The Sordariomycetes: an expanding resource with Big Data for mining in evolutionary genomics and transcriptomics.
Big Data
Fusarium
Neurospora
Sordariomycetes
Trichoderma
evolution
genomics
transcriptomics
Journal
Frontiers in fungal biology
ISSN: 2673-6128
Titre abrégé: Front Fungal Biol
Pays: Switzerland
ID NLM: 9918266300506676
Informations de publication
Date de publication:
2023
2023
Historique:
received:
30
04
2023
accepted:
06
06
2023
medline:
25
9
2023
pubmed:
25
9
2023
entrez:
25
9
2023
Statut:
epublish
Résumé
Advances in genomics and transcriptomics accompanying the rapid accumulation of omics data have provided new tools that have transformed and expanded the traditional concepts of model fungi. Evolutionary genomics and transcriptomics have flourished with the use of classical and newer fungal models that facilitate the study of diverse topics encompassing fungal biology and development. Technological advances have also created the opportunity to obtain and mine large datasets. One such continuously growing dataset is that of the Sordariomycetes, which exhibit a richness of species, ecological diversity, economic importance, and a profound research history on amenable models. Currently, 3,574 species of this class have been sequenced, comprising nearly one-third of the available ascomycete genomes. Among these genomes, multiple representatives of the model genera
Identifiants
pubmed: 37746130
doi: 10.3389/ffunb.2023.1214537
pmc: PMC10512317
doi:
Types de publication
Journal Article
Review
Langues
eng
Pagination
1214537Informations de copyright
Copyright © 2023 Wang, Kim, Wang, Yakubovich, Dong, Trail, Townsend and Yarden.
Déclaration de conflit d'intérêts
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Références
Biotechnol Biofuels. 2015 Feb 12;8:21
pubmed: 25691917
Elife. 2020 Dec 09;9:
pubmed: 33295874
BMC Biol. 2018 Jan 11;16(1):5
pubmed: 29325559
Nature. 2010 Dec 9;468(7325):815-8
pubmed: 21150997
Front Plant Sci. 2022 Oct 31;13:1034600
pubmed: 36388575
PLoS Genet. 2012;8(7):e1002820
pubmed: 22844246
PLoS Comput Biol. 2013;9(7):e1003126
pubmed: 23935467
PLoS Biol. 2023 Apr 12;21(4):e3002090
pubmed: 37043438
Genome Biol. 2008;9(5):R77
pubmed: 18460219
Fungal Genet Biol. 2005 Jun;42(6):528-33
pubmed: 15878295
Fungal Genet Biol. 2023 Mar;165:103768
pubmed: 36596442
BMC Genomics. 2019 May 4;20(1):337
pubmed: 31054562
Adv Genet. 2017;100:1-47
pubmed: 29153398
Genetics. 2019 Dec;213(4):1545-1563
pubmed: 31604798
Genome Biol. 2011;12(4):R40
pubmed: 21501500
mBio. 2022 Jun 28;13(3):e0110022
pubmed: 35638737
Proc Natl Acad Sci U S A. 1941 Nov 15;27(11):499-506
pubmed: 16588492
BMC Genomics. 2023 Mar 16;24(1):117
pubmed: 36927511
Front Microbiol. 2019 Jun 07;10:1247
pubmed: 31231336
Bioinformatics. 2023 Apr 3;39(4):
pubmed: 36944259
Mycologia. 2006 Nov-Dec;98(6):1029-40
pubmed: 17486978
Mycologia. 2006 Nov-Dec;98(6):838-49
pubmed: 17486961
Sci Rep. 2021 Feb 5;11(1):3217
pubmed: 33547391
J Fungi (Basel). 2021 Oct 28;7(11):
pubmed: 34829206
Protein Pept Lett. 2018 Feb 8;24(12):1120-1129
pubmed: 28933279
Front Fungal Biol. 2022 Sep 14;3:1002161
pubmed: 37746224
Proc Natl Acad Sci U S A. 2020 Dec 22;117(51):32528-32534
pubmed: 33257574
mBio. 2018 Aug 14;9(4):
pubmed: 30108170
Nat Commun. 2020 Nov 6;11(1):5627
pubmed: 33159072
Cell Mol Life Sci. 2019 Jan;76(2):329-340
pubmed: 30302531
Sci Rep. 2019 Feb 1;9(1):1108
pubmed: 30710113
Fungal Divers. 2021;109(1):27-55
pubmed: 34720775
Front Oncol. 2020 Oct 14;10:588221
pubmed: 33154949
Science. 2007 Sep 7;317(5843):1400-2
pubmed: 17823352
Microbiol Spectr. 2023 Mar 22;:e0480022
pubmed: 36946736
BMC Biol. 2020 Feb 11;18(1):12
pubmed: 32046716
Mol Ecol. 2012 Jun;21(11):2816-28
pubmed: 22486972
Zhongguo Zhong Yao Za Zhi. 2017 Apr;42(7):1281-1286
pubmed: 29052387
Annu Rev Microbiol. 2013;67:399-416
pubmed: 24024636
G3 (Bethesda). 2020 Aug 5;10(8):2573-2583
pubmed: 32580939
Microbiol Mol Biol Rev. 2022 Mar 16;86(1):e0001921
pubmed: 34817241
mBio. 2023 Feb 28;14(1):e0244222
pubmed: 36598191
BMC Evol Biol. 2015 Sep 16;15:198
pubmed: 26377599
PLoS Pathog. 2023 Apr 3;19(4):e1011251
pubmed: 37011084
Mol Ecol. 2018 Jan;27(1):216-232
pubmed: 29134709
Science. 1975 Apr 11;188(4184):107-16
pubmed: 1090005
PLoS One. 2013 Dec 20;8(12):e83109
pubmed: 24376646
Mycologia. 2006 Nov-Dec;98(6):1076-87
pubmed: 17486982
Stud Mycol. 2022 Jul;101:121-243
pubmed: 36059895
Proteomics. 2004 Jan;4(1):59-77
pubmed: 14730672
Microorganisms. 2019 Oct 29;7(11):
pubmed: 31671828
Sci Rep. 2012;2:483
pubmed: 22761991
mBio. 2022 Oct 31;13(6):e0221822
pubmed: 36314807
J Environ Monit. 2007 Aug;9(8):826-30
pubmed: 17671663
BMC Genomics. 2022 Jan 4;23(1):7
pubmed: 34983386
Genetics. 2014 Mar;196(3):729-44
pubmed: 24407906
Mycologia. 1975 Jul-Aug;67(4):852-62
pubmed: 1177970
PLoS Genet. 2018 Apr 9;14(4):e1007322
pubmed: 29630596
ISME J. 2023 May;17(5):733-747
pubmed: 36841903
FEMS Microbiol Lett. 2016 Oct 1;363(19):
pubmed: 27664058
Glob Chang Biol. 2018 Oct;24(10):4544-4553
pubmed: 30051940
Nat Methods. 2014 Nov;11(11):1114-25
pubmed: 25357241
Curr Biol. 2011 Jan 25;21(2):134-9
pubmed: 21194949
PLoS Genet. 2017 Jul 13;13(7):e1006867
pubmed: 28704372
Mol Plant Pathol. 2010 Sep;11(5):585-95
pubmed: 20695998
Mol Ecol. 2015 Nov;24(22):5657-75
pubmed: 26453896
Bioinformation. 2007 Mar 27;1(9):376-8
pubmed: 17597925
Eukaryot Cell. 2014 Jan;13(1):154-69
pubmed: 24243796
Proc Natl Acad Sci U S A. 2016 Mar 29;113(13):3567-72
pubmed: 26976598
Nat Commun. 2021 Dec 10;12(1):7198
pubmed: 34893601
Fungal Genet Biol. 2012 Aug;49(8):663-73
pubmed: 22705880
Biology (Basel). 2016 Jun 08;5(2):
pubmed: 27338490
Adv Virus Res. 2020;106:123-144
pubmed: 32327146
Fungal Biol Biotechnol. 2020 Apr 2;7:5
pubmed: 32280481
Front Plant Sci. 2017 Feb 03;8:119
pubmed: 28217138
Genome Biol. 2008;9(5):223
pubmed: 18492226
BMC Biol. 2017 Jun 29;15(1):55
pubmed: 28662661
Nat Commun. 2020 Oct 12;11(1):5125
pubmed: 33046698
Nat Commun. 2023 Feb 24;14(1):1059
pubmed: 36828814
PLoS One. 2011;6(6):e21476
pubmed: 21738678
OMICS. 2016 Mar;20(3):127-38
pubmed: 26885725
PLoS Negl Trop Dis. 2023 Mar 9;17(3):e0011136
pubmed: 36893096
Mol Biol Evol. 2020 Aug 1;37(8):2228-2240
pubmed: 32191325
BMC Genomics. 2019 Jun 12;20(1):485
pubmed: 31189469
J Fungi (Basel). 2023 Mar 29;9(4):
pubmed: 37108879
Mol Biol Evol. 2021 May 19;38(6):2475-2492
pubmed: 33555341
Proc Natl Acad Sci U S A. 2023 Mar 7;120(10):e2214076120
pubmed: 36848567
Mol Biol Rep. 2023 Apr;50(4):3885-3901
pubmed: 36826681
G3 (Bethesda). 2012 Feb;2(2):261-70
pubmed: 22384404
Sci Rep. 2019 Jan 29;9(1):898
pubmed: 30696919
Phytopathology. 2022 Apr;112(4):741-751
pubmed: 34491796
Adv Genet. 2016;94:67-105
pubmed: 27131323
Trends Genet. 2007 Nov;23(11):533-9
pubmed: 18029048
mBio. 2019 Dec 10;10(6):
pubmed: 31822585
Gene Regul Syst Bio. 2007 Nov 08;1:227-34
pubmed: 19936091
PLoS Biol. 2023 Jan 5;21(1):e3001961
pubmed: 36603054
Mol Biol Evol. 2016 Apr;33(4):959-70
pubmed: 26659563
Pathogens. 2020 May 01;9(5):
pubmed: 32369942
J Vis Exp. 2012 Mar 29;(61):
pubmed: 22491175
Microbiol Mol Biol Rev. 2004 Mar;68(1):1-108
pubmed: 15007097
World J Microbiol Biotechnol. 2017 Aug;33(8):155
pubmed: 28695465
Appl Environ Microbiol. 2011 Jun;77(12):4180-8
pubmed: 21531835
Mol Plant Microbe Interact. 2003 Oct;16(10):859-66
pubmed: 14558687
Microbiol Spectr. 2017 Jul;5(4):
pubmed: 28820125
Front Bioeng Biotechnol. 2021 Mar 15;9:649906
pubmed: 33791289
Annu Rev Microbiol. 2020 Sep 8;74:291-313
pubmed: 32660385
mBio. 2019 Oct 15;10(5):
pubmed: 31615963
Phytopathology. 2019 Jan;109(1):6-16
pubmed: 30412012
Plants (Basel). 2023 Mar 14;12(6):
pubmed: 36986993
Genome Announc. 2015 Feb 26;3(1):
pubmed: 25720678
Proc Natl Acad Sci U S A. 2014 Jul 8;111(27):9923-8
pubmed: 24958869
Arch Insect Biochem Physiol. 2022 Dec;111(4):e21968
pubmed: 36116100
FEMS Microbiol Lett. 2019 Jan 1;366(1):
pubmed: 30535195
Microbiology (Reading). 2007 Jan;153(Pt 1):1-6
pubmed: 17185529
BMC Genomics. 2016 Sep 29;17(1):763
pubmed: 27681232
Nature. 2005 Apr 21;434(7036):980-6
pubmed: 15846337
Methods Mol Biol. 2023;2642:295-318
pubmed: 36944885
Nat Commun. 2023 Mar 27;14(1):1684
pubmed: 36973282
Proc Natl Acad Sci U S A. 2006 Jul 5;103(27):10352-10357
pubmed: 16801547
Commun Integr Biol. 2009 Sep;2(5):448-51
pubmed: 19907715
Genome Res. 2016 Apr;26(4):486-98
pubmed: 26893460
Proc Natl Acad Sci U S A. 2023 Mar 7;120(10):e2216922120
pubmed: 36848561
Appl Microbiol Biotechnol. 2020 May;104(9):3691-3704
pubmed: 32162092
Appl Environ Microbiol. 2020 Jul 20;86(15):
pubmed: 32471912
Environ Microbiol. 2019 Aug;21(8):3011-3026
pubmed: 31136075
Syst Biol. 2012 May;61(3):539-42
pubmed: 22357727
Food Microbiol. 2018 Apr;70:28-32
pubmed: 29173636
Front Plant Sci. 2022 Sep 09;13:955254
pubmed: 36160954
PLoS Genet. 2019 Aug 14;15(8):e1008086
pubmed: 31412020
Nucleic Acids Res. 2014 Jan;42(Database issue):D699-704
pubmed: 24297253
Proc Natl Acad Sci U S A. 2020 Mar 17;117(11):6003-6013
pubmed: 32111691
Trends Cell Biol. 2016 Nov;26(11):818-824
pubmed: 27639630
Genetics. 1996 Jun;143(2):789-99
pubmed: 8725227
3 Biotech. 2020 Apr;10(4):172
pubmed: 32206506
Nat Commun. 2022 Dec 22;13(1):7897
pubmed: 36550124
G3 (Bethesda). 2017 Jan 5;7(1):129-142
pubmed: 27856696
Genetics. 2019 Jul;212(3):691-710
pubmed: 31068340
Nat Commun. 2017 Oct 26;8(1):1140
pubmed: 29074958
Genome Res. 2016 Apr;26(4):499-509
pubmed: 26934920
mBio. 2020 Sep 8;11(5):
pubmed: 32900807
Front Cell Infect Microbiol. 2019 Jul 18;9:257
pubmed: 31380300
BMC Genomics. 2022 Dec 29;23(1):859
pubmed: 36581831
Dev Biol. 2017 Sep 1;429(1):285-305
pubmed: 28629791
Proc Biol Sci. 2013 Jun 19;280(1764):20130862
pubmed: 23782882
J Fungi (Basel). 2022 Aug 15;8(8):
pubmed: 36012842
Viruses. 2022 Jul 14;14(7):
pubmed: 35891512
Toxins (Basel). 2011 Aug;3(8):1020-37
pubmed: 22069755
PLoS One. 2020 Oct 28;15(10):e0240191
pubmed: 33112870
Biol Rev Camb Philos Soc. 2020 Oct;95(5):1198-1232
pubmed: 32301582
BMC Genomics. 2014 Aug 07;15:660
pubmed: 25102932
Persoonia. 2016 Jun;36:83-133
pubmed: 27616789
New Phytol. 2021 Mar;229(5):2470-2491
pubmed: 33113229
Mycologia. 2006 Nov-Dec;98(6):1053-64
pubmed: 17486980
mSphere. 2021 Oct 27;6(5):e0056421
pubmed: 34523983
Adv Genet. 2014;87:199-244
pubmed: 25311923
Fungal Genet Biol. 2023 Jan;164:103766
pubmed: 36513262
mSystems. 2022 Jun 28;7(3):e0023222
pubmed: 35638725
PLoS Biol. 2023 Apr 11;21(4):e3002052
pubmed: 37040332
J Insect Sci. 2004;4:24
pubmed: 15861239
Front Microbiol. 2018 Apr 06;9:660
pubmed: 29681893
Fungal Biol Rev. 2015 Dec 1;29(3-4):220-229
pubmed: 26688691
J Appl Microbiol. 2020 Sep;129(3):486-495
pubmed: 32115828
BMC Bioinformatics. 2017 Aug 10;18(1):367
pubmed: 28797229
Genetics. 1992 Apr;130(4):687-701
pubmed: 1582553
BMC Genomics. 2016 Dec 1;17(1):986
pubmed: 27905873
Mycologia. 2011 Jul-Aug;103(4):863-82
pubmed: 21307161
Mol Biol Evol. 2015 Aug;32(8):2130-40
pubmed: 25901014
FEMS Microbiol Rev. 2012 Jan;36(1):165-92
pubmed: 22091779
Microbiol Spectr. 2022 Aug 31;10(4):e0017122
pubmed: 35950855
Curr Genomics. 2020 Sep;21(6):411-428
pubmed: 33093804
Nat Rev Microbiol. 2011 Sep 16;9(10):749-59
pubmed: 21921934
Methods Mol Biol. 2010;638:33-40
pubmed: 20238259
Front Microbiol. 2022 Sep 08;13:983243
pubmed: 36160203
PLoS One. 2014 Oct 20;9(10):e110398
pubmed: 25329823
Mol Biol Evol. 2015 May;32(5):1221-31
pubmed: 25631928
Mol Ecol. 2023 Oct 16;:
pubmed: 37843462
PLoS Genet. 2023 Feb 10;19(2):e1010347
pubmed: 36763677
New Phytol. 2022 Feb;233(3):1317-1330
pubmed: 34797921
Biotechnol Adv. 2021 Jul-Aug;49:107739
pubmed: 33794304
Curr Med Chem. 2016;23(37):4221-4230
pubmed: 27686657
J Fungi (Basel). 2023 Feb 28;9(3):
pubmed: 36983479
Annu Rev Microbiol. 2010;64:585-610
pubmed: 20533875
FEMS Microbiol Lett. 2007 Nov;276(1):12-8
pubmed: 17784861
PLoS Genet. 2010 Apr 08;6(4):e1000891
pubmed: 20386741
J Fungi (Basel). 2022 Dec 17;8(12):
pubmed: 36547648
Front Fungal Biol. 2022 Jul 15;3:935993
pubmed: 37746178
Genome Biol Evol. 2017 Apr 1;9(4):855-868
pubmed: 28338982
Genome Biol. 2011 Nov 23;12(11):R116
pubmed: 22112802
Nat Biotechnol. 2008 May;26(5):553-60
pubmed: 18454138
Sci Rep. 2015 Mar 30;5:9448
pubmed: 25819715
Proc Natl Acad Sci U S A. 2009 Aug 18;106(33):13909-14
pubmed: 19667182
Adv Genet. 2007;57:49-96
pubmed: 17352902
Proc Natl Acad Sci U S A. 2014 Dec 2;111(48):16995-7002
pubmed: 25362047
Genome Res. 2005 Dec;15(12):1620-31
pubmed: 16339359
mBio. 2016 Mar 08;7(2):e02148
pubmed: 26956589
PLoS Genet. 2011 Jan 06;7(1):e1001264
pubmed: 21253567
Proc Natl Acad Sci U S A. 2017 Sep 12;114(37):E7756-E7765
pubmed: 28847945
mBio. 2019 Mar 26;10(2):
pubmed: 30914504
Monoclon Antib Immunodiagn Immunother. 2014 Dec;33(6):428-37
pubmed: 25495488
Annu Rev Phytopathol. 2013;51:105-29
pubmed: 23915132
Microbiol Resour Announc. 2022 Feb 17;11(2):e0099521
pubmed: 35175124
Nature. 2010 Mar 18;464(7287):367-73
pubmed: 20237561
G3 (Bethesda). 2022 May 6;12(5):
pubmed: 35244156
Nat Ecol Evol. 2022 Jul;6(7):1007-1023
pubmed: 35680998
Elife. 2022 Aug 30;11:
pubmed: 36040303
Curr Biol. 2022 Jul 25;32(14):3146-3153.e3
pubmed: 35675809
New Phytol. 2013 Sep;199(4):895-907
pubmed: 23782262
mBio. 2020 Sep 1;11(5):
pubmed: 32873760
PLoS Biol. 2005 Jul;3(7):e245
pubmed: 16000021
Nat Rev Microbiol. 2023 May;21(5):312-326
pubmed: 36414835
PLoS Genet. 2022 Mar 31;18(3):e1010097
pubmed: 35358178
J Mol Endocrinol. 2018 Jul 13;:
pubmed: 30006342
Biotechnol Biofuels. 2019 Sep 04;12:210
pubmed: 31508149
Mol Ecol. 2021 Dec;30(23):6289-6308
pubmed: 34041794
Nat Rev Drug Discov. 2021 Mar;20(3):200-216
pubmed: 33510482
J Fungi (Basel). 2022 Nov 23;8(12):
pubmed: 36547571
Mol Plant. 2022 Apr 4;15(4):723-739
pubmed: 35217224
Mol Genet Genomics. 2019 Feb;294(1):177-190
pubmed: 30288581
Mol Ecol. 2023 Mar 2;:
pubmed: 36862075
Appl Microbiol Biotechnol. 2014 Dec;98(24):9953-66
pubmed: 25363558