Copy number variants and fixed duplications among 198 rhesus macaques (Macaca mulatta).
Animals
Chromosome Mapping
/ veterinary
DNA Copy Number Variations
/ physiology
Female
Gene Duplication
/ physiology
Genetics, Population
Genome
High-Throughput Nucleotide Sequencing
/ veterinary
Humans
Macaca mulatta
/ classification
Male
Open Reading Frames
/ genetics
Phylogeny
Sequence Analysis, DNA
/ veterinary
Species Specificity
Journal
PLoS genetics
ISSN: 1553-7404
Titre abrégé: PLoS Genet
Pays: United States
ID NLM: 101239074
Informations de publication
Date de publication:
05 2020
05 2020
Historique:
received:
16
08
2019
accepted:
27
03
2020
revised:
21
05
2020
pubmed:
12
5
2020
medline:
31
7
2020
entrez:
12
5
2020
Statut:
epublish
Résumé
The rhesus macaque is an abundant species of Old World monkeys and a valuable model organism for biomedical research due to its close phylogenetic relationship to humans. Copy number variation is one of the main sources of genomic diversity within and between species and a widely recognized cause of inter-individual differences in disease risk. However, copy number differences among rhesus macaques and between the human and macaque genomes, as well as the relevance of this diversity to research involving this nonhuman primate, remain understudied. Here we present a high-resolution map of sequence copy number for the rhesus macaque genome constructed from a dataset of 198 individuals. Our results show that about one-eighth of the rhesus macaque reference genome is composed of recently duplicated regions, either copy number variable regions or fixed duplications. Comparison with human genomic copy number maps based on previously published data shows that, despite overall similarities in the genome-wide distribution of these regions, there are specific differences at the chromosome level. Some of these create differences in the copy number profile between human disease genes and their rhesus macaque orthologs. Our results highlight the importance of addressing the number of copies of target genes in the design of experiments and cautions against human-centered assumptions in research conducted with model organisms. Overall, we present a genome-wide copy number map from a large sample of rhesus macaque individuals representing an important novel contribution concerning the evolution of copy number in primate genomes.
Identifiants
pubmed: 32392208
doi: 10.1371/journal.pgen.1008742
pii: PGENETICS-D-19-01374
pmc: PMC7241854
doi:
Types de publication
Comparative Study
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e1008742Subventions
Organisme : NIH HHS
ID : R24 OD011173
Pays : United States
Organisme : NHGRI NIH HHS
ID : UM1 HG008898
Pays : United States
Organisme : Howard Hughes Medical Institute
Pays : United States
Organisme : NIH HHS
ID : R24 OD010962
Pays : United States
Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
Références
BMC Biol. 2017 Nov 16;15(1):110
pubmed: 29145861
BMC Genomics. 2017 Mar 6;18(1):222
pubmed: 28264649
Nature. 2015 Oct 1;526(7571):75-81
pubmed: 26432246
Nat Genet. 2007 Nov;39(11):1361-8
pubmed: 17922013
Dev Biol. 2012 Apr 15;364(2):114-27
pubmed: 22326227
PLoS One. 2007 Nov 14;2(11):e1152
pubmed: 18000532
Mol Psychiatry. 2011 Nov;16(11):1130-8
pubmed: 21116278
Nucleic Acids Res. 2018 Jan 4;46(D1):D754-D761
pubmed: 29155950
Biol Direct. 2014 Oct 14;9(1):20
pubmed: 25319552
Genome Biol. 2015 Dec 10;16:277
pubmed: 26653294
Nat Genet. 2009 Oct;41(10):1061-7
pubmed: 19718026
Genome Res. 2013 Sep;23(9):1373-82
pubmed: 23825009
Cold Spring Harb Symp Quant Biol. 2009;74:355-62
pubmed: 19717539
Immunol Rev. 2015 Sep;267(1):228-45
pubmed: 26284481
Neurobiol Aging. 2012 Oct;33(10):2357-72
pubmed: 22192242
Psychiatry Clin Neurosci. 2014 Feb;68(2):85-95
pubmed: 24372918
Annu Rev Med. 2010;61:437-55
pubmed: 20059347
PLoS Pathog. 2011 Dec;7(12):e1002436
pubmed: 22194686
Nature. 2016 Jul 13;535(7612):367-75
pubmed: 27409810
Curr Opin Neurol. 2016 Apr;29(2):158-67
pubmed: 26886358
Nature. 2013 Oct 3;502(7469):100-4
pubmed: 24025770
Proc Natl Acad Sci U S A. 2013 Sep 24;110(39):15764-9
pubmed: 24014587
Genome Res. 2016 Dec;26(12):1651-1662
pubmed: 27934697
PLoS One. 2016 Mar 23;11(3):e0152164
pubmed: 27007437
Sci Adv. 2019 Jan 30;5(1):eaau6947
pubmed: 30854422
Nature. 2004 Aug 19;430(7002):857-64
pubmed: 15318213
Science. 2002 Aug 9;297(5583):1003-7
pubmed: 12169732
Curr Opin Genet Dev. 1996 Dec;6(6):743-8
pubmed: 8994846
Nature. 2014 Jul 31;511(7511):601-5
pubmed: 25043006
Proc Biol Sci. 2012 Dec 22;279(1749):5048-57
pubmed: 22977152
Mol Psychiatry. 2013 Jun;18(6):700-7
pubmed: 23147386
J Virol. 2012 Dec;86(23):13103-7
pubmed: 23015705
PLoS One. 2011;6(10):e26049
pubmed: 22016809
Biol Open. 2013 Dec 15;2(12):1402-11
pubmed: 24285712
Science. 2018 Jun 8;360(6393):
pubmed: 29880660
Mol Biol Evol. 2019 Aug 1;36(8):1746-1763
pubmed: 31070747
Science. 2017 Apr 28;356(6336):442-445
pubmed: 28450643
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D493-6
pubmed: 14681465
Genome Biol Evol. 2017 Dec 1;9(12):3260-3264
pubmed: 28985367
J Virol. 2013 May;87(9):5305-10
pubmed: 23449795
Nucleic Acids Res. 1999 Jan 15;27(2):573-80
pubmed: 9862982
Nucleic Acids Res. 2017 Jan 4;45(D1):D833-D839
pubmed: 27924018
Trends Genet. 2012 Jun;28(6):245-57
pubmed: 22483647
Cortex. 2018 Jan;98:218-227
pubmed: 28258716
Nat Rev Genet. 2006 Jul;7(7):552-64
pubmed: 16770338
Nat Ecol Evol. 2017;1(3):69
pubmed: 28580430
Nature. 2016 Oct 13;538(7624):201-206
pubmed: 27654912
PLoS One. 2010 Apr 14;5(4):e10171
pubmed: 20418953
PLoS Genet. 2019 Jan 24;15(1):e1007902
pubmed: 30677042
Cancer Genet. 2013 Dec;206(12):432-40
pubmed: 24405614
Genome Res. 2008 Dec;18(12):1865-74
pubmed: 18842824
Brain Struct Funct. 2015 Sep;220(5):3053-60
pubmed: 24957859
Hum Mol Genet. 2008 Apr 15;17(8):1127-36
pubmed: 18180252
Nature. 2004 Apr 1;428(6982):529-35
pubmed: 15057824
Genome Biol. 2013 Jan 29;14(1):R9
pubmed: 23360670
Trends Genet. 2009 Oct;25(10):443-54
pubmed: 19796838
Nucleic Acids Res. 2018 Aug 21;46(14):7070-7084
pubmed: 29982784
Genomics. 2017 Jul;109(3-4):214-220
pubmed: 28438488
J Infect Dis. 2018 May 25;217(12):1865-1874
pubmed: 29432596
Open Biol. 2019 Oct 31;9(10):190094
pubmed: 31615332
Lancet. 2003 Nov 22;362(9397):1714-9
pubmed: 14643120
Hum Mol Genet. 2014 Nov 15;23(22):5866-78
pubmed: 24939910
Nucleic Acids Res. 2017 Jan 4;45(D1):D896-D901
pubmed: 27899670
Am J Primatol. 2014 Sep;76(9):801-27
pubmed: 24723482
Nat Methods. 2012 Dec;9(12):1185-8
pubmed: 23103880
BMC Genomics. 2017 Dec 19;18(1):977
pubmed: 29258433
Hum Mol Genet. 2010 Oct 15;19(20):4072-82
pubmed: 20663923
BMC Evol Biol. 2014 Sep 04;14:176
pubmed: 25209564
Sci Rep. 2015 Nov 20;5:16894
pubmed: 26586576
Hum Genet. 2014 Oct;133(10):1217-33
pubmed: 25110110
J Pediatr Genet. 2015 Sep;4(3):159-67
pubmed: 27617127
Exp Neurol. 2018 Jan;299(Pt A):252-265
pubmed: 28774750
Genome Biol Evol. 2014 Oct 27;6(11):3025-38
pubmed: 25349268
Genome Biol Evol. 2018 Nov 1;10(11):2899-2905
pubmed: 30364947
PLoS Genet. 2009 Jan;5(1):e1000346
pubmed: 19165326
J Cell Biol. 2004 Oct 25;167(2):257-67
pubmed: 15492043