Genome-wide survey and identification of AP2/ERF genes involved in shoot and leaf development in Liriodendron chinense.
AP2/ERF family
Leaf development
Liriodendron chinense
Shoot-specific
Transcription factors
Journal
BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258
Informations de publication
Date de publication:
08 Nov 2021
08 Nov 2021
Historique:
received:
28
07
2020
accepted:
23
10
2021
entrez:
9
11
2021
pubmed:
10
11
2021
medline:
11
11
2021
Statut:
epublish
Résumé
Liriodendron chinense is a distinctive ornamental tree species due to its unique leaves and tulip-like flowers. The discovery of genes involved in leaf development and morphogenesis is critical for uncovering the underlying genetic basis of these traits. Genes in the AP2/ERF family are recognized as plant-specific transcription factors that contribute to plant growth, hormone-induced development, ethylene response factors, and stress responses. In this study, we identified 104 putative AP2/ERF genes in the recently released L. chinense genome and transcriptome database. In addition, all 104 genes were grouped into four subfamilies, the AP2, ERF, RAV, and Soloist subfamilies. This classification was further supported by the results of gene structure and conserved motif analyses. Intriguingly, after application of a series test of cluster analysis, three AP2 genes, LcERF 94, LcERF 96, and LcERF 98, were identified as tissue-specific in buds based on the expression profiles of various tissues. These results were further validated via RT-qPCR assays and were highly consistent with the STC analysis. We further investigated the dynamic changes of immature leaves by dissecting fresh shoots into seven discontinuous periods, which were empirically identified as shoot apical meristem (SAM), leaf primordia and tender leaf developmental stages according to the anatomic structure. Subsequently, these three candidates were highly expressed in SAM and leaf primordia but rarely in tender leaves, indicating that they were mainly involved in early leaf development and morphogenesis. Moreover, these three genes displayed nuclear subcellular localizations through the transient transformation of tobacco epidermal cells. Overall, we identified 104 AP2/ERF family members at the genome-wide level and discerned three candidate genes that might participate in the development and morphogenesis of the leaf primordium in L. chinense.
Sections du résumé
BACKGROUND
BACKGROUND
Liriodendron chinense is a distinctive ornamental tree species due to its unique leaves and tulip-like flowers. The discovery of genes involved in leaf development and morphogenesis is critical for uncovering the underlying genetic basis of these traits. Genes in the AP2/ERF family are recognized as plant-specific transcription factors that contribute to plant growth, hormone-induced development, ethylene response factors, and stress responses.
RESULTS
RESULTS
In this study, we identified 104 putative AP2/ERF genes in the recently released L. chinense genome and transcriptome database. In addition, all 104 genes were grouped into four subfamilies, the AP2, ERF, RAV, and Soloist subfamilies. This classification was further supported by the results of gene structure and conserved motif analyses. Intriguingly, after application of a series test of cluster analysis, three AP2 genes, LcERF 94, LcERF 96, and LcERF 98, were identified as tissue-specific in buds based on the expression profiles of various tissues. These results were further validated via RT-qPCR assays and were highly consistent with the STC analysis. We further investigated the dynamic changes of immature leaves by dissecting fresh shoots into seven discontinuous periods, which were empirically identified as shoot apical meristem (SAM), leaf primordia and tender leaf developmental stages according to the anatomic structure. Subsequently, these three candidates were highly expressed in SAM and leaf primordia but rarely in tender leaves, indicating that they were mainly involved in early leaf development and morphogenesis. Moreover, these three genes displayed nuclear subcellular localizations through the transient transformation of tobacco epidermal cells.
CONCLUSIONS
CONCLUSIONS
Overall, we identified 104 AP2/ERF family members at the genome-wide level and discerned three candidate genes that might participate in the development and morphogenesis of the leaf primordium in L. chinense.
Identifiants
pubmed: 34749659
doi: 10.1186/s12864-021-08119-7
pii: 10.1186/s12864-021-08119-7
pmc: PMC8576965
doi:
Substances chimiques
Plant Proteins
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
807Subventions
Organisme : National Natural Science Foundation of China
ID : 31770718
Organisme : National Natural Science Foundation of China
ID : 31470660
Informations de copyright
© 2021. The Author(s).
Références
Sci Rep. 2018 Oct 23;8(1):15612
pubmed: 30353116
Bioinformatics. 2005 Jun;21 Suppl 1:i159-68
pubmed: 15961453
Plant Biotechnol J. 2016 Jul;14(7):1563-77
pubmed: 26800652
Plant Physiol Biochem. 2021 May;162:706-715
pubmed: 33799182
Genes (Basel). 2018 Nov 27;9(12):
pubmed: 30486397
BMC Genomics. 2020 Jan 20;21(1):62
pubmed: 31959122
Genome Biol. 2013 Apr 25;14(4):R36
pubmed: 23618408
Plant Cell. 2002 Aug;14(8):1737-49
pubmed: 12172019
Plant Physiol. 2007 Nov;145(3):1073-85
pubmed: 17873090
Development. 2006 Jan;133(2):251-61
pubmed: 16339187
Mol Biol Evol. 2018 Jun 1;35(6):1547-1549
pubmed: 29722887
Plant Cell Environ. 2011 Aug;34(8):1345-59
pubmed: 21486303
Plant Cell Physiol. 2011 Feb;52(2):344-60
pubmed: 21169347
Nature. 2007 Oct 25;449(7165):1053-7
pubmed: 17960244
Genomics. 2021 Mar;113(2):474-489
pubmed: 33359830
Biochem Biophys Res Commun. 2002 Jan 25;290(3):998-1009
pubmed: 11798174
Plant Mol Biol. 2006 Dec;62(6):825-43
pubmed: 17096212
Development. 2000 Nov;127(22):4971-80
pubmed: 11044410
Sex Plant Reprod. 2009 Dec;22(4):277-89
pubmed: 20033449
Plant Physiol Biochem. 2011 Mar;49(3):346-51
pubmed: 21296583
Proc Natl Acad Sci U S A. 2000 Jan 18;97(2):942-7
pubmed: 10639184
Annu Rev Plant Biol. 2006;57:781-803
pubmed: 16669782
Development. 2001 Apr;128(7):1127-35
pubmed: 11245578
Nat Protoc. 2012 Mar 01;7(3):562-78
pubmed: 22383036
Plant Mol Biol. 2011 Mar;75(4-5):321-31
pubmed: 21246258
Mol Plant. 2020 Aug 3;13(8):1194-1202
pubmed: 32585190
Nat Genet. 2008 Sep;40(9):1136-41
pubmed: 19165928
Plant Physiol. 2006 Feb;140(2):411-32
pubmed: 16407444
Plant Biol (Stuttg). 2019 Jul;21(4):571-584
pubmed: 30468551
Plants (Basel). 2019 Oct 22;8(10):
pubmed: 31652517
Trends Plant Sci. 2014 Mar;19(3):146-57
pubmed: 24280109
Plant Cell. 2001 Dec;13(12):2609-18
pubmed: 11752375
Front Plant Sci. 2016 Jan 19;6:1247
pubmed: 26834762
Plant Physiol. 2005 Oct;139(2):949-59
pubmed: 16183832
BMC Plant Biol. 2018 Mar 20;18(1):46
pubmed: 29558898
Plant Cell. 1996 Feb;8(2):155-68
pubmed: 8742707
Plant Cell. 2006 Feb;18(2):295-307
pubmed: 16387832
Plant Cell. 2006 May;18(5):1292-309
pubmed: 16617101
3 Biotech. 2020 Mar;10(3):139
pubmed: 32158635
Plant Mol Biol. 2005 Mar;57(5):613-28
pubmed: 15988559
New Phytol. 2013 Aug;199(3):639-49
pubmed: 24010138
BMC Plant Biol. 2019 Feb 20;19(1):84
pubmed: 30786863
J Biol Chem. 1998 Oct 9;273(41):26857-61
pubmed: 9756931
Plant Cell. 1998 Aug;10(8):1391-406
pubmed: 9707537
BMC Genomics. 2015 May 27;16:407
pubmed: 26014501
Trends Plant Sci. 2018 Feb;23(2):151-162
pubmed: 29074232
Cell. 2004 Oct 1;119(1):109-20
pubmed: 15454085
Biol Chem. 1998 Jun;379(6):633-46
pubmed: 9687012
Nat Plants. 2016 Oct 31;2(11):16167
pubmed: 27797353
Plant Cell Physiol. 2013 Nov;54(11):1822-36
pubmed: 24009335
Front Plant Sci. 2020 Sep 23;11:578100
pubmed: 33072153
Arabidopsis Book. 2009;7:e0120
pubmed: 22303246
FEBS Lett. 2006 Feb 20;580(5):1303-8
pubmed: 16457823
Eur J Biochem. 1999 Jun;262(2):247-57
pubmed: 10336605
Curr Biol. 2011 Jul 12;21(13):1123-8
pubmed: 21700457
J Integr Plant Biol. 2021 Jul;63(7):1181-1196
pubmed: 33615731
Plant Sci. 2011 Jul;181(1):39-46
pubmed: 21600396
Plant Cell. 1994 Sep;6(9):1211-25
pubmed: 7919989
BMC Plant Biol. 2017 Jun 19;17(1):106
pubmed: 28629320
Proc Natl Acad Sci U S A. 2006 Jul 18;103(29):11081-5
pubmed: 16832061
Nat Plants. 2019 Jan;5(1):18-25
pubmed: 30559417
Plant J. 2012 Jul;71(1):108-21
pubmed: 22380923
J Exp Bot. 2013 May;64(8):2499-510
pubmed: 23599278
Biochem Biophys Res Commun. 2008 Jul 4;371(3):468-74
pubmed: 18442469