Comprehensive dissection of transcript and metabolite shifts during seed germination and post-germination stages in poplar.
Candidate genes
Data integration
Metabolomics
Poplar
Seed germination and post-germination stages
Transcriptomics
Journal
BMC plant biology
ISSN: 1471-2229
Titre abrégé: BMC Plant Biol
Pays: England
ID NLM: 100967807
Informations de publication
Date de publication:
26 Jun 2019
26 Jun 2019
Historique:
received:
15
01
2019
accepted:
31
05
2019
entrez:
28
6
2019
pubmed:
28
6
2019
medline:
3
8
2019
Statut:
epublish
Résumé
Seed germination, a complex, physiological-morphogenetic process, is a critical stage in the life cycle of plants. Biological changes in germinating seeds have not been investigated in poplar, a model woody plant. In this study, we exploited next-generation sequencing and metabolomics analysis and uncovered a series of significantly different genes and metabolites at various stages of seed germination and post germination. The K-means method was used to identify multiple transcription factors, including AP2/EREBP, DOF, and YABBY, involved in specific seed germination and post-germination stages. A weighted gene coexpression network analysis revealed that cell wall, amino acid metabolism, and transport-related pathways were significantly enriched during stages 3 and 5, with no significant enrichment observed in primary metabolic processes such as glycolysis and the tricarboxylic acid cycle. A metabolomics analysis detected significant changes in intermediate metabolites in these primary metabolic processes, while a targeted correlation network analysis identified the gene family members most relevant to these changing metabolites. Taken together, our results provide important insights into the molecular networks underlying poplar seed germination and post-germination processes. The targeted correlation network analysis approach developed in this study can be applied to search for key candidate genes in specific biochemical reactions and represents a new strategy for joint multiomics analyses.
Sections du résumé
BACKGROUND
BACKGROUND
Seed germination, a complex, physiological-morphogenetic process, is a critical stage in the life cycle of plants. Biological changes in germinating seeds have not been investigated in poplar, a model woody plant.
RESULTS
RESULTS
In this study, we exploited next-generation sequencing and metabolomics analysis and uncovered a series of significantly different genes and metabolites at various stages of seed germination and post germination. The K-means method was used to identify multiple transcription factors, including AP2/EREBP, DOF, and YABBY, involved in specific seed germination and post-germination stages. A weighted gene coexpression network analysis revealed that cell wall, amino acid metabolism, and transport-related pathways were significantly enriched during stages 3 and 5, with no significant enrichment observed in primary metabolic processes such as glycolysis and the tricarboxylic acid cycle. A metabolomics analysis detected significant changes in intermediate metabolites in these primary metabolic processes, while a targeted correlation network analysis identified the gene family members most relevant to these changing metabolites.
CONCLUSIONS
CONCLUSIONS
Taken together, our results provide important insights into the molecular networks underlying poplar seed germination and post-germination processes. The targeted correlation network analysis approach developed in this study can be applied to search for key candidate genes in specific biochemical reactions and represents a new strategy for joint multiomics analyses.
Identifiants
pubmed: 31242858
doi: 10.1186/s12870-019-1862-3
pii: 10.1186/s12870-019-1862-3
pmc: PMC6595626
doi:
Substances chimiques
Plant Proteins
0
Transcription Factors
0
Types de publication
Journal Article
Langues
eng
Pagination
279Subventions
Organisme : the Fundamental Research Funds for the Central Universities
ID : 2572017CA01
Organisme : National Natural Science Foundation of China
ID : No. 31570648
Organisme : National Natural Science Foundation of China
ID : No. 31600534
Références
Plant Cell. 1999 Jul;11(7):1217-26
pubmed: 10402424
Plant J. 2000 Jun;22(6):483-93
pubmed: 10886768
Plant Physiol. 2000 Dec;124(4):1570-81
pubmed: 11115875
Trends Plant Sci. 2001 Feb;6(2):72-8
pubmed: 11173291
Biosci Biotechnol Biochem. 2001 Mar;65(3):662-5
pubmed: 11330685
Plant Physiol. 2001 Jun;126(2):835-48
pubmed: 11402211
Plant J. 2001 Nov;28(4):443-53
pubmed: 11737781
Curr Opin Plant Biol. 2002 Feb;5(1):33-6
pubmed: 11788305
Funct Integr Genomics. 2002 May;2(1-2):28-39
pubmed: 12021848
Plant Cell. 1997 Jul;9(7):1055-1066
pubmed: 12237375
Biotechniques. 2003 Feb;34(2):374-8
pubmed: 12613259
Genome Res. 2003 Nov;13(11):2498-504
pubmed: 14597658
Plant J. 2004 Mar;37(6):914-39
pubmed: 14996223
Plant Physiol. 2005 Jan;137(1):354-68
pubmed: 15618428
Sci STKE. 2005 Nov 15;2005(310):cm12
pubmed: 16291769
Anal Chem. 2006 Feb 1;78(3):779-87
pubmed: 16448051
Plant Physiol. 1969 May;44(5):733-8
pubmed: 16657125
Plant Physiol. 1973 Sep;52(3):274-7
pubmed: 16658546
New Phytol. 2006;171(3):501-23
pubmed: 16866955
Plant Physiol. 2006 Nov;142(3):839-54
pubmed: 16963520
Plant Cell Physiol. 2007 Jul;48(7):984-99
pubmed: 17540691
Proteomics. 2007 Sep;7(18):3358-68
pubmed: 17849412
J Plant Physiol. 2008 Jun 16;165(9):911-9
pubmed: 18155318
Plant Physiol. 2008 Apr;146(4):1738-58
pubmed: 18281415
Sci China C Life Sci. 2008 Apr;51(4):336-45
pubmed: 18368311
Plant Physiol. 2009 Feb;149(2):961-80
pubmed: 19074628
BMC Bioinformatics. 2008 Dec 29;9:559
pubmed: 19114008
J Plant Physiol. 2009 Aug 15;166(12):1329-35
pubmed: 19286275
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Plant Physiol. 2009 Nov;151(3):1531-45
pubmed: 19759340
Plant Mol Biol. 2010 May;73(1-2):119-29
pubmed: 20099072
Nat Protoc. 2010 Jun;5(6):1005-18
pubmed: 20448546
Plant Physiol. 2010 Oct;154(2):691-704
pubmed: 20720170
New Phytol. 2011 Jan;189(1):148-59
pubmed: 20946418
Plant Sci. 2011 May;180(5):679-85
pubmed: 21421418
J Exp Bot. 2011 Jun;62(10):3289-309
pubmed: 21430292
Proteomics. 2011 Jul;11(13):2693-713
pubmed: 21630451
Plant Physiol. 2011 Oct;157(2):866-75
pubmed: 21825108
Annu Rev Plant Biol. 2012;63:507-33
pubmed: 22136565
J Exp Bot. 2012 Sep;63(14):5017-33
pubmed: 22936829
Plant Physiol. 2013 Sep;163(1):205-15
pubmed: 23858430
BMC Genomics. 2013 Jul 16;14:477
pubmed: 23865409
Planta. 1987 Feb;170(2):209-16
pubmed: 24232880
Plant Physiol. 2014 May 14;165(3):1062-1075
pubmed: 24828307
Plant Physiol Biochem. 2015 Jan;86:1-15
pubmed: 25461695
Nat Methods. 2015 Apr;12(4):357-60
pubmed: 25751142
PLoS One. 2015 Jul 14;10(7):e0132509
pubmed: 26172265
Nucleic Acids Res. 2015 Dec 2;43(21):e140
pubmed: 26184878
Environ Monit Assess. 2015 Nov;187(11):663
pubmed: 26433900
Front Plant Sci. 2017 Feb 08;8:92
pubmed: 28228764
J Plant Physiol. 2017 Jun;213:134-147
pubmed: 28384531
Tree Physiol. 2017 Dec 1;37(12):1752-1766
pubmed: 28985382
Eur J Biochem. 1995 Aug 15;232(1):77-83
pubmed: 7556174