Phylogenomic Analyses of Non-Dikarya Fungi Supports Horizontal Gene Transfer Driving Diversification of Secondary Metabolism in the Amphibian Gastrointestinal Symbiont,

Basidiobolus horizontal gene transfer secondary metabolism siderophores zygomycetes

Journal

G3 (Bethesda, Md.)
ISSN: 2160-1836
Titre abrégé: G3 (Bethesda)
Pays: England
ID NLM: 101566598

Informations de publication

Date de publication:
02 09 2020
Historique:
pubmed: 31 7 2020
medline: 22 6 2021
entrez: 31 7 2020
Statut: epublish

Résumé

Research into secondary metabolism (SM) production by fungi has resulted in the discovery of diverse, biologically active compounds with significant medicinal applications. The fungi rich in SM production are taxonomically concentrated in the subkingdom Dikarya, which comprises the phyla Ascomycota and Basidiomycota. Here, we explore the potential for SM production in Mucoromycota and Zoopagomycota, two phyla of nonflagellated fungi that are not members of Dikarya, by predicting and identifying core genes and gene clusters involved in SM. The majority of non-Dikarya have few genes and gene clusters involved in SM production except for the amphibian gut symbionts in the genus

Identifiants

pubmed: 32727924
pii: g3.120.401516
doi: 10.1534/g3.120.401516
pmc: PMC7466969
doi:

Types de publication

Journal Article Research Support, U.S. Gov't, Non-P.H.S.

Langues

eng

Sous-ensembles de citation

IM

Pagination

3417-3433

Informations de copyright

Copyright © 2020 Tabima et al.

Références

Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15670-5
pubmed: 14676319
New Phytol. 2018 Feb;217(3):1213-1229
pubmed: 29315638
G3 (Bethesda). 2015 Sep 28;5(12):2539-45
pubmed: 26416668
Proc Natl Acad Sci U S A. 2016 Dec 27;113(52):15102-15107
pubmed: 27956601
Nat Commun. 2016 Dec 15;7:13699
pubmed: 27976718
mBio. 2012 Sep 04;3(5):e00259-12
pubmed: 22951933
BMC Genomics. 2014 Jan 17;15:34
pubmed: 24438332
Eukaryot Cell. 2010 Dec;9(12):1891-900
pubmed: 20889720
Nat Prod Rep. 2020 Jul 1;37(7):868-878
pubmed: 31898704
Bioinformatics. 2015 Jan 15;31(2):166-9
pubmed: 25260700
Fungal Genet Biol. 2010 Sep;47(9):736-41
pubmed: 20554054
Microbiome. 2018 Dec 17;6(1):225
pubmed: 30558682
New Phytol. 2018 Dec;220(4):1161-1171
pubmed: 29355972
PLoS Comput Biol. 2013;9(8):e1003118
pubmed: 23950696
Org Lett. 2019 Mar 1;21(5):1444-1448
pubmed: 30789272
Nucleic Acids Res. 2010 Jan;38(Database issue):D211-22
pubmed: 19920124
Proc Natl Acad Sci U S A. 2011 Feb 8;108(6):2504-9
pubmed: 21262841
PLoS Pathog. 2011 Sep;7(9):e1002179
pubmed: 21909256
Mol Biol Evol. 2016 Oct;33(10):2544-54
pubmed: 27343289
Mol Biol Evol. 2018 Aug 1;35(8):1840-1854
pubmed: 29771364
Science. 2012 Jun 29;336(6089):1715-9
pubmed: 22745431
Mycol Res. 2007 Dec;111(Pt 12):1437-49
pubmed: 18035528
mSystems. 2019 Aug 27;4(4):
pubmed: 31455637
Nat Rev Microbiol. 2005 Dec;3(12):937-47
pubmed: 16322742
Bioinformatics. 2014 May 1;30(9):1312-3
pubmed: 24451623
Sci Rep. 2012;2:483
pubmed: 22761991
Front Plant Sci. 2014 Jun 26;5:299
pubmed: 25018762
Genome Announc. 2016 Aug 18;4(4):
pubmed: 27540072
Environ Microbiol Rep. 2013 Dec;5(6):899-903
pubmed: 24249298
Evol Lett. 2018 Feb 27;2(2):88-101
pubmed: 30283667
Appl Microbiol Biotechnol. 1999 May;51(5):553-63
pubmed: 10390813
Curr Biol. 2016 Jun 20;26(12):1577-1584
pubmed: 27238284
Fungal Genet Biol. 2007 Nov;44(11):1096-108
pubmed: 17822929
Clin Infect Dis. 2012 Jun;54(12):1685-91
pubmed: 22441651
BMC Genomics. 2015 Jun 16;16:461
pubmed: 26076695
Plant Physiol. 2010 Oct;154(2):531-5
pubmed: 20921179
Mol Biol Evol. 2016 Apr;33(4):959-70
pubmed: 26659563
Nat Prod Rep. 2018 Sep 19;35(9):992-1014
pubmed: 29774351
New Phytol. 2019 Apr;222(1):511-525
pubmed: 30485448
Phytopathology. 2020 Jun;110(6):1180-1188
pubmed: 32207662
Nat Commun. 2016 Jul 22;7:12218
pubmed: 27447865
J Vet Med Sci. 2015 Oct;77(10):1311-3
pubmed: 25960121
Nature. 2008 Mar 6;452(7183):88-92
pubmed: 18322534
Proc Natl Acad Sci U S A. 2014 Jul 8;111(27):9923-8
pubmed: 24958869
Genome Announc. 2013 Feb 28;1(2):e0019512
pubmed: 23516228
Mol Ecol. 2016 Aug;25(16):3776-800
pubmed: 27297628
Appl Environ Microbiol. 2012 Apr;78(7):2272-81
pubmed: 22247176
PLoS Pathog. 2011 Oct;7(10):e1002290
pubmed: 22022265
Bioinformatics. 2010 Jan 1;26(1):139-40
pubmed: 19910308
Fitoterapia. 2020 Jun 18;146:104671
pubmed: 32565347
Nat Microbiol. 2017 May 30;2:17087
pubmed: 28555641
Stud Mycol. 2020 Feb 01;96:141-153
pubmed: 32206138
Proc Natl Acad Sci U S A. 2013 Dec 10;110(50):20117-22
pubmed: 24277808
PLoS Genet. 2013 Jun;9(6):e1003496
pubmed: 23818858
Stud Mycol. 2017 Mar;86:1-28
pubmed: 28348446
Nucleic Acids Res. 2014 Jan;42(Database issue):D699-704
pubmed: 24297253
BMC Microbiol. 2014 Apr 14;14:93
pubmed: 24731286
Biotechnology (N Y). 1990 Jan;8(1):39-41
pubmed: 1368505
Nat Prod Rep. 2014 Oct;31(10):1449-73
pubmed: 25171145
Nucleic Acids Res. 2000 Jan 1;28(1):231-4
pubmed: 10592234
BMC Evol Biol. 2010 Jan 26;10:26
pubmed: 20100353
PLoS Genet. 2014 Aug 14;10(8):e1004496
pubmed: 25121733
Nat Commun. 2017 Feb 08;8:14444
pubmed: 28176784
Nat Genet. 2017 Jun;49(6):964-968
pubmed: 28481340
Nat Rev Microbiol. 2018 Dec;16(12):731-744
pubmed: 30194403
Fungal Genet Biol. 2012 Mar;49(3):217-26
pubmed: 22326418
ISME J. 2010 Nov;4(11):1375-85
pubmed: 20520652
Genome Announc. 2014 Sep 18;2(5):
pubmed: 25291769
Mycologia. 2016 Sep;108(5):1028-1046
pubmed: 27738200
Nat Genet. 2015 Apr;47(4):410-5
pubmed: 25706625
PLoS Genet. 2009 Jul;5(7):e1000549
pubmed: 19578406
Genome Biol. 2011;12(1):R7
pubmed: 21247460
Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
pubmed: 9254694
Mol Biol Evol. 2004 Oct;21(10):1884-94
pubmed: 15240837
PLoS Genet. 2013;9(1):e1003233
pubmed: 23357949
New Phytol. 2008;179(1):196-208
pubmed: 18433432
Nat Methods. 2015 Apr;12(4):357-60
pubmed: 25751142
Brief Bioinform. 2019 Jul 19;20(4):1160-1166
pubmed: 28968734
Microb Ecol. 2012 Oct;64(3):617-27
pubmed: 22526402
Nat Biotechnol. 2004 Oct;22(10):1315-6
pubmed: 15470472
Genome Biol Evol. 2015 May 14;7(6):1590-601
pubmed: 25977457
J Microbiol Methods. 2016 Feb;121:41-3
pubmed: 26712125
Elife. 2017 Nov 24;6:
pubmed: 29171834
Fungal Biol. 2012 Jan;116(1):90-7
pubmed: 22208604
Proc Natl Acad Sci U S A. 2012 Oct 23;109(43):17501-6
pubmed: 23045686
PLoS Genet. 2014 Dec 04;10(12):e1004816
pubmed: 25474404
BMC Genomics. 2019 Jul 23;20(1):605
pubmed: 31337355
Iran J Med Sci. 2015 Mar;40(2):90-7
pubmed: 25821287
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Nucleic Acids Res. 2017 Jul 3;45(W1):W36-W41
pubmed: 28460038
Nat Microbiol. 2018 Dec;3(12):1417-1428
pubmed: 30297742
BMC Genomics. 2014 Jul 01;15:549
pubmed: 24984952
Appl Environ Microbiol. 2013 Aug;79(15):4620-34
pubmed: 23709508
Mol Biol Evol. 2010 Sep;27(9):2141-51
pubmed: 20403964
Nucleic Acids Res. 2016 Jan 4;44(D1):D733-45
pubmed: 26553804
Environ Microbiol. 2017 Aug;19(8):2964-2983
pubmed: 28076891
Nat Rev Microbiol. 2013 Jan;11(1):21-32
pubmed: 23178386
Mob Genet Elements. 2011 May;1(1):75-77
pubmed: 22016848
Genome Biol. 2015 Aug 06;16:157
pubmed: 26243257
Appl Environ Microbiol. 2019 Jul 18;85(15):
pubmed: 31126947
PLoS Pathog. 2012;8(12):e1003037
pubmed: 23236275
BMC Evol Biol. 2013 Feb 13;13:40
pubmed: 23405862
Nat Genet. 2018 Dec;50(12):1688-1695
pubmed: 30349117

Auteurs

Javier F Tabima (JF)

Department of Botany and Plant Pathology, College of Agricultural Sciences, Oregon State University, Corvallis tabimaj@oregonstate.edu.

Ian A Trautman (IA)

Department of Botany and Plant Pathology, College of Agricultural Sciences, Oregon State University, Corvallis.

Ying Chang (Y)

Department of Botany and Plant Pathology, College of Agricultural Sciences, Oregon State University, Corvallis.

Yan Wang (Y)

Department of Microbiology and Plant Pathology, University of California-Riverside, California.
Institute for Integrative Genome Biology, University of California-Riverside, California.

Stephen Mondo (S)

US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, California.

Alan Kuo (A)

US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, California.

Asaf Salamov (A)

US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, California.

Igor V Grigoriev (IV)

Department of Plant and Microbial Biology, University of California-Berkeley, California.
US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, California.

Jason E Stajich (JE)

Department of Microbiology and Plant Pathology, University of California-Riverside, California.
Institute for Integrative Genome Biology, University of California-Riverside, California.

Joseph W Spatafora (JW)

Department of Botany and Plant Pathology, College of Agricultural Sciences, Oregon State University, Corvallis.

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