Genome-wide identification and characterization of bZIP transcription factors and their expression profile under abiotic stresses in Chinese pear (Pyrus bretschneideri).
Abscisic Acid
/ pharmacology
Basic-Leucine Zipper Transcription Factors
/ genetics
Chromosomes, Plant
Exons
Fragaria
/ genetics
Fruit
/ genetics
Gene Duplication
Gene Expression Regulation, Plant
Genome, Plant
Genome-Wide Association Study
Introns
Multigene Family
Phylogeny
Plant Proteins
/ genetics
Pyrus
/ drug effects
Salicylates
/ pharmacology
Salicylic Acid
/ pharmacology
Stress, Physiological
/ genetics
Synteny
Expansion
Expression analysis
PbbZIP gene family
Phylogenetic analysis
Stress response
Journal
BMC plant biology
ISSN: 1471-2229
Titre abrégé: BMC Plant Biol
Pays: England
ID NLM: 100967807
Informations de publication
Date de publication:
09 Sep 2021
09 Sep 2021
Historique:
received:
10
04
2021
accepted:
28
08
2021
entrez:
10
9
2021
pubmed:
11
9
2021
medline:
21
9
2021
Statut:
epublish
Résumé
In plants, basic leucine zipper transcription factors (TFs) play important roles in multiple biological processes such as anthesis, fruit growth & development and stress responses. However, systematic investigation and characterization of bZIP-TFs remain unclear in Chinese white pear. Chinese white pear is a fruit crop that has important nutritional and medicinal values. In this study, 62 bZIP genes were comprehensively identified from Chinese Pear, and 54 genes were distributed among 17 chromosomes. Frequent whole-genome duplication (WGD) and dispersed duplication (DSD) were the major driving forces underlying the bZIP gene family in Chinese white pear. bZIP-TFs are classified into 13 subfamilies according to the phylogenetic tree. Subsequently, purifying selection plays an important role in the evolution process of PbbZIPs. Synteny analysis of bZIP genes revealed that 196 orthologous gene pairs were identified between Pyrus bretschneideri, Fragaria vesca, Prunus mume, and Prunus persica. Moreover, cis-elements that respond to various stresses and hormones were found on the promoter regions of PbbZIP, which were induced by stimuli. Gene structure (intron/exon) and different compositions of motifs revealed that functional divergence among subfamilies. Expression pattern of PbbZIP genes differential expressed under hormonal treatment abscisic acid, salicylic acid, and methyl jasmonate in pear fruits by real-time qRT-PCR. Collectively, a systematic analysis of gene structure, motif composition, subcellular localization, synteny analysis, and calculation of synonymous (Ks) and non-synonymous (Ka) was performed in Chinese white pear. Sixty-two bZIP-TFs in Chinese pear were identified, and their expression profiles were comprehensively analyzed under ABA, SA, and MeJa hormones, which respond to multiple abiotic stresses and fruit growth and development. PbbZIP gene occurred through Whole-genome duplication and dispersed duplication events. These results provide a basic framework for further elucidating the biological function characterizations under multiple developmental stages and abiotic stress responses.
Sections du résumé
BACKGROUND
BACKGROUND
In plants, basic leucine zipper transcription factors (TFs) play important roles in multiple biological processes such as anthesis, fruit growth & development and stress responses. However, systematic investigation and characterization of bZIP-TFs remain unclear in Chinese white pear. Chinese white pear is a fruit crop that has important nutritional and medicinal values.
RESULTS
RESULTS
In this study, 62 bZIP genes were comprehensively identified from Chinese Pear, and 54 genes were distributed among 17 chromosomes. Frequent whole-genome duplication (WGD) and dispersed duplication (DSD) were the major driving forces underlying the bZIP gene family in Chinese white pear. bZIP-TFs are classified into 13 subfamilies according to the phylogenetic tree. Subsequently, purifying selection plays an important role in the evolution process of PbbZIPs. Synteny analysis of bZIP genes revealed that 196 orthologous gene pairs were identified between Pyrus bretschneideri, Fragaria vesca, Prunus mume, and Prunus persica. Moreover, cis-elements that respond to various stresses and hormones were found on the promoter regions of PbbZIP, which were induced by stimuli. Gene structure (intron/exon) and different compositions of motifs revealed that functional divergence among subfamilies. Expression pattern of PbbZIP genes differential expressed under hormonal treatment abscisic acid, salicylic acid, and methyl jasmonate in pear fruits by real-time qRT-PCR.
CONCLUSIONS
CONCLUSIONS
Collectively, a systematic analysis of gene structure, motif composition, subcellular localization, synteny analysis, and calculation of synonymous (Ks) and non-synonymous (Ka) was performed in Chinese white pear. Sixty-two bZIP-TFs in Chinese pear were identified, and their expression profiles were comprehensively analyzed under ABA, SA, and MeJa hormones, which respond to multiple abiotic stresses and fruit growth and development. PbbZIP gene occurred through Whole-genome duplication and dispersed duplication events. These results provide a basic framework for further elucidating the biological function characterizations under multiple developmental stages and abiotic stress responses.
Identifiants
pubmed: 34503442
doi: 10.1186/s12870-021-03191-3
pii: 10.1186/s12870-021-03191-3
pmc: PMC8427902
doi:
Substances chimiques
Basic-Leucine Zipper Transcription Factors
0
Plant Proteins
0
Salicylates
0
Abscisic Acid
72S9A8J5GW
methyl salicylate
LAV5U5022Y
Salicylic Acid
O414PZ4LPZ
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
413Informations de copyright
© 2021. The Author(s).
Références
Plant Mol Biol. 2014 Jan;84(1-2):19-36
pubmed: 23918260
BMC Genomics. 2015 Mar 22;16:227
pubmed: 25887221
BMC Genomics. 2015 Dec 10;16:1053
pubmed: 26651343
Mol Biol Evol. 2018 Jun 1;35(6):1547-1549
pubmed: 29722887
BMC Genomics. 2014 Apr 13;15:281
pubmed: 24725365
Plant Physiol Biochem. 2020 Nov;156:135-145
pubmed: 32937268
Funct Integr Genomics. 2018 Nov;18(6):673-684
pubmed: 29948460
BMC Plant Biol. 2010 Oct 25;10:229
pubmed: 20973957
Nucleic Acids Res. 2012 Jan;40(Database issue):D302-5
pubmed: 22053084
Planta. 2008 Jul;228(2):225-40
pubmed: 18365246
Proteins. 2006 Aug 15;64(3):643-51
pubmed: 16752418
Physiol Mol Biol Plants. 2020 Mar;26(3):433-444
pubmed: 32205921
Front Plant Sci. 2018 Feb 13;9:161
pubmed: 29487610
Genes (Basel). 2017 Oct 24;8(10):
pubmed: 29064393
Genomics Proteomics Bioinformatics. 2010 Mar;8(1):77-80
pubmed: 20451164
Nucleic Acids Res. 2012 Apr;40(7):e49
pubmed: 22217600
Front Plant Sci. 2020 Feb 26;11:139
pubmed: 32174937
Annu Rev Plant Biol. 2013;64:477-99
pubmed: 23330794
Plant Cell Environ. 2008 Dec;31(12):1735-43
pubmed: 18721266
Plant Physiol. 2000 Apr;122(4):1179-86
pubmed: 10759513
J Biol Chem. 2000 Jan 21;275(3):1723-30
pubmed: 10636868
Bioinformatics. 2015 Apr 15;31(8):1296-7
pubmed: 25504850
Planta. 2012 Jun;235(6):1157-69
pubmed: 22189955
Int J Genomics. 2017;2017:3981031
pubmed: 28487861
BMC Genomics. 2019 Dec 19;20(1):993
pubmed: 31856713
BMC Plant Biol. 2019 Oct 11;19(1):417
pubmed: 31604417
Mol Plant. 2020 Aug 3;13(8):1194-1202
pubmed: 32585190
Plant Cell. 2000 Jun;12(6):901-15
pubmed: 10852936
Plant Physiol. 2008 Feb;146(2):333-50
pubmed: 18065552
Plant Mol Biol. 2009 Jan;69(1-2):107-19
pubmed: 18841482
Mol Plant. 2012 Jul;5(4):831-40
pubmed: 22207719
Ann N Y Acad Sci. 2012 May;1256:1-14
pubmed: 22257007
Plant J. 2009 Oct;60(2):207-17
pubmed: 19519801
Plant J. 2011 Dec;68(6):999-1013
pubmed: 21851430
Plant Cell. 2015 Aug;27(8):2244-60
pubmed: 26276836
BMC Plant Biol. 2015 Jan 21;15:12
pubmed: 25604453
Nucleic Acids Res. 2019 Jul 2;47(W1):W256-W259
pubmed: 30931475
BMC Plant Biol. 2012 Sep 28;12:174
pubmed: 23016701
Plant J. 2005 Oct;44(1):100-13
pubmed: 16167899
Molecules. 2018 May 11;23(5):
pubmed: 29751599
Plant Cell Environ. 2015 Jan;38(1):35-49
pubmed: 24738645
J Plant Res. 2012 May;125(3):429-38
pubmed: 21938515
BMC Genomics. 2015 Nov 18;16:976
pubmed: 26581444
Plant Cell Rep. 2006 Nov;25(11):1233-45
pubmed: 16802118
Front Plant Sci. 2017 Dec 18;8:2145
pubmed: 29326742
Mol Biol Rep. 2019 Apr;46(2):2153-2175
pubmed: 30734172
Plant Mol Biol. 2009 Jul;70(5):581-601
pubmed: 19449183
Genes (Basel). 2017 Dec 20;8(12):
pubmed: 29261143
Genomics. 2020 Sep;112(5):3803-3814
pubmed: 32145381
Plant Cell Physiol. 2013 Dec;54(12):2020-33
pubmed: 24092882
Front Genet. 2018 Mar 02;9:64
pubmed: 29552026
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D247-51
pubmed: 16381856
Nature. 2000 May 25;405(6785):462-6
pubmed: 10839542
Plant J. 2011 Oct;68(1):88-99
pubmed: 21645149
Plant Cell Physiol. 2010 Nov;51(11):1821-39
pubmed: 20980270
Genome Res. 2002 Jan;12(1):47-56
pubmed: 11779830
Front Genet. 2018 Oct 09;9:357
pubmed: 30356782
Plant J. 2010 Feb;61(4):672-85
pubmed: 19947981
Plant J. 2007 Sep;51(5):897-909
pubmed: 17662035
J Exp Bot. 2014 Jun;65(9):2351-63
pubmed: 24659489
Microorganisms. 2020 Jul 14;8(7):
pubmed: 32674413
Proc Natl Acad Sci U S A. 2004 Feb 3;101(5):1397-402
pubmed: 14739338
Planta. 2014 Feb;239(2):299-312
pubmed: 24165825
Bioinformatics. 2001 Sep;17(9):847-8
pubmed: 11590104
Plant J. 2001 Sep;27(6):529-38
pubmed: 11576436
Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15682-7
pubmed: 14671323
Methods. 2001 Dec;25(4):402-8
pubmed: 11846609
Plant Cell Environ. 2010 Dec;33(12):2191-208
pubmed: 20807374
Front Genet. 2019 Jul 05;10:632
pubmed: 31333718
J Plant Physiol. 2010 Nov 15;167(17):1512-20
pubmed: 20576316
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W597-603
pubmed: 22661580
Plant Mol Biol. 2005 Aug;58(6):899-914
pubmed: 16240181
BMC Genomics. 2020 Jul 14;21(1):483
pubmed: 32664853
Plant Cell Physiol. 2005 Oct;46(10):1623-34
pubmed: 16051676
Genome Res. 2013 Feb;23(2):396-408
pubmed: 23149293
Nucleic Acids Res. 2010 Jan;38(Database issue):D822-7
pubmed: 19858103
Nucleic Acids Res. 2002 Jan 1;30(1):325-7
pubmed: 11752327
Trends Plant Sci. 2002 Mar;7(3):106-11
pubmed: 11906833
EMBO J. 1997 Sep 1;16(17):5247-59
pubmed: 9311985
DNA Res. 2012 Dec;19(6):463-76
pubmed: 23103471
Plant Cell. 2012 Nov;24(11):4590-606
pubmed: 23150635
Comput Biol Chem. 2020 Oct;88:107346
pubmed: 32759051
J Hered. 2002 Jan-Feb;93(1):77-8
pubmed: 12011185
J Integr Plant Biol. 2011 Mar;53(3):212-31
pubmed: 21205183
Plant Cell. 1994 Sep;6(9):1277-87
pubmed: 7919992
Int J Genomics. 2015;2015:536943
pubmed: 26770968
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W202-8
pubmed: 19458158
BMC Genomics. 2015 Oct 12;16:771
pubmed: 26459863