Oomycete Gene Table: an online database for comparative genomic analyses of the oomycete microorganisms.
Journal
Database : the journal of biological databases and curation
ISSN: 1758-0463
Titre abrégé: Database (Oxford)
Pays: England
ID NLM: 101517697
Informations de publication
Date de publication:
01 01 2019
01 01 2019
Historique:
received:
07
09
2018
revised:
01
05
2019
accepted:
29
05
2019
entrez:
2
7
2019
pubmed:
2
7
2019
medline:
9
1
2020
Statut:
ppublish
Résumé
Oomycetes form a unique group of the fungal-like, aquatic, eukaryotic microorganisms. Lifestyle and pathogenicity of the oomycetes are diverse. Many pathogenic oomycetes affect a broad range of plants and cause enormous economic loss annually. Some pathogenic oomycetes cause destructive and deadly diseases in a variety of animals, including humans. No effective antimicrobial agent against the oomycetes is available. Genomic data of many oomycetes are currently available. Comparative analyses of the oomycete genomes must be performed to better understand the oomycete biology and virulence, as well as to identify conserved and biologically important proteins that are potential diagnostic and therapeutic targets of these organisms. However, a tool that facilitates comparative genomic studies of the oomycetes is lacking. Here, we described in detail the Oomycete Gene Table, which is an online user-friendly bioinformatic tool, designed to search, analyze, compare and visualize gene contents of 20 oomycetes in a customizable table. Genomic contents of other oomycete species, when available, can be added to the existing database. Some of the applications of the Oomycete Gene Table include investigations of phylogenomic relationships, as well as identifications of biologically important and pathogenesis-related genes of oomycetes. In summary, the Oomycete Gene Table is a simple and useful tool for comparative genomic analyses of oomycetes.
Identifiants
pubmed: 31260041
pii: 5525202
doi: 10.1093/database/baz082
pmc: PMC6601393
pii:
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© The Author(s) 2019. Published by Oxford University Press.
Références
Data Brief. 2017 Oct 26;15:896-900
pubmed: 29159227
PLoS Pathog. 2014 Dec 11;10(12):e1004472
pubmed: 25501953
Nucleic Acids Res. 2000 Jan 1;28(1):87-90
pubmed: 10592189
Science. 2010 Dec 10;330(6010):1549-1551
pubmed: 21148394
Nucleic Acids Res. 2015 Jan;43(Database issue):D261-9
pubmed: 25428365
Eukaryot Cell. 2003 Apr;2(2):191-9
pubmed: 12684368
Cold Spring Harb Perspect Biol. 2014 May 01;6(5):a016147
pubmed: 24789819
Science. 2006 Sep 1;313(5791):1261-6
pubmed: 16946064
mSphere. 2017 Apr 12;2(2):
pubmed: 28435885
J Clin Microbiol. 2011 Oct;49(10):3710-3
pubmed: 21813724
PLoS Pathog. 2014 May 15;10(5):e1004062
pubmed: 24831297
Nucleic Acids Res. 2012 Jan;40(Database issue):D675-81
pubmed: 22064857
Mol Plant Pathol. 2015 May;16(4):413-34
pubmed: 25178392
Genome Announc. 2015 Jun 18;3(3):
pubmed: 26089407
Plant Physiol. 2005 Nov;139(3):1155-62
pubmed: 16244137
Protoplasma. 2012 Jan;249(1):3-19
pubmed: 21424613
Infect Immun. 2000 Feb;68(2):443-8
pubmed: 10639402
PLoS One. 2011;6(7):e22420
pubmed: 21811606
Clin Infect Dis. 2006 Sep 1;43(5):569-76
pubmed: 16886148
Mol Plant Microbe Interact. 2012 Oct;25(10):1350-60
pubmed: 22712506
Genome Biol. 2010;11(7):R73
pubmed: 20626842
Genom Data. 2015 Nov 23;7:60-1
pubmed: 26981361
BMC Bioinformatics. 2003 Sep 11;4:41
pubmed: 12969510
Mol Plant Pathol. 2018 Jan;19(1):227-237
pubmed: 27785876
PLoS One. 2013 Oct 04;8(10):e75072
pubmed: 24124466
Mol Genet Genomics. 2005 Mar;273(1):20-32
pubmed: 15702346
PeerJ. 2018 Jun 5;6:e4821
pubmed: 29888122
PLoS Genet. 2013 Jun;9(6):e1003272
pubmed: 23785293
J Clin Microbiol. 2013 Aug;51(8):2778-80
pubmed: 23740721
Mol Biol Evol. 2006 Feb;23(2):338-51
pubmed: 16237208
Nature. 2009 Sep 17;461(7262):393-8
pubmed: 19741609
Sci Rep. 2018 Mar 7;8(1):4135
pubmed: 29515152
Data Brief. 2017 Nov 07;16:47-50
pubmed: 29541657