A gene expression atlas for kiwifruit (Actinidia chinensis) and network analysis of transcription factors.
Actinidia
Transcription factors
eFP browser
Journal
BMC plant biology
ISSN: 1471-2229
Titre abrégé: BMC Plant Biol
Pays: England
ID NLM: 100967807
Informations de publication
Date de publication:
27 Feb 2021
27 Feb 2021
Historique:
received:
13
10
2020
accepted:
18
02
2021
entrez:
28
2
2021
pubmed:
1
3
2021
medline:
30
4
2021
Statut:
epublish
Résumé
Transcriptomic studies combined with a well annotated genome have laid the foundations for new understanding of molecular processes. Tools which visualise gene expression patterns have further added to these resources. The manual annotation of the Actinidia chinensis (kiwifruit) genome has resulted in a high quality set of 33,044 genes. Here we investigate gene expression patterns in diverse tissues, visualised in an Electronic Fluorescent Pictograph (eFP) browser, to study the relationship of transcription factor (TF) expression using network analysis. Sixty-one samples covering diverse tissues at different developmental time points were selected for RNA-seq analysis and an eFP browser was generated to visualise this dataset. 2839 TFs representing 57 different classes were identified and named. Network analysis of the TF expression patterns separated TFs into 14 different modules. Two modules consisting of 237 TFs were correlated with floral bud and flower development, a further two modules containing 160 TFs were associated with fruit development and maturation. A single module of 480 TFs was associated with ethylene-induced fruit ripening. Three "hub" genes correlated with flower and fruit development consisted of a HAF-like gene central to gynoecium development, an ERF and a DOF gene. Maturing and ripening hub genes included a KNOX gene that was associated with seed maturation, and a GRAS-like TF. This study provides an insight into the complexity of the transcriptional control of flower and fruit development, as well as providing a new resource to the plant community. The Actinidia eFP browser is provided in an accessible format that allows researchers to download and work internally.
Sections du résumé
BACKGROUND
BACKGROUND
Transcriptomic studies combined with a well annotated genome have laid the foundations for new understanding of molecular processes. Tools which visualise gene expression patterns have further added to these resources. The manual annotation of the Actinidia chinensis (kiwifruit) genome has resulted in a high quality set of 33,044 genes. Here we investigate gene expression patterns in diverse tissues, visualised in an Electronic Fluorescent Pictograph (eFP) browser, to study the relationship of transcription factor (TF) expression using network analysis.
RESULTS
RESULTS
Sixty-one samples covering diverse tissues at different developmental time points were selected for RNA-seq analysis and an eFP browser was generated to visualise this dataset. 2839 TFs representing 57 different classes were identified and named. Network analysis of the TF expression patterns separated TFs into 14 different modules. Two modules consisting of 237 TFs were correlated with floral bud and flower development, a further two modules containing 160 TFs were associated with fruit development and maturation. A single module of 480 TFs was associated with ethylene-induced fruit ripening. Three "hub" genes correlated with flower and fruit development consisted of a HAF-like gene central to gynoecium development, an ERF and a DOF gene. Maturing and ripening hub genes included a KNOX gene that was associated with seed maturation, and a GRAS-like TF.
CONCLUSIONS
CONCLUSIONS
This study provides an insight into the complexity of the transcriptional control of flower and fruit development, as well as providing a new resource to the plant community. The Actinidia eFP browser is provided in an accessible format that allows researchers to download and work internally.
Identifiants
pubmed: 33639842
doi: 10.1186/s12870-021-02894-x
pii: 10.1186/s12870-021-02894-x
pmc: PMC7913447
doi:
Substances chimiques
RNA, Plant
0
Transcription Factors
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
121Références
Sci Rep. 2017 Dec 4;7(1):16861
pubmed: 29203778
BMC Plant Biol. 2011 Dec 28;11:182
pubmed: 22204446
Genome Biol. 2014;15(12):550
pubmed: 25516281
New Phytol. 2019 Jan;221(1):309-325
pubmed: 30067292
Mol Biol Evol. 2017 Apr 1;34(4):925-942
pubmed: 28087776
Planta. 2013 May;237(5):1199-211
pubmed: 23328896
Plant Physiol. 2015 Apr;167(4):1243-58
pubmed: 25649633
Bioinformatics. 2017 Aug 1;33(15):2397-2398
pubmed: 28379331
Methods Mol Biol. 2009;537:113-37
pubmed: 19378142
PLoS One. 2019 May 13;14(5):e0216120
pubmed: 31083658
Curr Opin Plant Biol. 2007 Oct;10(5):453-60
pubmed: 17900969
Plant Cell Rep. 2011 Nov;30(11):2059-73
pubmed: 21735233
Hortic Res. 2017 Jun 21;4:17029
pubmed: 28674614
PLoS One. 2014 Jan 10;9(1):e84203
pubmed: 24427281
PeerJ. 2018 Dec 4;6:e6028
pubmed: 30564517
J Exp Bot. 2015 Aug;66(15):4699-710
pubmed: 25979999
Nat Commun. 2013;4:2640
pubmed: 24136039
BMC Genomics. 2018 Apr 16;19(1):257
pubmed: 29661190
Cell. 1998 Jun 26;93(7):1219-29
pubmed: 9657154
Bioinformatics. 2012 Jun 15;28(12):1647-9
pubmed: 22543367
Nucleic Acids Res. 2014 Jan;42(Database issue):D222-30
pubmed: 24288371
Biochim Biophys Acta Gene Regul Mech. 2017 Jan;1860(1):3-20
pubmed: 27522016
PLoS One. 2007 Aug 08;2(8):e718
pubmed: 17684564
Plant Biotechnol J. 2019 May;17(5):869-880
pubmed: 30302894
J Exp Bot. 2012 Jan;63(2):797-807
pubmed: 22071267
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
Plant Cell. 2017 Jun;29(6):1278-1292
pubmed: 28584165
J Exp Bot. 2002 Oct;53(377):2001-22
pubmed: 12324525
BMC Bioinformatics. 2008 Dec 29;9:559
pubmed: 19114008
Nature. 1991 Sep 5;353(6339):31-7
pubmed: 1715520
Genome Biol. 2013 Aug 30;14(8):R93
pubmed: 24000942
J Exp Bot. 2011 Jul;62(11):3821-35
pubmed: 21511911
Development. 2011 Jul;138(14):2999-3009
pubmed: 21693516
Science. 2000 Dec 15;290(5499):2105-10
pubmed: 11118137
Curr Biol. 2004 Nov 9;14(21):1935-40
pubmed: 15530395
BMC Plant Biol. 2011 Apr 27;11:72
pubmed: 21521532
BMC Plant Biol. 2015 Dec 29;15:304
pubmed: 26714876
BMC Plant Biol. 2020 Mar 6;20(1):103
pubmed: 32138665
Genes Genomics. 2018 Apr;40(4):429-446
pubmed: 29892845
Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
pubmed: 15034147
EMBO J. 1999 Sep 1;18(17):4679-88
pubmed: 10469647
Plant J. 2011 Jan;65(1):62-76
pubmed: 21175890
Mol Phylogenet Evol. 2003 Dec;29(3):464-89
pubmed: 14615187
Plant Physiol. 2018 Oct;178(2):850-863
pubmed: 30135096