The Tiger Rattlesnake genome reveals a complex genotype underlying a simple venom phenotype.
chromatin
gene regulation
genotype–phenotype
methylation
Journal
Proceedings of the National Academy of Sciences of the United States of America
ISSN: 1091-6490
Titre abrégé: Proc Natl Acad Sci U S A
Pays: United States
ID NLM: 7505876
Informations de publication
Date de publication:
26 01 2021
26 01 2021
Historique:
entrez:
20
1
2021
pubmed:
21
1
2021
medline:
12
6
2021
Statut:
ppublish
Résumé
Variation in gene regulation is ubiquitous, yet identifying the mechanisms producing such variation, especially for complex traits, is challenging. Snake venoms provide a model system for studying the phenotypic impacts of regulatory variation in complex traits because of their genetic tractability. Here, we sequence the genome of the Tiger Rattlesnake, which possesses the simplest and most toxic venom of any rattlesnake species, to determine whether the simple venom phenotype is the result of a simple genotype through gene loss or a complex genotype mediated through regulatory mechanisms. We generate the most contiguous snake-genome assembly to date and use this genome to show that gene loss, chromatin accessibility, and methylation levels all contribute to the production of the simplest, most toxic rattlesnake venom. We provide the most complete characterization of the venom gene-regulatory network to date and identify key mechanisms mediating phenotypic variation across a polygenic regulatory network.
Identifiants
pubmed: 33468678
pii: 2014634118
doi: 10.1073/pnas.2014634118
pmc: PMC7848695
pii:
doi:
Substances chimiques
Crotalid Venoms
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : NIGMS NIH HHS
ID : P20 GM109094
Pays : United States
Organisme : NHGRI NIH HHS
ID : R21 HG010403
Pays : United States
Déclaration de conflit d'intérêts
The authors declare no competing interest.
Références
Int J Cancer. 2017 Jun 15;140(12):2634-2641
pubmed: 28076901
Nat Methods. 2015 Apr;12(4):357-60
pubmed: 25751142
Nat Protoc. 2016 Sep;11(9):1650-67
pubmed: 27560171
BMC Genomics. 2013 Apr 10;14:234
pubmed: 23575160
Curr Biol. 2018 Apr 2;28(7):1016-1026.e4
pubmed: 29576471
Nat Rev Genet. 2011 Dec 06;13(1):59-69
pubmed: 22143240
Science. 2016 Apr 1;352(6281):aae0344
pubmed: 27034376
BMC Genomics. 2012 Jul 16;13:312
pubmed: 23025625
Evolution. 2007 May;61(5):995-1016
pubmed: 17492956
Nat Commun. 2016 Oct 06;7:13107
pubmed: 27708285
Genome Biol. 2006;7 Suppl 1:S10.1-12
pubmed: 16925832
Nat Commun. 2018 Jan 15;9(1):189
pubmed: 29335486
Science. 2019 Apr 5;364(6435):74-78
pubmed: 30948549
Comp Funct Genomics. 2008;:545269
pubmed: 18815629
Mol Biol Evol. 2013 Apr;30(4):772-80
pubmed: 23329690
Bioinformatics. 2013 Nov 1;29(21):2669-77
pubmed: 23990416
Nat Rev Mol Cell Biol. 2007 May;8(5):369-78
pubmed: 17377526
J Proteomics. 2014 Jan 16;96:145-58
pubmed: 24231107
Genome Biol. 2012 Oct 03;13(10):R83
pubmed: 23034175
Science. 2017 May 5;356(6337):
pubmed: 28473536
Comp Biochem Physiol Pharmacol Toxicol Endocrinol. 1994 Mar;107(3):337-46
pubmed: 8061939
Genome Biol. 2014;15(12):550
pubmed: 25516281
Nature. 1996 Feb 8;379(6565):537-40
pubmed: 8596631
Nat Ecol Evol. 2017;1(3):52
pubmed: 28523290
Proc Natl Acad Sci U S A. 2013 Dec 17;110(51):20651-6
pubmed: 24297900
Nature. 2011 Aug 31;477(7366):587-91
pubmed: 21881562
Curr Biol. 2016 Sep 26;26(18):2434-2445
pubmed: 27641771
Nucleic Acids Res. 2019 Jan 8;47(D1):D145-D154
pubmed: 30380113
J Proteome Res. 2010 Jan;9(1):528-44
pubmed: 19863078
Proc Natl Acad Sci U S A. 2013 Dec 10;110(50):E4858-66
pubmed: 24277850
Genome Res. 2019 Jun;29(6):969-977
pubmed: 31160376
J Proteomics. 2011 Sep 6;74(10):2169-79
pubmed: 21722760
Bioinformatics. 2015 Oct 1;31(19):3210-2
pubmed: 26059717
Bioinformatics. 2014 Oct;30(19):2811-2
pubmed: 24930139
Genome Res. 2008 Jan;18(1):188-96
pubmed: 18025269
Genetics. 2005 Aug;170(4):1449-57
pubmed: 15944361
Mol Endocrinol. 2014 Jun;28(6):949-64
pubmed: 24801505
Nature. 2008 Mar 27;452(7186):470-2
pubmed: 18368117
Proc Natl Acad Sci U S A. 2010 May 11;107(19):8689-94
pubmed: 20395551
Nat Biotechnol. 2015 Mar;33(3):290-5
pubmed: 25690850
Nat Rev Genet. 2013 Nov;14(11):807-20
pubmed: 24136507
Genome Res. 2019 Apr;29(4):590-601
pubmed: 30898880
Curr Protoc Mol Biol. 2015 Jan 05;109:21.29.1-21.29.9
pubmed: 25559105
Evolution. 2018 Jun;72(6):1242-1260
pubmed: 29676774
Trends Genet. 2017 Jul;33(7):436-447
pubmed: 28528721
J Proteome Res. 2012 Feb 3;11(2):1382-90
pubmed: 22181673
Nature. 2012 Sep 6;489(7414):75-82
pubmed: 22955617
Proc Biol Sci. 2016 Apr 27;283(1829):
pubmed: 27122552
J R Soc Interface. 2018 Jan;15(138):
pubmed: 29321269
Bioinformatics. 2010 Jan 1;26(1):139-40
pubmed: 19910308
Bioinformatics. 2020 Apr 15;36(8):2628-2629
pubmed: 31882993
G3 (Bethesda). 2015 Sep 09;5(11):2375-82
pubmed: 26358130
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
Science. 2016 Apr 22;352(6284):470-4
pubmed: 27102486
BMC Evol Biol. 2007 Jan 18;7:2
pubmed: 17233905
Mol Cell. 2010 May 28;38(4):576-89
pubmed: 20513432
Sci Rep. 2018 Dec 4;8(1):17622
pubmed: 30514908
Nat Commun. 2018 Feb 22;9(1):781
pubmed: 29472610
Nat Genet. 2020 Jan;52(1):106-117
pubmed: 31907489
Mol Biol Evol. 2019 Feb 1;36(2):271-282
pubmed: 30395254
Nat Methods. 2015 Mar;12(3):230-2, 1 p following 232
pubmed: 25362363
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W187-91
pubmed: 24799436
Mol Biol Evol. 2019 Jan 1;36(1):159-173
pubmed: 30452724
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W465-7
pubmed: 15980513
Nature. 2017 Mar 2;543(7643):72-77
pubmed: 28225755
Bioinformatics. 2011 Jun 1;27(11):1571-2
pubmed: 21493656
Evolution. 2000 Feb;54(1):13-20
pubmed: 10937178
Genome Biol. 2019 Oct 28;20(1):224
pubmed: 31661016
Genome Biol. 2020 Feb 3;21(1):22
pubmed: 32014034
Proc Natl Acad Sci U S A. 2020 May 19;117(20):10911-10920
pubmed: 32366667
Proc Natl Acad Sci U S A. 2014 Jun 24;111(25):9205-10
pubmed: 24927555
Nat Commun. 2016 May 06;7:11485
pubmed: 27151365
Toxicon. 2016 Sep 1;119:28-38
pubmed: 27179420
Biochem J. 1971 Feb;121(4):609-12
pubmed: 4940047
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
Mol Biol Evol. 2017 Dec 1;34(12):3099-3110
pubmed: 28962003
Transl Res. 2012 Feb;159(2):64-79
pubmed: 22243791
Trends Genet. 2019 Nov;35(11):818-827
pubmed: 31399242
Mol Ecol. 2015 Jul;24(13):3405-20
pubmed: 25988233
PLoS One. 2018 Feb 7;13(2):e0192414
pubmed: 29415017
Nat Commun. 2016 Jun 15;7:11769
pubmed: 27302525
Toxins (Basel). 2018 Jun 19;10(6):
pubmed: 29921759
Cell. 2008 Jul 11;134(1):25-36
pubmed: 18614008
Nat Ecol Evol. 2019 Aug;3(8):1241-1252
pubmed: 31358948