Transcriptome profiling reveals the effects of drought tolerance in Giant Juncao.
Drought resistance
Giant Juncao
RNA-sequence
Transcription factors
Transcriptome
Journal
BMC plant biology
ISSN: 1471-2229
Titre abrégé: BMC Plant Biol
Pays: England
ID NLM: 100967807
Informations de publication
Date de publication:
04 Jan 2021
04 Jan 2021
Historique:
received:
30
05
2020
accepted:
06
12
2020
entrez:
4
1
2021
pubmed:
5
1
2021
medline:
4
5
2021
Statut:
epublish
Résumé
Giant Juncao is often used as feed for livestock because of its huge biomass. However, drought stress reduces forage production by affecting the normal growth and development of plants. Therefore, investigating the molecular mechanisms of drought tolerance will provide important information for the improvement of drought tolerance in this grass. A total of 144.96 Gb of clean data was generated and assembled into 144,806 transcripts and 93,907 unigenes. After 7 and 14 days of drought stress, a total of 16,726 and 46,492 differentially expressed genes (DEGs) were observed, respectively. Compared with normal irrigation, 16,247, 23,503, and 11,598 DEGs were observed in 1, 5, and 9 days following rehydration, respectively. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed abiotic stress-responsive genes and pathways related to catalytic activity, methyltransferase activity, transferase activity, and superoxide metabolic process. We also identified transcription factors belonging to several families, including basic helix-loop-helix (bHLH), WRKY, NAM (no apical meristem), ATAF1/2 and CUC2 (cup-shaped cotyledon) (NAC), fatty acyl-CoA reductase (FAR1), B3, myeloblastosis (MYB)-related, and basic leucine zipper (bZIP) families, which are important drought-rehydration-responsive proteins. Weighted gene co-expression network analysis was also used to analyze the RNA-seq data to predict the interrelationship between genes. Twenty modules were obtained, and four of these modules may be involved in photosynthesis and plant hormone signal transduction that respond to drought and rehydration conditions. Our research is the first to provide a more comprehensive understanding of DEGs involved in drought stress at the transcriptome level in Giant Juncao with different drought and recovery conditions. These results may reveal insights into the molecular mechanisms of drought tolerance in Giant Juncao and provide diverse genetic resources involved in drought tolerance research.
Sections du résumé
BACKGROUND
BACKGROUND
Giant Juncao is often used as feed for livestock because of its huge biomass. However, drought stress reduces forage production by affecting the normal growth and development of plants. Therefore, investigating the molecular mechanisms of drought tolerance will provide important information for the improvement of drought tolerance in this grass.
RESULTS
RESULTS
A total of 144.96 Gb of clean data was generated and assembled into 144,806 transcripts and 93,907 unigenes. After 7 and 14 days of drought stress, a total of 16,726 and 46,492 differentially expressed genes (DEGs) were observed, respectively. Compared with normal irrigation, 16,247, 23,503, and 11,598 DEGs were observed in 1, 5, and 9 days following rehydration, respectively. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed abiotic stress-responsive genes and pathways related to catalytic activity, methyltransferase activity, transferase activity, and superoxide metabolic process. We also identified transcription factors belonging to several families, including basic helix-loop-helix (bHLH), WRKY, NAM (no apical meristem), ATAF1/2 and CUC2 (cup-shaped cotyledon) (NAC), fatty acyl-CoA reductase (FAR1), B3, myeloblastosis (MYB)-related, and basic leucine zipper (bZIP) families, which are important drought-rehydration-responsive proteins. Weighted gene co-expression network analysis was also used to analyze the RNA-seq data to predict the interrelationship between genes. Twenty modules were obtained, and four of these modules may be involved in photosynthesis and plant hormone signal transduction that respond to drought and rehydration conditions.
CONCLUSIONS
CONCLUSIONS
Our research is the first to provide a more comprehensive understanding of DEGs involved in drought stress at the transcriptome level in Giant Juncao with different drought and recovery conditions. These results may reveal insights into the molecular mechanisms of drought tolerance in Giant Juncao and provide diverse genetic resources involved in drought tolerance research.
Identifiants
pubmed: 33390157
doi: 10.1186/s12870-020-02785-7
pii: 10.1186/s12870-020-02785-7
pmc: PMC7780708
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
2Subventions
Organisme : Natural Science Foundation of Fujian Province
ID : 2019J05053
Organisme : Education department of Fujian Province
ID : JT180120
Organisme : National Natural Science Foundation of China
ID : 41775105
Références
Physiol Plant. 2007 Oct;131(2):201-10
pubmed: 18251892
Plant Cell. 2005 Dec;17(12):3470-88
pubmed: 16284313
J Exp Bot. 2015 Jul;66(13):4075-90
pubmed: 25956882
Nat Biotechnol. 2010 May;28(5):511-5
pubmed: 20436464
J Photochem Photobiol B. 2014 Aug;137:31-8
pubmed: 24935099
Plant J. 2011 Mar;65(6):907-21
pubmed: 21332845
Mol Genet Genomics. 2014 Feb;289(1):77-91
pubmed: 24241166
PLoS One. 2016 Jan 11;11(1):e0146242
pubmed: 26752408
Plant J. 2004 Oct;40(1):75-87
pubmed: 15361142
Nat Biotechnol. 1999 Jan;17(1):76-80
pubmed: 9920274
PLoS One. 2015 May 18;10(5):e0125302
pubmed: 25984726
Bioinformatics. 2005 Oct 1;21(19):3787-93
pubmed: 15817693
J Integr Plant Biol. 2013 Nov;55(11):1147-65
pubmed: 24034274
Nucleic Acids Res. 2014 Jan;42(Database issue):D1182-7
pubmed: 24174544
Proc Natl Acad Sci U S A. 2015 Jul 14;112(28):8529-36
pubmed: 26124102
Nat Biotechnol. 2011 May 15;29(7):644-52
pubmed: 21572440
Front Plant Sci. 2016 Jul 19;7:1044
pubmed: 27486466
Tree Physiol. 2007 Oct;27(10):1423-31
pubmed: 17669733
BMC Plant Biol. 2016 Nov 9;16(1):248
pubmed: 27829376
J Integr Plant Biol. 2019 Jul;61(7):817-835
pubmed: 30761734
Plant Cell Rep. 2009 Jun;28(6):975-84
pubmed: 19381641
Genome Biol. 2010;11(2):R14
pubmed: 20132535
Funct Integr Genomics. 2018 Sep;18(5):489-503
pubmed: 29651641
New Phytol. 2020 May;226(4):1042-1054
pubmed: 31917861
Front Plant Sci. 2020 May 14;11:577
pubmed: 32477388
Biochem Biophys Res Commun. 2016 May 13;473(4):1321-1327
pubmed: 27091431
Front Plant Sci. 2013 Apr 01;4:66
pubmed: 23554602
BMC Genomics. 2017 Aug 15;18(1):619
pubmed: 28810832
Int J Mol Sci. 2013 Jun 19;14(6):12827-42
pubmed: 23783278
BMC Bioinformatics. 2011 Aug 04;12:323
pubmed: 21816040
BMC Genet. 2016 Apr 12;17:57
pubmed: 27068810
BMC Plant Biol. 2019 Jan 21;19(1):33
pubmed: 30665359
Funct Plant Biol. 2016 Apr;43(4):337-345
pubmed: 32480465
Bioinformatics. 2010 Jan 1;26(1):139-40
pubmed: 19910308
J Exp Bot. 2009;60(13):3737-49
pubmed: 19596698
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
Methods Mol Biol. 2018;1754:15-27
pubmed: 29536435
J Immunol. 2003 Mar 15;170(6):2993-3001
pubmed: 12626552
J Exp Bot. 2017 Apr 1;68(9):2135-2148
pubmed: 28419345
J Exp Bot. 2012 May;63(8):3001-9
pubmed: 22323273
Front Plant Sci. 2018 Feb 19;9:187
pubmed: 29515605
Plant Physiol. 2014 Apr;164(4):1759-71
pubmed: 24515831
Int J Mol Sci. 2019 Mar 14;20(6):
pubmed: 30875790
Plant Mol Biol. 2011 Jul;76(3-5):407-23
pubmed: 21327516
Planta. 2006 Apr;223(5):901-9
pubmed: 16283377
Front Plant Sci. 2017 Apr 11;8:480
pubmed: 28443104
Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
pubmed: 9254694
BMC Bioinformatics. 2008 Dec 29;9:559
pubmed: 19114008
BMC Genomics. 2014 May 16;15:378
pubmed: 24886190
Ecotoxicol Environ Saf. 2019 Aug 30;178:9-16
pubmed: 30980964
BMC Plant Biol. 2018 Nov 29;18(1):309
pubmed: 30497403
J Plant Physiol. 2010 Nov 15;167(17):1512-20
pubmed: 20576316
Plant Cell. 2003 Nov;15(11):2497-502
pubmed: 14600211
Bioinformatics. 2012 Nov 15;28(22):2914-21
pubmed: 23060617
Int J Mol Sci. 2019 Jan 15;20(2):
pubmed: 30650531
Nat Protoc. 2013 Aug;8(8):1494-512
pubmed: 23845962
Plant Physiol. 2010 Jul;153(3):1398-412
pubmed: 20472752
Front Plant Sci. 2019 Mar 20;10:314
pubmed: 30949189
Sci China Life Sci. 2020 May;63(5):635-674
pubmed: 32246404
J Mol Biol. 1990 Oct 5;215(3):403-10
pubmed: 2231712
BMC Plant Biol. 2016 May 21;16(1):115
pubmed: 27208977
BMC Genomics. 2019 Feb 6;20(1):110
pubmed: 30727949
Tree Physiol. 2018 Mar 1;38(3):423-441
pubmed: 29177514
Mol Biol Evol. 2012 Jan;29(1):367-79
pubmed: 21903677
J Biol Chem. 2005 Jan 21;280(3):1921-30
pubmed: 15536088