macaque, owl monkey, and marmoset. We identified 1,338,997 lineage -specific fixed structural variants (SVs) disrupting 1,561 protein -coding genes and 136,932 regulatory elements, including the most complete set of human -specific fixed differences. We estimate that 819.47 Mbp or -27% of the genome has been affected by SVs across primate evolution. We identify 1,607 structurally divergent regions wherein recurrent structural variation contributes to creating SV hotspots where genes are recurrently lost (e.g., CARD , C4 , and OLAH gene families) and additional lineage -specific genes are generated (e.g., CKAP2 , VPS36 , ACBD7 , and NEK5 paralogs), becoming targets of rapid chromosomal diversification and positive selection (e.g., RGPD gene family). High-fidelity long -read sequencing has made these dynamic regions of the genome accessible for sequence -level analyses within and between primate species.

引用

页码：1547 / 1562.e13

页数：30

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