Mining and evolution analysis of lateral organ boundaries domain (LBD) genes in Chinese white pear (Pyrus bretschneideri).
Anthocyanins biosynthesis
Gene expression
LBD gene family
Pyrus
Synteny analysis
Journal
BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258
Informations de publication
Date de publication:
21 Sep 2020
21 Sep 2020
Historique:
received:
24
02
2020
accepted:
17
08
2020
entrez:
22
9
2020
pubmed:
23
9
2020
medline:
15
4
2021
Statut:
epublish
Résumé
The lateral organ boundaries domain (LBD) gene is a plant-specific transcription factor that plays a critical role in diverse biological processes. However, the evolution and functional divergence of the LBD gene family has not yet been characterized for the Chinese White Pear. In our study, a total of 60 PbrLBDs were identified in the pear genome. The PbrLBD gene family was divided into two classes based on gene structure and phylogenetic analysis: class I (53) and class II (7). Cis-acting element analysis results suggested that PbrLBDs may participate in various biological processes, such as flavonoid biosynthetic and stress response. Synteny analysis results indicated that segmental duplication played a key role in the expansion of the PbrLBD gene family. The mean Ks and 4DTv values showed that the PbrLBD gene family had undergone only one recent whole-genome duplication event occurring at 30-45 MYA. Purifying selection was a primary force during the PbrLBD gene family evolution process. Transcriptome data analysis revealed that 10 PbrLBDs were expressed in all six examined tissues, and 73.33% of members in the PbrLBD gene family were expressed in pear sepal. qRT-PCR was conducted to verify the expression levels of 11 PbrLBDs in these six tissues. Specifically, PbrLBD20, PbrLBD35 and PbrLBD53 genes were down-regulated when anthocyanin concentrations were high, whereas PbrLBD33 was significantly up-regulated in pear when anthocyanin concentrations were high. Furthermore, PbrLBD20, one of the candidate genes related to anthocyanins was localized in the nucleus. Our analysis provides valuable information for understanding the evolution of the PbrLBD gene family, and provides new insights into the regulation of pear pigment metabolism and lays a foundation for the future disclosure of the molecular mechanism of LBD gene regulating flavonoid metabolism.
Sections du résumé
BACKGROUND
BACKGROUND
The lateral organ boundaries domain (LBD) gene is a plant-specific transcription factor that plays a critical role in diverse biological processes. However, the evolution and functional divergence of the LBD gene family has not yet been characterized for the Chinese White Pear.
RESULTS
RESULTS
In our study, a total of 60 PbrLBDs were identified in the pear genome. The PbrLBD gene family was divided into two classes based on gene structure and phylogenetic analysis: class I (53) and class II (7). Cis-acting element analysis results suggested that PbrLBDs may participate in various biological processes, such as flavonoid biosynthetic and stress response. Synteny analysis results indicated that segmental duplication played a key role in the expansion of the PbrLBD gene family. The mean Ks and 4DTv values showed that the PbrLBD gene family had undergone only one recent whole-genome duplication event occurring at 30-45 MYA. Purifying selection was a primary force during the PbrLBD gene family evolution process. Transcriptome data analysis revealed that 10 PbrLBDs were expressed in all six examined tissues, and 73.33% of members in the PbrLBD gene family were expressed in pear sepal. qRT-PCR was conducted to verify the expression levels of 11 PbrLBDs in these six tissues. Specifically, PbrLBD20, PbrLBD35 and PbrLBD53 genes were down-regulated when anthocyanin concentrations were high, whereas PbrLBD33 was significantly up-regulated in pear when anthocyanin concentrations were high. Furthermore, PbrLBD20, one of the candidate genes related to anthocyanins was localized in the nucleus.
CONCLUSIONS
CONCLUSIONS
Our analysis provides valuable information for understanding the evolution of the PbrLBD gene family, and provides new insights into the regulation of pear pigment metabolism and lays a foundation for the future disclosure of the molecular mechanism of LBD gene regulating flavonoid metabolism.
Identifiants
pubmed: 32957912
doi: 10.1186/s12864-020-06999-9
pii: 10.1186/s12864-020-06999-9
pmc: PMC7504654
doi:
Substances chimiques
Anthocyanins
0
Plant Proteins
0
Transcription Factors
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
644Subventions
Organisme : National Natural Science Foundation of China
ID : 31820103012,31672111
Organisme : The Earmarked Fund for Jiangsu Agricultural Industry Technology System
ID : JATS[2018]277
Organisme : The Earmarked Fund for China Agriculture Research System
ID : CARS-28
Références
Genome Res. 2006 Apr;16(4):510-9
pubmed: 16520461
J Exp Bot. 2019 Mar 27;70(6):1801-1814
pubmed: 30715420
Development. 2013 May;140(9):1958-69
pubmed: 23571218
Yi Chuan. 2015 Jul;37(7):720-30
pubmed: 26351172
Plant Physiol. 2013 Apr;161(4):1844-61
pubmed: 23396833
Proc Int Conf Intell Syst Mol Biol. 1994;2:28-36
pubmed: 7584402
Genetics. 2001 Jul;158(3):1227-34
pubmed: 11454770
Annu Rev Plant Biol. 2009;60:433-53
pubmed: 19575588
Genome Res. 2013 Feb;23(2):396-408
pubmed: 23149293
Plant Mol Biol. 2018 Sep;98(1-2):1-18
pubmed: 30167900
PeerJ. 2017 Sep 11;5:e3776
pubmed: 28924499
Nucleic Acids Res. 2019 Jan 8;47(D1):D427-D432
pubmed: 30357350
Plant Physiol. 2002 Jun;129(2):747-61
pubmed: 12068116
Hortic Res. 2019 Dec 1;6:134
pubmed: 31814987
Plant Cell. 2007 Jan;19(1):118-30
pubmed: 17259263
PLoS One. 2013;8(2):e57044
pubmed: 23468909
Genomics Proteomics Bioinformatics. 2010 Mar;8(1):77-80
pubmed: 20451164
Nucleic Acids Res. 2012 Apr;40(7):e49
pubmed: 22217600
Mol Plant. 2020 Aug 3;13(8):1194-1202
pubmed: 32585190
J Genet. 2014 Apr;93(1):79-91
pubmed: 24840825
Plant Cell Physiol. 2002 May;43(5):467-78
pubmed: 12040093
Plant Cell. 2006 Mar;18(3):574-85
pubmed: 16399802
BMC Plant Biol. 2015 Jan 21;15:12
pubmed: 25604453
BMC Plant Biol. 2018 Mar 20;18(1):46
pubmed: 29558898
BMC Plant Biol. 2004 Jun 01;4:10
pubmed: 15171794
Hortic Res. 2019 Mar 1;6:34
pubmed: 30854211
Plant Cell Rep. 2016 Mar;35(3):641-53
pubmed: 26703384
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W569-72
pubmed: 22695796
Gene. 2019 Jun 20;702:133-142
pubmed: 30904717
Int J Mol Sci. 2019 Dec 16;20(24):
pubmed: 31888167
J Exp Bot. 2015 Jan;66(1):99-112
pubmed: 25324400
Plant J. 2009 May;58(3):525-37
pubmed: 19154202
Biochem Biophys Res Commun. 2012 Mar 23;419(4):779-81
pubmed: 22390928
Curr Protoc Bioinformatics. 2002 Aug;Chapter 2:Unit 2.3
pubmed: 18792934
Plant J. 2013 Jan;73(2):212-24
pubmed: 22974309
Plant Cell. 2009 Nov;21(11):3567-84
pubmed: 19933203
Plant Mol Biol. 2005 Mar;57(4):559-75
pubmed: 15821980
Methods. 2001 Dec;25(4):402-8
pubmed: 11846609
Genome Biol. 2019 Feb 21;20(1):38
pubmed: 30791939
Annu Rev Immunol. 2003;21:139-76
pubmed: 12414722
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W597-603
pubmed: 22661580
J Genet. 2016 Sep;95(3):515-26
pubmed: 27659322
Plant Cell Physiol. 2016 Apr;57(4):824-47
pubmed: 26872835
Nucleic Acids Res. 2002 Jan 1;30(1):325-7
pubmed: 11752327
Front Plant Sci. 2018 Sep 10;9:1282
pubmed: 30298074
Proc Natl Acad Sci U S A. 2009 Apr 7;106(14):5737-42
pubmed: 19325131
Biosci Biotechnol Biochem. 2007 May;71(5):1269-78
pubmed: 17485849
Plant Physiol. 2009 Nov;151(3):1377-89
pubmed: 19717544
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
J Hered. 2002 Jan-Feb;93(1):77-8
pubmed: 12011185