A unique chromatin profile defines adaptive genomic regions in a fungal plant pathogen.
DNA methylation
atac sequencing
chromatin
epigenome
evolutionary biology
histone modification
infectious disease
microbiology
verticillium dahliae
Journal
eLife
ISSN: 2050-084X
Titre abrégé: Elife
Pays: England
ID NLM: 101579614
Informations de publication
Date de publication:
18 12 2020
18 12 2020
Historique:
received:
18
08
2020
accepted:
17
12
2020
pubmed:
19
12
2020
medline:
19
3
2021
entrez:
18
12
2020
Statut:
epublish
Résumé
Genomes store information at scales beyond the linear nucleotide sequence, which impacts genome function at the level of an individual, while influences on populations and long-term genome function remains unclear. Here, we addressed how physical and chemical DNA characteristics influence genome evolution in the plant pathogenic fungus
Identifiants
pubmed: 33337321
doi: 10.7554/eLife.62208
pii: 62208
pmc: PMC7781603
doi:
pii:
Substances chimiques
Chromatin
0
DNA, Fungal
0
Histones
0
Banques de données
SRA
['PRJNA592220']
Types de publication
Journal Article
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 : European Molecular Biology Organization
ID : ALTF 969-2013
Pays : International
Organisme : Human Frontier Science Program
ID : LT000627/2014-L
Pays : International
Organisme : European Molecular Biology Organization
ID : XC 2048/1 – PROJECT ID: 390686111
Pays : International
Organisme : United States Department of Agriculture
ID : 2018-67013-28492
Pays : International
Organisme : National Science Foundation
ID : 1936800
Pays : International
Informations de copyright
© 2020, Cook et al.
Déclaration de conflit d'intérêts
DC, HK, DT, MS, BT No competing interests declared
Références
Genome Biol Evol. 2019 May 1;11(5):1487-1500
pubmed: 31028389
PLoS Genet. 2019 Apr 22;15(4):e1008093
pubmed: 31009462
Mol Plant Pathol. 2018 Sep;19(9):2094-2110
pubmed: 29569316
Cell. 2015 Mar 12;160(6):1049-59
pubmed: 25768903
PLoS One. 2011 Jan 31;6(1):e16526
pubmed: 21304975
Mol Biol Evol. 2019 Aug 1;36(8):1624-1627
pubmed: 31077317
Genetics. 2018 Oct;210(2):517-529
pubmed: 30072376
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Genome Biol. 2014 Jul 31;15(7):411
pubmed: 25091826
Proc Natl Acad Sci U S A. 2012 Mar 27;109(13):5110-5
pubmed: 22416119
BMC Bioinformatics. 2009 Jul 27;10:232
pubmed: 19635165
PLoS Comput Biol. 2013;9(8):e1003118
pubmed: 23950696
Environ Microbiol. 2016 Nov;18(11):4037-4054
pubmed: 27348741
PLoS Biol. 2008 May 6;6(5):e110
pubmed: 18462019
PLoS Pathog. 2011 Jul;7(7):e1002137
pubmed: 21829347
Nat Rev Microbiol. 2017 Dec;15(12):756-771
pubmed: 28781365
Nucleic Acids Res. 2009 Nov;37(21):7002-13
pubmed: 19786494
Plant Physiol. 2014 Feb;164(2):513-24
pubmed: 24306534
Elife. 2020 Dec 18;9:
pubmed: 33337321
PLoS One. 2014 May 02;9(5):e91929
pubmed: 24786468
Prog Mol Subcell Biol. 2017;56:85-109
pubmed: 28840234
Mol Biol Evol. 2013 Apr;30(4):772-80
pubmed: 23329690
Genome Res. 2013 Aug;23(8):1271-82
pubmed: 23685541
Science. 2002 Nov 1;298(5595):1039-43
pubmed: 12351676
Theory Biosci. 2012 Dec;131(4):281-5
pubmed: 22872506
Nature. 2001 Nov 15;414(6861):277-83
pubmed: 11713521
Genome Biol. 2014;15(12):550
pubmed: 25516281
Chromosoma. 2006 Apr;115(2):110-22
pubmed: 16506022
Trends Genet. 2000 Jun;16(6):276-7
pubmed: 10827456
Mol Cell Biol. 2008 Oct;28(19):6044-55
pubmed: 18678653
Nat Biotechnol. 2016 May;34(5):525-7
pubmed: 27043002
Nature. 2011 Jan 20;469(7330):343-9
pubmed: 21248841
Annu Rev Cell Dev Biol. 2018 Oct 6;34:265-288
pubmed: 30044650
Annu Rev Phytopathol. 2015;53:541-63
pubmed: 26047564
BMC Genomics. 2012 Jul 16;13:314
pubmed: 22800085
PLoS Pathog. 2016 Nov 3;12(11):e1005920
pubmed: 27812218
Curr Opin Plant Biol. 2012 Nov;15(5):523-9
pubmed: 22999383
Nat Methods. 2020 Mar;17(3):261-272
pubmed: 32015543
Genome Res. 2016 Jan;26(1):97-107
pubmed: 26537359
Nature. 2003 Apr 24;422(6934):893-7
pubmed: 12712205
Bioessays. 2014 Apr;36(4):335-45
pubmed: 24531982
Curr Protoc Mol Biol. 2015 Jan 05;109:21.29.1-21.29.9
pubmed: 25559105
Mol Microbiol. 2014 Apr;92(2):413-34
pubmed: 24571357
Nature. 2001 Mar 1;410(6824):120-4
pubmed: 11242054
BMC Bioinformatics. 2008 Jan 14;9:18
pubmed: 18194517
PLoS Genet. 2014 Mar 06;10(3):e1004227
pubmed: 24603691
Genome Res. 2009 Jun;19(6):959-66
pubmed: 19273618
Science. 2010 Dec 10;330(6010):1540-3
pubmed: 21148391
Fungal Genet Biol. 2016 May;90:24-30
pubmed: 26342853
Nat Biotechnol. 2019 Apr;37(4):420-423
pubmed: 30778233
Methods Mol Biol. 2012;835:509-17
pubmed: 22183674
Mol Cell Biol. 2011 Jun;31(12):2528-42
pubmed: 21505064
BMC Bioinformatics. 2011 Mar 17;12:77
pubmed: 21414208
Genome Biol. 2018 Oct 31;19(1):181
pubmed: 30382931
Nat Methods. 2013 Dec;10(12):1213-8
pubmed: 24097267
Curr Opin Genet Dev. 2015 Dec;35:57-65
pubmed: 26451981
mBio. 2020 Sep 8;11(5):
pubmed: 32900804
EMBO J. 2001 Aug 1;20(15):4309-23
pubmed: 11483533
Cell. 2015 Jan 15;160(1-2):204-18
pubmed: 25533783
Elife. 2020 Jan 20;9:
pubmed: 31958060
Trends Ecol Evol. 2010 Jul;25(7):387-95
pubmed: 20434790
Environ Microbiol. 2018 Apr;20(4):1362-1373
pubmed: 29282842
Nat Rev Microbiol. 2012 May 08;10(6):417-30
pubmed: 22565130
Trends Genet. 2012 Dec;28(12):583-5
pubmed: 23131467
Science. 2008 Jan 4;319(5859):94-7
pubmed: 18174443
Mol Cell. 2004 Feb 13;13(3):427-34
pubmed: 14967149
Nature. 2000 Aug 10;406(6796):593-9
pubmed: 10949293
Nat Commun. 2011 Feb 15;2:202
pubmed: 21326234
Genome Res. 2011 Feb;21(2):147-63
pubmed: 21177972
Epigenetics Chromatin. 2021 May 3;14(1):21
pubmed: 33941240
Nat Genet. 2017 Jun;49(6):964-968
pubmed: 28481340
PeerJ. 2016 Oct 18;4:e2584
pubmed: 27781170
Annu Rev Plant Biol. 2018 Apr 29;69:267-299
pubmed: 29719165
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
Sci Rep. 2019 Jun 27;9(1):9354
pubmed: 31249361
Proc Natl Acad Sci U S A. 2016 Dec 27;113(52):15048-15053
pubmed: 27856763
Nat Rev Immunol. 2016 Sep;16(9):537-52
pubmed: 27477127
Genome Biol Evol. 2016 Feb 12;8(3):681-704
pubmed: 26872771
Nature. 2011 May 5;473(7345):43-9
pubmed: 21441907
BMC Mol Biol. 2008 Aug 01;9:70
pubmed: 18673530
Science. 2014 Sep 19;345(6203):1515-8
pubmed: 25237104
Mol Plant Pathol. 2017 May;18(4):596-608
pubmed: 27911046
Curr Opin Microbiol. 2015 Aug;26:92-101
pubmed: 26162502
J Mol Evol. 1990 May;30(5):463-76
pubmed: 2111858
Genome Res. 2009 Mar;19(3):427-37
pubmed: 19092133
PLoS Genet. 2011 Jun;7(6):e1002070
pubmed: 21695235
Nature. 2006 Nov 16;444(7117):323-9
pubmed: 17108957
Genome Res. 2018 Oct;28(10):1543-1554
pubmed: 30143598
Nat Genet. 2005 Aug;37(8):809-19
pubmed: 15976807
PLoS One. 2015 Mar 04;10(3):e0118432
pubmed: 25738806
Proc Natl Acad Sci U S A. 2002 Jun 25;99(13):8802-7
pubmed: 12072568
PLoS Genet. 2019 Sep 12;15(9):e1008272
pubmed: 31513573
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
Nature. 2010 Mar 18;464(7287):367-73
pubmed: 20237561
Nat Rev Genet. 2007 Dec;8(12):973-82
pubmed: 17984973
PLoS Genet. 2013 Oct;9(10):e1003916
pubmed: 24204317
Nucleic Acids Res. 1994 Aug 11;22(15):2990-7
pubmed: 8065911
Annu Rev Microbiol. 2017 Sep 8;71:413-439
pubmed: 28715960
Genome Res. 2016 Aug;26(8):1069-80
pubmed: 27260477
J Mol Biol. 2021 Mar 19;433(6):166676
pubmed: 33065112
mBio. 2015 Aug 18;6(4):
pubmed: 26286689
Chromosome Res. 2012 Jul;20(5):635-56
pubmed: 22752455
Cell. 2012 Feb 3;148(3):458-72
pubmed: 22265598
Epigenetics Chromatin. 2015 Oct 01;8:41
pubmed: 26430472
Bioinformatics. 2015 Aug 1;31(15):2595-7
pubmed: 25810428
Genome Res. 2016 Aug;26(8):1091-100
pubmed: 27325116
Annu Rev Genet. 2016 Nov 23;50:371-392
pubmed: 27732794