Identification of Transcriptional Networks Involved in De Novo Organ Formation in Tomato Hypocotyl Explants

Some of the hormone crosstalk and transcription factors (TFs) involved in wound-induced organ regeneration have been extensively studied in the model plant . In previous work, we established "Micro-Tom" explants without the addition of exogenous hormones as a model to investigate wound-ind...

Full description

Saved in:
Bibliographic Details
Published inInternational journal of molecular sciences Vol. 23; no. 24; p. 16112
Main Authors Larriba, Eduardo, Nicolás-Albujer, Míriam, Sánchez-García, Ana Belén, Pérez-Pérez, José Manuel
Format Journal Article
LanguageEnglish
Published Switzerland MDPI AG 17.12.2022
MDPI
Subjects
Arabidopsis - metabolism
Arabidopsis Proteins - genetics
Cell activation
Cell cycle
Cytokinins
de novo root formation
de novo shoot regeneration
Explants
Flowers & plants
Gene expression
Gene Expression Regulation, Plant
Gene Regulatory Networks
Hormones
Hypocotyl - genetics
Hypocotyl - metabolism
Indoleacetic Acids - metabolism
Plant Roots - metabolism
Plant Shoots - metabolism
Plants - metabolism
Solanum lycopersicum
Solanum lycopersicum - genetics
time-course RNA-Seq
Transcription factors
Transcriptomics
wound-induced cell reprogramming
Wounds
gene regulatory networks
time-course RNA-Seq
wound-induced cell reprogramming
de novo shoot regeneration
de novo root formation
Online AccessGet full text

Cover

Abstract Some of the hormone crosstalk and transcription factors (TFs) involved in wound-induced organ regeneration have been extensively studied in the model plant . In previous work, we established "Micro-Tom" explants without the addition of exogenous hormones as a model to investigate wound-induced de novo organ formation. The current working model indicates that cell reprogramming and founder cell activation requires spatial and temporal regulation of auxin-to-cytokinin (CK) gradients in the apical and basal regions of the hypocotyl combined with extensive metabolic reprogramming of some cells in the apical region. In this work, we extended our transcriptomic analysis to identify some of the gene regulatory networks involved in wound-induced organ regeneration in tomato. Our results highlight a functional conservation of key TF modules whose function is conserved during de novo organ formation in plants, which will serve as a valuable resource for future studies.
AbstractList Some of the hormone crosstalk and transcription factors (TFs) involved in wound-induced organ regeneration have been extensively studied in the model plant Arabidopsis thaliana. In previous work, we established Solanum lycopersicum “Micro-Tom” explants without the addition of exogenous hormones as a model to investigate wound-induced de novo organ formation. The current working model indicates that cell reprogramming and founder cell activation requires spatial and temporal regulation of auxin-to-cytokinin (CK) gradients in the apical and basal regions of the hypocotyl combined with extensive metabolic reprogramming of some cells in the apical region. In this work, we extended our transcriptomic analysis to identify some of the gene regulatory networks involved in wound-induced organ regeneration in tomato. Our results highlight a functional conservation of key TF modules whose function is conserved during de novo organ formation in plants, which will serve as a valuable resource for future studies.
Some of the hormone crosstalk and transcription factors (TFs) involved in wound-induced organ regeneration have been extensively studied in the model plant Arabidopsis thaliana . In previous work, we established Solanum lycopersicum “Micro-Tom” explants without the addition of exogenous hormones as a model to investigate wound-induced de novo organ formation. The current working model indicates that cell reprogramming and founder cell activation requires spatial and temporal regulation of auxin-to-cytokinin (CK) gradients in the apical and basal regions of the hypocotyl combined with extensive metabolic reprogramming of some cells in the apical region. In this work, we extended our transcriptomic analysis to identify some of the gene regulatory networks involved in wound-induced organ regeneration in tomato. Our results highlight a functional conservation of key TF modules whose function is conserved during de novo organ formation in plants, which will serve as a valuable resource for future studies.
Some of the hormone crosstalk and transcription factors (TFs) involved in wound-induced organ regeneration have been extensively studied in the model plant Arabidopsis thaliana. In previous work, we established Solanum lycopersicum "Micro-Tom" explants without the addition of exogenous hormones as a model to investigate wound-induced de novo organ formation. The current working model indicates that cell reprogramming and founder cell activation requires spatial and temporal regulation of auxin-to-cytokinin (CK) gradients in the apical and basal regions of the hypocotyl combined with extensive metabolic reprogramming of some cells in the apical region. In this work, we extended our transcriptomic analysis to identify some of the gene regulatory networks involved in wound-induced organ regeneration in tomato. Our results highlight a functional conservation of key TF modules whose function is conserved during de novo organ formation in plants, which will serve as a valuable resource for future studies.Some of the hormone crosstalk and transcription factors (TFs) involved in wound-induced organ regeneration have been extensively studied in the model plant Arabidopsis thaliana. In previous work, we established Solanum lycopersicum "Micro-Tom" explants without the addition of exogenous hormones as a model to investigate wound-induced de novo organ formation. The current working model indicates that cell reprogramming and founder cell activation requires spatial and temporal regulation of auxin-to-cytokinin (CK) gradients in the apical and basal regions of the hypocotyl combined with extensive metabolic reprogramming of some cells in the apical region. In this work, we extended our transcriptomic analysis to identify some of the gene regulatory networks involved in wound-induced organ regeneration in tomato. Our results highlight a functional conservation of key TF modules whose function is conserved during de novo organ formation in plants, which will serve as a valuable resource for future studies.
Some of the hormone crosstalk and transcription factors (TFs) involved in wound-induced organ regeneration have been extensively studied in the model plant . In previous work, we established "Micro-Tom" explants without the addition of exogenous hormones as a model to investigate wound-induced de novo organ formation. The current working model indicates that cell reprogramming and founder cell activation requires spatial and temporal regulation of auxin-to-cytokinin (CK) gradients in the apical and basal regions of the hypocotyl combined with extensive metabolic reprogramming of some cells in the apical region. In this work, we extended our transcriptomic analysis to identify some of the gene regulatory networks involved in wound-induced organ regeneration in tomato. Our results highlight a functional conservation of key TF modules whose function is conserved during de novo organ formation in plants, which will serve as a valuable resource for future studies.
Author Nicolás-Albujer, Míriam
Pérez-Pérez, José Manuel
Larriba, Eduardo
Sánchez-García, Ana Belén
AuthorAffiliation Instituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain
AuthorAffiliation_xml – name: Instituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain
Author_xml – sequence: 1
  givenname: Eduardo
  orcidid: 0000-0001-8838-4974
  surname: Larriba
  fullname: Larriba, Eduardo
  organization: Instituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain
– sequence: 2
  givenname: Míriam
  surname: Nicolás-Albujer
  fullname: Nicolás-Albujer, Míriam
  organization: Instituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain
– sequence: 3
  givenname: Ana Belén
  surname: Sánchez-García
  fullname: Sánchez-García, Ana Belén
  organization: Instituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain
– sequence: 4
  givenname: José Manuel
  orcidid: 0000-0003-2848-4919
  surname: Pérez-Pérez
  fullname: Pérez-Pérez, José Manuel
  organization: Instituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain
BackLink https://www.ncbi.nlm.nih.gov/pubmed/36555756$$D View this record in MEDLINE/PubMed
BookMark eNpdkstvEzEQxi1URB9w5IosceGyxY_1IxckVPqIVLWXcLZmbW9wurte7E1K_nucplQNJ49mfv5mPP5O0dEQB4_QR0rOOZ-Rr2HVZ8ZZTSWl7A06oTVjFSFSHb2Kj9FpzitCCihm79Axl0IIJeQJepg7P0yhDRamEAccW7xIMGSbwrhLQIfv_PQY00PG82ETu413OAz4h8d3cRPxfVrCgK9i6vf3S2kRSxzxzXaMNk7bDl_-GTsYpvwevW2hy_7D83mGfl5dLi5uqtv76_nF99vK1ppOldeaMEcVA8mpawirJRFKtkQ7yaCZ0ZZ6Ck4JDqwFx72mQkrQXnPmrLX8DM33ui7Cyowp9JC2JkIwT4mYlgbSFGznjdNc6hqgtJF1TXlTGupWtQB1Ixqrita3vda4bnrvbFlWgu5A9LAyhF9mGTdmprSmkheBL88CKf5e-zyZPmTru7IRH9fZMCU0JUqzHfr5P3QV16l8wRMlFdeMzApV7SmbYs7Jty_DUGJ2ljAHlij8p9cveKH_eYD_BVw2tbw
CitedBy_id crossref_primary_10_1007_s00425_024_04341_1
Cites_doi 10.1111/tpj.15010
10.1016/j.phytochem.2014.06.008
10.1101/gad.252503
10.1038/cr.2012.63
10.1242/dev.134668
10.1016/j.celrep.2016.02.003
10.1016/j.cell.2019.03.006
10.1186/s12864-015-1249-2
10.4161/psb.27432
10.1016/j.csbj.2022.06.033
10.1007/s10265-015-0714-y
10.1242/dev.071928
10.1186/s12864-020-6689-7
10.1016/j.plaphy.2015.07.025
10.1016/j.devcel.2015.10.022
10.3389/fpls.2022.838421
10.1093/pcp/pcaa083
10.1016/j.redox.2019.101247
10.1093/pcp/pcac146
10.7717/peerj.7929
10.1093/plcell/koac218
10.1016/j.freeradbiomed.2012.10.538
10.1126/science.220.4601.1049
10.1371/journal.pone.0177381
10.1242/dev.097444
10.1016/j.jplph.2011.02.014
10.1080/15592324.2020.1794147
10.1016/j.cub.2011.02.020
10.1016/j.cell.2004.09.018
10.1186/s12864-015-1990-6
10.1105/tpc.19.00378
10.1126/science.abf4368
10.1093/pcp/pcw091
10.3389/fpls.2022.861556
10.1105/tpc.20.00208
10.1186/1471-2105-14-321
10.1073/pnas.1320457111
10.1016/B978-0-12-391498-9.00009-7
10.1073/pnas.1110443108
10.1186/1471-2105-12-124
10.1093/jxb/eraa088
10.3390/genes11121435
10.3389/fpls.2017.00660
10.1111/pce.14001
10.1016/j.ydbio.2014.06.008
10.1016/j.plantsci.2019.110323
10.1016/j.plaphy.2010.08.016
10.1242/dev.00596
10.1038/s42003-021-01895-8
10.1146/annurev-arplant-050718-100434
10.1242/dev.195347
10.1016/j.cub.2014.07.050
10.3389/fpls.2020.582020
10.1186/s12870-021-03329-3
10.1007/s00438-012-0696-6
10.1104/pp.15.01556
10.1073/pnas.1617146114
10.1093/plphys/kiab510
10.1038/nplants.2016.165
10.3390/ijms222111843
10.1016/j.cell.2010.10.020
10.1007/s00438-014-0861-1
10.3390/genes9090457
10.1093/pcp/pcy013
10.1104/pp.17.00633
10.1105/tpc.109.069948
10.1007/s00438-013-0733-0
10.3390/ijms20020238
10.1016/j.celrep.2019.08.099
10.1105/tpc.16.00623
10.1016/j.cub.2004.12.038
10.1016/j.cub.2015.02.022
10.1038/s41477-021-01015-8
10.3390/ijms20122961
10.1186/s12864-015-2334-2
10.1111/pce.12838
10.1016/j.bbrc.2015.11.010
10.1016/j.cell.2016.04.046
10.1111/nph.13738
10.1093/pcp/pcx168
10.1016/j.molp.2022.08.008
10.1007/s00299-010-0817-9
10.1105/tpc.19.00226
10.1105/tpc.15.00744
10.15252/embj.201490899
10.1016/j.devcel.2012.12.013
10.1111/nph.14304
10.1073/pnas.1718263115
10.1186/s12859-018-2486-6
10.1038/s41587-020-0703-0
10.1111/nph.14315
10.1093/nar/gkw982
10.3390/antiox10020332
10.1111/nph.14313
10.1111/nph.17594
10.1016/j.molp.2016.09.014
10.1242/dev.006296
10.7717/peerj.3955
10.1093/jxb/erac079
10.1016/j.tplants.2017.09.016
10.1038/s41477-019-0408-x
10.1007/s00299-020-02633-w
10.1111/nph.16065
10.1105/tpc.019398
10.3390/ijms18051056
10.1016/j.cell.2021.02.001
10.1016/j.cell.2017.08.030
10.1093/bioinformatics/btz931
10.1101/2021.04.29.441912
10.1093/plphys/kiaa062
10.1186/1471-2105-7-191
10.3390/plants8020038
ContentType Journal Article
Copyright 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.
2022 by the authors. 2022
Copyright_xml – notice: 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.
– notice: 2022 by the authors. 2022
DBID CGR
CUY
CVF
ECM
EIF
NPM
AAYXX
CITATION
3V.
7X7
7XB
88E
8FI
8FJ
8FK
8G5
ABUWG
AFKRA
AZQEC
BENPR
CCPQU
DWQXO
FYUFA
GHDGH
GNUQQ
GUQSH
K9.
M0S
M1P
M2O
MBDVC
PIMPY
PQEST
PQQKQ
PQUKI
PRINS
Q9U
7X8
5PM
DOA
DOI 10.3390/ijms232416112
DatabaseName Medline
MEDLINE
MEDLINE (Ovid)
MEDLINE
MEDLINE
PubMed
CrossRef
ProQuest Central (Corporate)
Health & Medical Collection (Proquest)
ProQuest Central (purchase pre-March 2016)
Medical Database (Alumni Edition)
Hospital Premium Collection
Hospital Premium Collection (Alumni Edition)
ProQuest Central (Alumni) (purchase pre-March 2016)
Research Library (Alumni Edition)
ProQuest Central (Alumni)
ProQuest Central
ProQuest Central Essentials
ProQuest Central
ProQuest One Community College
ProQuest Central Korea
Health Research Premium Collection
Health Research Premium Collection (Alumni)
ProQuest Central Student
Research Library Prep
ProQuest Health & Medical Complete (Alumni)
Health & Medical Collection (Alumni Edition)
Medical Database
ProQuest research library
Research Library (Corporate)
Publicly Available Content (ProQuest)
ProQuest One Academic Eastern Edition (DO NOT USE)
ProQuest One Academic
ProQuest One Academic UKI Edition
ProQuest Central China
ProQuest Central Basic
MEDLINE - Academic
PubMed Central (Full Participant titles)
DOAJ Directory of Open Access Journals
DatabaseTitle MEDLINE
Medline Complete
MEDLINE with Full Text
PubMed
MEDLINE (Ovid)
CrossRef
Publicly Available Content Database
Research Library Prep
ProQuest Central Student
ProQuest Central Essentials
ProQuest Health & Medical Complete (Alumni)
ProQuest Central (Alumni Edition)
ProQuest One Community College
Research Library (Alumni Edition)
ProQuest Central China
ProQuest Central
Health Research Premium Collection
Health and Medicine Complete (Alumni Edition)
ProQuest Central Korea
ProQuest Research Library
ProQuest Medical Library (Alumni)
ProQuest Central Basic
ProQuest One Academic Eastern Edition
ProQuest Hospital Collection
Health Research Premium Collection (Alumni)
ProQuest Hospital Collection (Alumni)
ProQuest Health & Medical Complete
ProQuest Medical Library
ProQuest One Academic UKI Edition
ProQuest One Academic
ProQuest Central (Alumni)
MEDLINE - Academic
DatabaseTitleList

Publicly Available Content Database
MEDLINE - Academic
MEDLINE
CrossRef
Database_xml – sequence: 1
  dbid: DOA
  name: DOAJ Directory of Open Access Journals
  url: https://www.doaj.org/
  sourceTypes: Open Website
– sequence: 2
  dbid: NPM
  name: PubMed
  url: https://proxy.k.utb.cz/login?url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed
  sourceTypes: Index Database
– sequence: 3
  dbid: EIF
  name: MEDLINE
  url: https://proxy.k.utb.cz/login?url=https://www.webofscience.com/wos/medline/basic-search
  sourceTypes: Index Database
– sequence: 4
  dbid: BENPR
  name: ProQuest Central
  url: https://www.proquest.com/central
  sourceTypes: Aggregation Database
DeliveryMethod fulltext_linktorsrc
Discipline Biology
EISSN 1422-0067
ExternalDocumentID oai_doaj_org_article_d83684aadb064413b1db8f7faa4b5bc7
10_3390_ijms232416112
36555756
Genre Journal Article
GrantInformation_xml – fundername: Ministerio de Ciencia e Innovación of Spain
  grantid: BIO2015-64255-R
– fundername: Conselleria d'Educació, Cultura i Sport of the Generalitat Valenciana
  grantid: IDIFEDER/2018/016
– fundername: European Regional Development Fund (ERDF) of the European Commission
  grantid: RTI2018-096505-B-I00
– fundername: European Regional Development Fund (ERDF) of the European Commission
  grantid: IDIFEDER/2018/016
– fundername: European Regional Development Fund (ERDF) of the European Commission
  grantid: BIO2015-64255-R
– fundername: Conselleria d'Educació, Cultura i Sport of the Generalitat Valenciana
  grantid: PROMETEO/2019/117
– fundername: Ministerio de Ciencia e Innovación of Spain
  grantid: RTI2018-096505-B-I00
– fundername: Ministerio de Ciencia e Innovación of Spain
  grantid: BIO2015-64255-R; RTI2018-096505-B-I00
– fundername: Conselleria d’Educació, Cultura i Sport of the Generalitat Valenciana
  grantid: IDIFEDER/2018/016; PROMETEO/2019/117
– fundername: European Regional Development Fund (ERDF) of the European Commission
  grantid: EDGJID/2021/025
GroupedDBID ---
29J
2WC
3V.
53G
5GY
5VS
7X7
88E
8FE
8FG
8FH
8FI
8FJ
8G5
A8Z
AADQD
AAFWJ
AAHBH
ABDBF
ABJCF
ABUWG
ACGFO
ACIHN
ACIWK
ACPRK
ADBBV
AEAQA
AENEX
AFKRA
AFZYC
ALIPV
ALMA_UNASSIGNED_HOLDINGS
AOIJS
AZQEC
BAWUL
BBNVY
BCNDV
BENPR
BHPHI
BPHCQ
BVXVI
CCPQU
CGR
CS3
CUY
CVF
D1I
DIK
DU5
DWQXO
E3Z
EBD
EBS
ECM
EIF
EJD
ESTFP
ESX
F5P
FRP
FYUFA
GNUQQ
GROUPED_DOAJ
GUQSH
GX1
HCIFZ
HH5
HMCUK
HYE
IAO
ITC
KB.
KQ8
LK8
M1P
M2O
M48
M7P
MODMG
M~E
NPM
O5R
O5S
OK1
P2P
PDBOC
PIMPY
PQQKQ
PROAC
PSQYO
RIG
RNS
RPM
TR2
TUS
UKHRP
~8M
AAYXX
AFPKN
CITATION
7XB
8FK
K9.
MBDVC
PQEST
PQUKI
PRINS
Q9U
7X8
5PM
ID FETCH-LOGICAL-c481t-e8802d172a631db02460576f08d62ab91f1e1ad753a2fad3e81566a8e832dccc3
IEDL.DBID RPM
ISSN 1422-0067
1661-6596
IngestDate Fri Jul 05 11:57:08 EDT 2024
Tue Sep 17 21:32:21 EDT 2024
Mon Sep 09 17:31:24 EDT 2024
Thu Oct 10 22:50:33 EDT 2024
Wed Aug 14 12:34:39 EDT 2024
Sun Oct 13 10:14:38 EDT 2024
IsDoiOpenAccess true
IsOpenAccess true
IsPeerReviewed true
IsScholarly true
Issue 24
Keywords gene regulatory networks
time-course RNA-Seq
wound-induced cell reprogramming
de novo shoot regeneration
de novo root formation
Language English
License Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
LinkModel DirectLink
MergedId FETCHMERGED-LOGICAL-c481t-e8802d172a631db02460576f08d62ab91f1e1ad753a2fad3e81566a8e832dccc3
Notes ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
ORCID 0000-0001-8838-4974
0000-0003-2848-4919
OpenAccessLink https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9788163/
PMID 36555756
PQID 2756738209
PQPubID 2032341
ParticipantIDs doaj_primary_oai_doaj_org_article_d83684aadb064413b1db8f7faa4b5bc7
pubmedcentral_primary_oai_pubmedcentral_nih_gov_9788163
proquest_miscellaneous_2758107823
proquest_journals_2756738209
crossref_primary_10_3390_ijms232416112
pubmed_primary_36555756
PublicationCentury 2000
PublicationDate 20221217
PublicationDateYYYYMMDD 2022-12-17
PublicationDate_xml – month: 12
  year: 2022
  text: 20221217
  day: 17
PublicationDecade 2020
PublicationPlace Switzerland
PublicationPlace_xml – name: Switzerland
– name: Basel
PublicationTitle International journal of molecular sciences
PublicationTitleAlternate Int J Mol Sci
PublicationYear 2022
Publisher MDPI AG
MDPI
Publisher_xml – name: MDPI AG
– name: MDPI
References ref_94
Jin (ref_71) 2017; 45
ref_92
ref_90
Kobayashi (ref_53) 2015; 34
Asahina (ref_48) 2011; 108
Molina (ref_67) 2017; 8
ref_14
ref_13
Reinhardt (ref_31) 2003; 130
Carrillo (ref_38) 2020; 11
Efroni (ref_114) 2016; 165
Ranftl (ref_20) 2016; 170
ref_97
ref_95
Melnyk (ref_102) 2018; 115
Hendelman (ref_40) 2021; 184
Willems (ref_52) 2020; 32
Albacete (ref_12) 2021; 44
Yang (ref_121) 2020; 61
Xu (ref_60) 2018; 59
Xu (ref_96) 2014; 289
Gude (ref_109) 2017; 213
Heyman (ref_115) 2016; 2
Goh (ref_19) 2019; 224
Bae (ref_6) 2022; 20
Iwase (ref_11) 2021; 232
Matsuoka (ref_49) 2021; 4
Canher (ref_112) 2022; 15
Takahashi (ref_24) 2010; 29
ref_23
ref_120
Cejudo (ref_54) 2020; 186
Shigeto (ref_59) 2016; 209
Tsukagoshi (ref_56) 2010; 143
Capua (ref_35) 2017; 114
Hu (ref_86) 2019; 7
Saegusa (ref_100) 2014; 24
Durgaprasad (ref_106) 2019; 29
Iwase (ref_7) 2011; 21
Yu (ref_99) 2015; 468
ref_72
Joshi (ref_118) 2022; 13
Iwase (ref_9) 2015; 128
Aida (ref_22) 2004; 119
ref_79
ref_76
Ernst (ref_16) 2006; 7
ref_75
ref_74
ref_73
Goh (ref_21) 2012; 139
Mhimdi (ref_55) 2020; 11
ref_82
Mathew (ref_4) 2021; 148
ref_81
Yoshida (ref_51) 2013; 24
Huang (ref_85) 2013; 288
Sagi (ref_28) 2004; 16
Kouklas (ref_50) 2015; 35
Zheng (ref_70) 2016; 9
Yuan (ref_98) 2018; 20
ref_89
Sabatini (ref_116) 2003; 17
Zhai (ref_122) 2021; 7
Zhou (ref_44) 2019; 177
ref_88
Tang (ref_107) 2017; 213
ref_87
Bergmann (ref_108) 2007; 134
Iwase (ref_10) 2017; 29
Peng (ref_25) 2014; 393
Chandler (ref_104) 2018; 23
Bellande (ref_41) 2022; 73
Iwase (ref_8) 2013; 8
Hassani (ref_123) 2022; 13
Ge (ref_15) 2018; 19
Galbraith (ref_80) 1983; 220
Niu (ref_93) 2017; 5
Li (ref_91) 2016; 57
Desvoyes (ref_57) 2017; 213
Hawkins (ref_65) 2016; 14
Ye (ref_111) 2020; 32
Dai (ref_37) 2020; 293
Feller (ref_68) 1995; 47
Pu (ref_113) 2016; 28
Gill (ref_29) 2010; 48
Lemmon (ref_32) 2017; 171
Gao (ref_83) 2015; 96
Kareem (ref_39) 2015; 25
Devireddy (ref_27) 2021; 105
Motte (ref_119) 2011; 168
Vlieghe (ref_18) 2005; 15
Sakakibara (ref_47) 2014; 141
Kim (ref_101) 2019; 8
ref_69
Bolt (ref_42) 2017; 40
ref_66
Ikeuchi (ref_46) 2022; 188
ref_64
Xu (ref_3) 2014; 108
Han (ref_103) 2020; 32
Ikeuchi (ref_1) 2016; 143
Koenig (ref_33) 2009; 21
Ikeuchi (ref_5) 2018; 59
Fan (ref_61) 2012; 22
Zhang (ref_43) 2019; 5
Sakamoto (ref_36) 2022; 34
Huang (ref_84) 2012; 287
Zhang (ref_62) 2018; 176
Ge (ref_78) 2020; 36
Omary (ref_17) 2022; 375
Sengupta (ref_105) 2020; 15
Minibayeva (ref_58) 2015; 112
Zhang (ref_110) 2021; 40
ref_45
Debernardi (ref_117) 2020; 38
Schiessl (ref_34) 2014; 111
Ikeuchi (ref_2) 2019; 70
Carrillo (ref_30) 2020; 71
Tian (ref_77) 2020; 48
Savelli (ref_26) 2019; 26
Suzuki (ref_63) 2012; 53
References_xml – volume: 105
  start-page: 459
  year: 2021
  ident: ref_27
  article-title: Integration of Reactive Oxygen Species and Hormone Signaling during Abiotic Stress
  publication-title: Plant J.
  doi: 10.1111/tpj.15010
  contributor:
    fullname: Devireddy
– volume: 112
  start-page: 122
  year: 2015
  ident: ref_58
  article-title: Roles of Apoplastic Peroxidases in Plant Response to Wounding
  publication-title: Phytochemistry
  doi: 10.1016/j.phytochem.2014.06.008
  contributor:
    fullname: Minibayeva
– volume: 17
  start-page: 354
  year: 2003
  ident: ref_116
  article-title: SCARECROW is involved in positioning the stem cell niche in the Arabidopsis root meristem
  publication-title: Genes Dev.
  doi: 10.1101/gad.252503
  contributor:
    fullname: Sabatini
– volume: 22
  start-page: 1169
  year: 2012
  ident: ref_61
  article-title: LATERAL ORGAN BOUNDARIES DOMAIN Transcription Factors Direct Callus Formation in Arabidopsis Regeneration
  publication-title: Cell Res.
  doi: 10.1038/cr.2012.63
  contributor:
    fullname: Fan
– volume: 143
  start-page: 1442
  year: 2016
  ident: ref_1
  article-title: Plant Regeneration: Cellular Origins and Molecular Mechanisms
  publication-title: Development
  doi: 10.1242/dev.134668
  contributor:
    fullname: Ikeuchi
– volume: 14
  start-page: 1883
  year: 2016
  ident: ref_65
  article-title: NRF2 Orchestrates the Metabolic Shift during Induced Pluripotent Stem Cell Reprogramming
  publication-title: Cell Rep.
  doi: 10.1016/j.celrep.2016.02.003
  contributor:
    fullname: Hawkins
– volume: 177
  start-page: 942
  year: 2019
  ident: ref_44
  article-title: A Jasmonate Signaling Network Activates Root Stem Cells and Promotes Regeneration
  publication-title: Cell
  doi: 10.1016/j.cell.2019.03.006
  contributor:
    fullname: Zhou
– ident: ref_94
  doi: 10.1186/s12864-015-1249-2
– volume: 8
  start-page: e27432
  year: 2013
  ident: ref_8
  article-title: Arabidopsis WIND1 Induces Callus Formation in Rapeseed, Tomato, and Tobacco
  publication-title: Plant Signal. Behav.
  doi: 10.4161/psb.27432
  contributor:
    fullname: Iwase
– volume: 20
  start-page: 3234
  year: 2022
  ident: ref_6
  article-title: REGENOMICS: A Web-Based Application for Plant REGENeration-Associated TranscriptOMICS Analyses
  publication-title: Comput. Struct. Biotechnol. J.
  doi: 10.1016/j.csbj.2022.06.033
  contributor:
    fullname: Bae
– volume: 128
  start-page: 389
  year: 2015
  ident: ref_9
  article-title: WIND1-Based Acquisition of Regeneration Competency in Arabidopsis and Rapeseed
  publication-title: J. Plant Res.
  doi: 10.1007/s10265-015-0714-y
  contributor:
    fullname: Iwase
– volume: 139
  start-page: 883
  year: 2012
  ident: ref_21
  article-title: The Establishment of Asymmetry in Arabidopsis Lateral Root Founder Cells Is Regulated by LBD16/ASL18 and Related LBD/ASL Proteins
  publication-title: Development
  doi: 10.1242/dev.071928
  contributor:
    fullname: Goh
– ident: ref_87
  doi: 10.1186/s12864-020-6689-7
– volume: 96
  start-page: 141
  year: 2015
  ident: ref_83
  article-title: Comprehensive analysis and expression profile of the homeodomain leucine zipper IV transcription factor family in tomato
  publication-title: Plant Physiol. Biochem.
  doi: 10.1016/j.plaphy.2015.07.025
  contributor:
    fullname: Gao
– volume: 35
  start-page: 432
  year: 2015
  ident: ref_50
  article-title: A BHLH-Based Feedback Loop Restricts Vascular Cell Proliferation in Plants
  publication-title: Dev. Cell
  doi: 10.1016/j.devcel.2015.10.022
  contributor:
    fullname: Kouklas
– volume: 13
  start-page: 838421
  year: 2022
  ident: ref_123
  article-title: Constitutive Overexpression of a Conifer WOX2 Homolog Affects Somatic Embryo Development in Pinus pinaster and Promotes Somatic Embryogenesis and Organogenesis in Arabidopsis Seedlings
  publication-title: Front. Plant Sci.
  doi: 10.3389/fpls.2022.838421
  contributor:
    fullname: Hassani
– volume: 61
  start-page: 1600
  year: 2020
  ident: ref_121
  article-title: De Novo Shoot Regeneration Controlled by HEN1 and TCP3/4 in Arabidopsis
  publication-title: Plant Cell Physiol.
  doi: 10.1093/pcp/pcaa083
  contributor:
    fullname: Yang
– volume: 26
  start-page: 101247
  year: 2019
  ident: ref_26
  article-title: RedoxiBase: A Database for ROS Homeostasis Regulated Proteins
  publication-title: Redox Biol.
  doi: 10.1016/j.redox.2019.101247
  contributor:
    fullname: Savelli
– ident: ref_45
  doi: 10.1093/pcp/pcac146
– volume: 7
  start-page: e7929
  year: 2019
  ident: ref_86
  article-title: Genome-wide identification of C2H2 zinc-finger genes and their expression patterns under heat stress in tomato (Solanum lycopersicum L.)
  publication-title: PeerJ
  doi: 10.7717/peerj.7929
  contributor:
    fullname: Hu
– volume: 34
  start-page: 4348
  year: 2022
  ident: ref_36
  article-title: Transcriptional Activation of Auxin Biosynthesis Drives Developmental Reprogramming of Differentiated Cells
  publication-title: Plant Cell
  doi: 10.1093/plcell/koac218
  contributor:
    fullname: Sakamoto
– volume: 47
  start-page: 217
  year: 1995
  ident: ref_68
  article-title: Phänologische Entwicklungsstadien von Gemüsepflanzen: II. Fruchtgemüse Und Hülsenfrüchte
  publication-title: Nachrichtenbl. Deut. Pflanzenschutzd.
  contributor:
    fullname: Feller
– volume: 53
  start-page: 2269
  year: 2012
  ident: ref_63
  article-title: Reactive Oxygen Species-Dependent Wound Responses in Animals and Plants
  publication-title: Free Radic. Biol. Med.
  doi: 10.1016/j.freeradbiomed.2012.10.538
  contributor:
    fullname: Suzuki
– volume: 220
  start-page: 1049
  year: 1983
  ident: ref_80
  article-title: Rapid Flow Cytometric Analysis of the Cell Cycle in Intact Plant Tissues
  publication-title: Science
  doi: 10.1126/science.220.4601.1049
  contributor:
    fullname: Galbraith
– ident: ref_82
  doi: 10.1371/journal.pone.0177381
– volume: 141
  start-page: 1660
  year: 2014
  ident: ref_47
  article-title: WOX13-like Genes Are Required for Reprogramming of Leaf and Protoplast Cells into Stem Cells in the Moss Physcomitrella Patens
  publication-title: Development
  doi: 10.1242/dev.097444
  contributor:
    fullname: Sakakibara
– volume: 168
  start-page: 1598
  year: 2011
  ident: ref_119
  article-title: CUC2 as an early marker for regeneration competence in Arabidopsis root explants
  publication-title: J. Plant Physiol.
  doi: 10.1016/j.jplph.2011.02.014
  contributor:
    fullname: Motte
– volume: 15
  start-page: 1794147
  year: 2020
  ident: ref_105
  article-title: ABI3 plays a role in de-novo root regeneration from Arabidopsis thaliana callus cells
  publication-title: Plant Signal Behav.
  doi: 10.1080/15592324.2020.1794147
  contributor:
    fullname: Sengupta
– volume: 21
  start-page: 508
  year: 2011
  ident: ref_7
  article-title: The AP2/ERF Transcription Factor WIND1 Controls Cell Dedifferentiation in Arabidopsis
  publication-title: Curr. Biol.
  doi: 10.1016/j.cub.2011.02.020
  contributor:
    fullname: Iwase
– volume: 119
  start-page: 109
  year: 2004
  ident: ref_22
  article-title: The PLETHORA Genes Mediate Patterning of the Arabidopsis Root Stem Cell Niche
  publication-title: Cell
  doi: 10.1016/j.cell.2004.09.018
  contributor:
    fullname: Aida
– ident: ref_89
  doi: 10.1186/s12864-015-1990-6
– volume: 32
  start-page: 226
  year: 2020
  ident: ref_111
  article-title: AP2/ERF Transcription Factors Integrate Age and Wound Signals for Root Regeneration
  publication-title: Plant Cell.
  doi: 10.1105/tpc.19.00378
  contributor:
    fullname: Ye
– volume: 375
  start-page: eabf4368
  year: 2022
  ident: ref_17
  article-title: A Conserved Superlocus Regulates Above- and Belowground Root Initiation
  publication-title: Science
  doi: 10.1126/science.abf4368
  contributor:
    fullname: Omary
– volume: 57
  start-page: 1657
  year: 2016
  ident: ref_91
  article-title: Genome-Wide Identification and Analysis of the MYB Transcription Factor Superfamily in Solanum lycopersicum
  publication-title: Plant Cell Physiol.
  doi: 10.1093/pcp/pcw091
  contributor:
    fullname: Li
– volume: 48
  start-page: D1104
  year: 2020
  ident: ref_77
  article-title: PlantRegMap: Charting Functional Regulatory Maps in Plants
  publication-title: Nucleic Acids Res.
  contributor:
    fullname: Tian
– volume: 13
  start-page: 861556
  year: 2022
  ident: ref_118
  article-title: AGL15 Promotion of Somatic Embryogenesis: Role and Molecular Mechanism
  publication-title: Front. Plant Sci.
  doi: 10.3389/fpls.2022.861556
  contributor:
    fullname: Joshi
– volume: 32
  start-page: 2979
  year: 2020
  ident: ref_52
  article-title: The Cyclin CYCA3;4 Is a Postprophase Target of the APC/CCCS52A2 E3-Ligase Controlling Formative Cell Divisions in Arabidopsis
  publication-title: Plant Cell
  doi: 10.1105/tpc.20.00208
  contributor:
    fullname: Willems
– ident: ref_72
  doi: 10.1186/1471-2105-14-321
– ident: ref_73
– volume: 111
  start-page: 2830
  year: 2014
  ident: ref_34
  article-title: Arabidopsis JAGGED Links Floral Organ Patterning to Tissue Growth by Repressing Kip-Related Cell Cycle Inhibitors
  publication-title: Proc. Natl. Acad. Sci. USA
  doi: 10.1073/pnas.1320457111
  contributor:
    fullname: Schiessl
– volume: 108
  start-page: 1
  year: 2014
  ident: ref_3
  article-title: Genetic and Epigenetic Controls of Plant Regeneration
  publication-title: Curr. Top. Dev. Biol.
  doi: 10.1016/B978-0-12-391498-9.00009-7
  contributor:
    fullname: Xu
– volume: 108
  start-page: 16128
  year: 2011
  ident: ref_48
  article-title: Spatially Selective Hormonal Control of RAP2.6L and ANAC071 Transcription Factors Involved in Tissue Reunion in Arabidopsis
  publication-title: Proc. Natl. Acad. Sci. USA
  doi: 10.1073/pnas.1110443108
  contributor:
    fullname: Asahina
– ident: ref_74
  doi: 10.1186/1471-2105-12-124
– ident: ref_75
– volume: 71
  start-page: 3803
  year: 2020
  ident: ref_30
  article-title: CDF Transcription Factors: Plant Regulators to Deal with Extreme Environmental Conditions
  publication-title: J. Exp. Bot.
  doi: 10.1093/jxb/eraa088
  contributor:
    fullname: Carrillo
– ident: ref_81
  doi: 10.3390/genes11121435
– volume: 8
  start-page: 660
  year: 2017
  ident: ref_67
  article-title: Ectopic Expression of CDF3 Genes in Tomato Enhances Biomass Production and Yield under Salinity Stress Conditions
  publication-title: Front. Plant Sci.
  doi: 10.3389/fpls.2017.00660
  contributor:
    fullname: Molina
– volume: 44
  start-page: 1642
  year: 2021
  ident: ref_12
  article-title: An Auxin-Mediated Regulatory Framework for Wound-Induced Adventitious Root Formation in Tomato Shoot Explants
  publication-title: Plant Cell Environ.
  doi: 10.1111/pce.14001
  contributor:
    fullname: Albacete
– volume: 393
  start-page: 160
  year: 2014
  ident: ref_25
  article-title: CYCP2;1 Integrates Genetic and Nutritional Information to Promote Meristem Cell Division in Arabidopsis
  publication-title: Dev. Biol.
  doi: 10.1016/j.ydbio.2014.06.008
  contributor:
    fullname: Peng
– volume: 293
  start-page: 110323
  year: 2020
  ident: ref_37
  article-title: MYB94 and MYB96 Additively Inhibit Callus Formation via Directly Repressing LBD29 Expression in Arabidopsis Thaliana
  publication-title: Plant Sci.
  doi: 10.1016/j.plantsci.2019.110323
  contributor:
    fullname: Dai
– volume: 48
  start-page: 909
  year: 2010
  ident: ref_29
  article-title: Reactive Oxygen Species and Antioxidant Machinery in Abiotic Stress Tolerance in Crop Plants
  publication-title: Plant Physiol. Biochem.
  doi: 10.1016/j.plaphy.2010.08.016
  contributor:
    fullname: Gill
– volume: 130
  start-page: 4073
  year: 2003
  ident: ref_31
  article-title: Microsurgical and Laser Ablation Analysis of Interactions between the Zones and Layers of the Tomato Shoot Apical Meristem
  publication-title: Development
  doi: 10.1242/dev.00596
  contributor:
    fullname: Reinhardt
– volume: 4
  start-page: 1
  year: 2021
  ident: ref_49
  article-title: Wound-Inducible ANAC071 and ANAC096 Transcription Factors Promote Cambial Cell Formation in Incised Arabidopsis Flowering Stems
  publication-title: Commun. Biol.
  doi: 10.1038/s42003-021-01895-8
  contributor:
    fullname: Matsuoka
– volume: 70
  start-page: 377
  year: 2019
  ident: ref_2
  article-title: Molecular Mechanisms of Plant Regeneration
  publication-title: Annu. Rev. Plant Biol.
  doi: 10.1146/annurev-arplant-050718-100434
  contributor:
    fullname: Ikeuchi
– volume: 148
  start-page: dev195347
  year: 2021
  ident: ref_4
  article-title: Model Systems for Regeneration: Arabidopsis
  publication-title: Development
  doi: 10.1242/dev.195347
  contributor:
    fullname: Mathew
– volume: 24
  start-page: 2053
  year: 2014
  ident: ref_100
  article-title: A bHLH complex activates vascular cell division via cytokinin action in root apical meristem
  publication-title: Curr. Biol.
  doi: 10.1016/j.cub.2014.07.050
  contributor:
    fullname: Saegusa
– volume: 11
  start-page: 1541
  year: 2020
  ident: ref_55
  article-title: Understanding of Adventitious Root Formation: What Can We Learn From Comparative Genetics?
  publication-title: Front. Plant Sci.
  doi: 10.3389/fpls.2020.582020
  contributor:
    fullname: Mhimdi
– ident: ref_97
  doi: 10.1186/s12870-021-03329-3
– volume: 287
  start-page: 495
  year: 2012
  ident: ref_84
  article-title: Genome-wide analysis of WRKY transcription factors in Solanum lycopersicum
  publication-title: Mol. Genet. Genom.
  doi: 10.1007/s00438-012-0696-6
  contributor:
    fullname: Huang
– volume: 170
  start-page: 2295
  year: 2016
  ident: ref_20
  article-title: LLM-Domain Containing B-GATA Factors Control Different Aspects of Cytokinin-Regulated Development in Arabidopsis Thaliana
  publication-title: Plant Physiol.
  doi: 10.1104/pp.15.01556
  contributor:
    fullname: Ranftl
– volume: 8
  start-page: bio039677
  year: 2019
  ident: ref_101
  article-title: Reprogramming of the cambium regulators during adventitious root development upon wounding of storage tap roots in radish (Raphanus sativus L.)
  publication-title: Biol. Open
  contributor:
    fullname: Kim
– volume: 114
  start-page: 3246
  year: 2017
  ident: ref_35
  article-title: Coordination of Auxin-Triggered Leaf Initiation by Tomato LEAFLESS
  publication-title: Proc. Natl. Acad. Sci. USA
  doi: 10.1073/pnas.1617146114
  contributor:
    fullname: Capua
– volume: 188
  start-page: 425
  year: 2022
  ident: ref_46
  article-title: Wound-Inducible WUSCHEL-RELATED HOMEOBOX 13 Is Required for Callus Growth and Organ Reconnection
  publication-title: Plant Physiol.
  doi: 10.1093/plphys/kiab510
  contributor:
    fullname: Ikeuchi
– volume: 2
  start-page: 16165
  year: 2016
  ident: ref_115
  article-title: The heterodimeric transcription factor complex ERF115-PAT1 grants regeneration competence
  publication-title: Nat. Plants
  doi: 10.1038/nplants.2016.165
  contributor:
    fullname: Heyman
– ident: ref_14
  doi: 10.3390/ijms222111843
– volume: 143
  start-page: 606
  year: 2010
  ident: ref_56
  article-title: Transcriptional Regulation of ROS Controls Transition from Proliferation to Differentiation in the Root
  publication-title: Cell
  doi: 10.1016/j.cell.2010.10.020
  contributor:
    fullname: Tsukagoshi
– volume: 289
  start-page: 965
  year: 2014
  ident: ref_96
  article-title: Genome-wide analysis and identification of stress-responsive genes of the CCCH zinc finger family in Solanum lycopersicum
  publication-title: Mol. Genet. Genom.
  doi: 10.1007/s00438-014-0861-1
  contributor:
    fullname: Xu
– ident: ref_92
  doi: 10.3390/genes9090457
– volume: 59
  start-page: 770
  year: 2018
  ident: ref_5
  article-title: A Gene Regulatory Network for Cellular Reprogramming in Plant Regeneration
  publication-title: Plant Cell Physiol.
  doi: 10.1093/pcp/pcy013
  contributor:
    fullname: Ikeuchi
– volume: 176
  start-page: 2231
  year: 2018
  ident: ref_62
  article-title: Thioredoxin-Mediated ROS Homeostasis Explains Natural Variation in Plant Regeneration
  publication-title: Plant Physiol.
  doi: 10.1104/pp.17.00633
  contributor:
    fullname: Zhang
– volume: 21
  start-page: 3093
  year: 2009
  ident: ref_33
  article-title: LYRATE Is a Key Regulator of Leaflet Initiation and Lamina Outgrowth in Tomato
  publication-title: Plant Cell
  doi: 10.1105/tpc.109.069948
  contributor:
    fullname: Koenig
– ident: ref_23
– volume: 20
  start-page: 1274
  year: 2018
  ident: ref_98
  article-title: A genome-wide analysis of GATA transcription factor family in tomato and analysis of expression patterns
  publication-title: Int. J. Agric. Biol.
  contributor:
    fullname: Yuan
– volume: 288
  start-page: 111
  year: 2013
  ident: ref_85
  article-title: Genome-wide identification, phylogeny and expression analysis of SUN, OFP and YABBY gene family in tomato
  publication-title: Mol. Genet. Genom.
  doi: 10.1007/s00438-013-0733-0
  contributor:
    fullname: Huang
– ident: ref_64
  doi: 10.3390/ijms20020238
– volume: 29
  start-page: 453
  year: 2019
  ident: ref_106
  article-title: Gradient Expression of Transcription Factor Imposes a Boundary on Organ Regeneration Potential in Plants
  publication-title: Cell Rep.
  doi: 10.1016/j.celrep.2019.08.099
  contributor:
    fullname: Durgaprasad
– volume: 29
  start-page: 54
  year: 2017
  ident: ref_10
  article-title: WIND1 Promotes Shoot Regeneration through Transcriptional Activation of ENHANCER OF SHOOT REGENERATION1 in Arabidopsis
  publication-title: Plant Cell
  doi: 10.1105/tpc.16.00623
  contributor:
    fullname: Iwase
– volume: 15
  start-page: 59
  year: 2005
  ident: ref_18
  article-title: The DP-E2F-like Gene DEL1 Controls the Endocycle in Arabidopsis Thaliana
  publication-title: Curr. Biol.
  doi: 10.1016/j.cub.2004.12.038
  contributor:
    fullname: Vlieghe
– volume: 25
  start-page: 1017
  year: 2015
  ident: ref_39
  article-title: PLETHORA Genes Control Regeneration by a Two-Step Mechanism
  publication-title: Curr. Biol.
  doi: 10.1016/j.cub.2015.02.022
  contributor:
    fullname: Kareem
– volume: 7
  start-page: 1453
  year: 2021
  ident: ref_122
  article-title: Pluripotency acquisition in the middle cell layer of callus is required for organ regeneration
  publication-title: Nat. Plants
  doi: 10.1038/s41477-021-01015-8
  contributor:
    fullname: Zhai
– ident: ref_95
  doi: 10.3390/ijms20122961
– ident: ref_69
– ident: ref_90
  doi: 10.1186/s12864-015-2334-2
– volume: 40
  start-page: 108
  year: 2017
  ident: ref_42
  article-title: ERF105 Is a Transcription Factor Gene of Arabidopsis Thaliana Required for Freezing Tolerance and Cold Acclimation
  publication-title: Plant Cell Environ.
  doi: 10.1111/pce.12838
  contributor:
    fullname: Bolt
– volume: 468
  start-page: 653
  year: 2015
  ident: ref_99
  article-title: Genome-wide identification and expression profiling analysis of trihelix gene family in tomato
  publication-title: Biochem. Biophys. Res. Commun.
  doi: 10.1016/j.bbrc.2015.11.010
  contributor:
    fullname: Yu
– volume: 165
  start-page: 1721
  year: 2016
  ident: ref_114
  article-title: Root Regeneration Triggers an Embryo-like Sequence Guided by Hormonal Interactions
  publication-title: Cell
  doi: 10.1016/j.cell.2016.04.046
  contributor:
    fullname: Efroni
– volume: 209
  start-page: 1395
  year: 2016
  ident: ref_59
  article-title: Diverse Functions and Reactions of Class III Peroxidases
  publication-title: New Phytol.
  doi: 10.1111/nph.13738
  contributor:
    fullname: Shigeto
– volume: 59
  start-page: 749
  year: 2018
  ident: ref_60
  article-title: Genome-Wide Identification of Arabidopsis LBD29 Target Genes Reveals the Molecular Events behind Auxin-Induced Cell Reprogramming during Callus Formation
  publication-title: Plant Cell Physiol.
  doi: 10.1093/pcp/pcx168
  contributor:
    fullname: Xu
– volume: 15
  start-page: 1543
  year: 2022
  ident: ref_112
  article-title: The regeneration factors ERF114 and ERF115 regulate auxin-mediated lateral root development in response to mechanical cues
  publication-title: Mol. Plant.
  doi: 10.1016/j.molp.2022.08.008
  contributor:
    fullname: Canher
– volume: 29
  start-page: 307
  year: 2010
  ident: ref_24
  article-title: Two Arabidopsis Cyclin A3s Possess G1 Cyclin-like Features
  publication-title: Plant Cell Rep.
  doi: 10.1007/s00299-010-0817-9
  contributor:
    fullname: Takahashi
– volume: 32
  start-page: 206
  year: 2020
  ident: ref_103
  article-title: Arabidopsis ZINC FINGER PROTEIN1 Acts Downstream of GL2 to Repress Root Hair Initiation and Elongation by Directly Suppressing bHLH Genes
  publication-title: Plant Cell
  doi: 10.1105/tpc.19.00226
  contributor:
    fullname: Han
– volume: 28
  start-page: 2616
  year: 2016
  ident: ref_113
  article-title: Transcriptional Regulation of Arabidopsis Polycomb Repressive Complex 2 Coordinates Cell-Type Proliferation and Differentiation
  publication-title: Plant Cell.
  doi: 10.1105/tpc.15.00744
  contributor:
    fullname: Pu
– volume: 34
  start-page: 1992
  year: 2015
  ident: ref_53
  article-title: Transcriptional Repression by MYB3R Proteins Regulates Plant Organ Growth
  publication-title: EMBO J.
  doi: 10.15252/embj.201490899
  contributor:
    fullname: Kobayashi
– volume: 24
  start-page: 426
  year: 2013
  ident: ref_51
  article-title: A BHLH Complex Controls Embryonic Vascular Tissue Establishment and Indeterminate Growth in Arabidopsis
  publication-title: Dev. Cell
  doi: 10.1016/j.devcel.2012.12.013
  contributor:
    fullname: Yoshida
– volume: 213
  start-page: 105
  year: 2017
  ident: ref_57
  article-title: Control of Arabidopsis Lateral Root Primordium Boundaries by MYB36
  publication-title: New Phytol.
  doi: 10.1111/nph.14304
  contributor:
    fullname: Desvoyes
– volume: 115
  start-page: E2447
  year: 2018
  ident: ref_102
  article-title: Transcriptome dynamics at Arabidopsis graft junctions reveal an intertissue recognition mechanism that activates vascular regeneration
  publication-title: Proc. Natl. Acad. Sci. USA
  doi: 10.1073/pnas.1718263115
  contributor:
    fullname: Melnyk
– volume: 19
  start-page: 1
  year: 2018
  ident: ref_15
  article-title: IDEP: An Integrated Web Application for Differential Expression and Pathway Analysis of RNA-Seq Data
  publication-title: BMC Bioinform.
  doi: 10.1186/s12859-018-2486-6
  contributor:
    fullname: Ge
– ident: ref_76
– volume: 38
  start-page: 1274
  year: 2020
  ident: ref_117
  article-title: A GRF-GIF chimeric protein improves the regeneration efficiency of transgenic plants
  publication-title: Nat. Biotechnol.
  doi: 10.1038/s41587-020-0703-0
  contributor:
    fullname: Debernardi
– volume: 213
  start-page: 1787
  year: 2017
  ident: ref_109
  article-title: The transcription factor OBP4 controls root growth and promotes callus formation
  publication-title: New Phytol.
  doi: 10.1111/nph.14315
  contributor:
    fullname: Gude
– volume: 45
  start-page: D1040
  year: 2017
  ident: ref_71
  article-title: PlantTFDB 4.0: Toward a Central Hub for Transcription Factors and Regulatory Interactions in Plants
  publication-title: Nucleic Acids Res.
  doi: 10.1093/nar/gkw982
  contributor:
    fullname: Jin
– ident: ref_66
  doi: 10.3390/antiox10020332
– volume: 213
  start-page: 1740
  year: 2017
  ident: ref_107
  article-title: FUSCA3 interacting with LEAFY COTYLEDON2 controls lateral root formation through regulating YUCCA4 gene expression in Arabidopsis thaliana
  publication-title: New Phytol.
  doi: 10.1111/nph.14313
  contributor:
    fullname: Tang
– volume: 232
  start-page: 734
  year: 2021
  ident: ref_11
  article-title: WIND Transcription Factors Orchestrate Wound-Induced Callus Formation, Vascular Reconnection and Defense Response in Arabidopsis
  publication-title: New Phytol.
  doi: 10.1111/nph.17594
  contributor:
    fullname: Iwase
– volume: 9
  start-page: 1667
  year: 2016
  ident: ref_70
  article-title: ITAK: A Program for Genome-Wide Prediction and Classification of Plant Transcription Factors, Transcriptional Regulators, and Protein Kinases
  publication-title: Mol. Plant
  doi: 10.1016/j.molp.2016.09.014
  contributor:
    fullname: Zheng
– volume: 134
  start-page: 2959
  year: 2007
  ident: ref_108
  article-title: Regulation of the Arabidopsis root vascular initial population by LONESOME HIGHWAY
  publication-title: Development
  doi: 10.1242/dev.006296
  contributor:
    fullname: Bergmann
– volume: 5
  start-page: e3955
  year: 2017
  ident: ref_93
  article-title: Genome-wide identification and characterization of GRAS transcription factors in tomato (Solanum lycopersicum)
  publication-title: PeerJ
  doi: 10.7717/peerj.3955
  contributor:
    fullname: Niu
– volume: 73
  start-page: 3496
  year: 2022
  ident: ref_41
  article-title: PUCHI Represses Early Meristem Formation in Developing Lateral Roots of Arabidopsis Thaliana
  publication-title: J. Exp. Bot.
  doi: 10.1093/jxb/erac079
  contributor:
    fullname: Bellande
– volume: 23
  start-page: 151
  year: 2018
  ident: ref_104
  article-title: Class VIIIb APETALA2 Ethylene Response Factors in Plant Development
  publication-title: Trends Plant Sci.
  doi: 10.1016/j.tplants.2017.09.016
  contributor:
    fullname: Chandler
– volume: 5
  start-page: 491
  year: 2019
  ident: ref_43
  article-title: Jasmonate-Mediated Wound Signalling Promotes Plant Regeneration
  publication-title: Nat. Plants
  doi: 10.1038/s41477-019-0408-x
  contributor:
    fullname: Zhang
– volume: 40
  start-page: 315
  year: 2021
  ident: ref_110
  article-title: ARF4 regulates shoot regeneration through coordination with ARF5 and IAA12
  publication-title: Plant Cell Rep.
  doi: 10.1007/s00299-020-02633-w
  contributor:
    fullname: Zhang
– volume: 224
  start-page: 749
  year: 2019
  ident: ref_19
  article-title: Lateral Root Initiation Requires the Sequential Induction of Transcription Factors LBD16 and PUCHI in Arabidopsis Thaliana
  publication-title: New Phytol.
  doi: 10.1111/nph.16065
  contributor:
    fullname: Goh
– ident: ref_79
– volume: 16
  start-page: 616
  year: 2004
  ident: ref_28
  article-title: Plant Respiratory Burst Oxidase Homologs Impinge on Wound Responsiveness and Development in Lycopersicon Esculentum
  publication-title: Plant Cell
  doi: 10.1105/tpc.019398
  contributor:
    fullname: Sagi
– ident: ref_88
  doi: 10.3390/ijms18051056
– volume: 184
  start-page: 1724
  year: 2021
  ident: ref_40
  article-title: Conserved Pleiotropy of an Ancient Plant Homeobox Gene Uncovered by Cis-Regulatory Dissection
  publication-title: Cell
  doi: 10.1016/j.cell.2021.02.001
  contributor:
    fullname: Hendelman
– volume: 171
  start-page: 470
  year: 2017
  ident: ref_32
  article-title: Engineering Quantitative Trait Variation for Crop Improvement by Genome Editing
  publication-title: Cell
  doi: 10.1016/j.cell.2017.08.030
  contributor:
    fullname: Lemmon
– volume: 11
  start-page: 1825
  year: 2020
  ident: ref_38
  article-title: The Arabidopsis Transcription Factor CDF3 Is Involved in Nitrogen Responses and Improves Nitrogen Use Efficiency in Tomato
  publication-title: Front. Plant Sci.
  contributor:
    fullname: Carrillo
– volume: 36
  start-page: 2628
  year: 2020
  ident: ref_78
  article-title: ShinyGO: A Graphical Gene-Set Enrichment Tool for Animals and Plants
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btz931
  contributor:
    fullname: Ge
– ident: ref_13
  doi: 10.1101/2021.04.29.441912
– volume: 186
  start-page: 9
  year: 2020
  ident: ref_54
  article-title: Redox Regulation of Chloroplast Metabolism
  publication-title: Plant Physiol.
  doi: 10.1093/plphys/kiaa062
  contributor:
    fullname: Cejudo
– volume: 7
  start-page: 1
  year: 2006
  ident: ref_16
  article-title: STEM: A Tool for the Analysis of Short Time Series Gene Expression Data
  publication-title: BMC Bioinform.
  doi: 10.1186/1471-2105-7-191
  contributor:
    fullname: Ernst
– ident: ref_120
  doi: 10.3390/plants8020038
SSID ssj0023259
Score 2.4216053
Snippet Some of the hormone crosstalk and transcription factors (TFs) involved in wound-induced organ regeneration have been extensively studied in the model plant ....
Some of the hormone crosstalk and transcription factors (TFs) involved in wound-induced organ regeneration have been extensively studied in the model plant...
SourceID doaj
pubmedcentral
proquest
crossref
pubmed
SourceType Open Website
Open Access Repository
Aggregation Database
Index Database
StartPage 16112
SubjectTerms Arabidopsis - metabolism
Arabidopsis Proteins - genetics
Cell activation
Cell cycle
Cytokinins
de novo root formation
de novo shoot regeneration
Explants
Flowers & plants
Gene expression
Gene Expression Regulation, Plant
Gene Regulatory Networks
Hormones
Hypocotyl - genetics
Hypocotyl - metabolism
Indoleacetic Acids - metabolism
Plant Roots - metabolism
Plant Shoots - metabolism
Plants - metabolism
Solanum lycopersicum
Solanum lycopersicum - genetics
time-course RNA-Seq
Transcription factors
Transcriptomics
wound-induced cell reprogramming
Wounds
SummonAdditionalLinks – databaseName: DOAJ Directory of Open Access Journals
  dbid: DOA
  link: http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwrV1La9wwEBYlEMglNG3aukmLCqU3E8uyZOmYR5dtoXtKIDejJ9k-rNDdBPbfZyTZS1wKuQR8sC0Z5BmP5ht55hNCnytPDVPUlI5LVjbggqJJVaUyRkpTi8qnBbcfCz6_ar5fs-tHW33FnLBMD5wFd2IF5aJRyuoqum6qidXCt16pRjNtch05YWMwNYRatE7bpBHwPiVnkmd2TQoB_sny559VhBEAdUg98UaJtP9_SPPfhMlHHmj2Eu0P0BGf5iEfoBeuf4V282aSm9foV6659cMiHA4eJ0c0Tgvw6CLnfK_wtx5mpXtn8bLHFw4vwn3AqSoTz8Zixth0GeA84PnmNpiw3vzGMWMvJs4coqvZ18vzeTlspVCaRpB16cBMawtgRXEKAgTHDGFMy30lLK-VlsQTR5SF2EXVXlnqIokMV8KBwVtjDH2DdvrQu3cIGy2EVF6L1rnGESYMzAptI2vtHFw2BfoyirS7zYwZHUQaUfbdRPYFOosC33aKRNfpBqi_G9TfPaX-Ah2P6uoG61t1kdK-pYBtZIE-bZvBbuLPENW7cJf6CBLxES3Q26zd7UgoZwxgLC9QO9H7ZKjTln55k7i5ZaTn5_T9c7zbEdqrY7EFgaM9Rjvrv3fuA0Cgtf6YvvYHNfIGfQ
  priority: 102
  providerName: Directory of Open Access Journals
– databaseName: ProQuest Technology Collection
  dbid: 8FG
  link: http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwfV3di9QwEB_0RPBF_LZ6SgTxrdymadPkSe7UdRXcpzu4t5Kkia4fzXq7d7D_vTNpu1oRoQ9t08KQdGZ-k878BuDlLAhXGeFyL3WVl-iCSKVmuXFOa1eoWUgbbp-WcnFWfjyvzocNt82QVjnaxGSo2-hoj_yIaMprgf5Kv17_zKlrFP1dHVpoXIcbnJjwqFJ8_n4fcIkiNUvj6INyWWnZc2wKDPOPVl9_bAhMIODhxcQnJer-f-HNv9Mm__BD8ztwewCQ7Lhf8btwzXf34GbfUnJ3H771lbdh2IpjMbDkjkbjgK8u-8zvDfvQoW268i1bdeytZ8t4FVmqzWTzsaSRhk4jnke22K2ji9vdd0Z5e5Q-8wDO5u9O3yzyoaFC7krFt7lHZS1ahCxGCt5adM8YzNQyzFQrC2M1D9xz02IEY4pgWuGJSkYa5VHtW-eceAgHXez8Y2DOKqVNsKr2vvS8Ug5tQ13qwnqPl2UGr8YpbdY9b0aD8QbNfTOZ-wxOaML3DxHddboRLz43g_Y0rRJSlcagzITfhEXpVaiDMaWtrKszOByXqxl0cNP8_mIyeLEfRu2hXyKm8_EyPaM4oSSRwaN-dfeSCFlVCGZlBvVk3SeiTke61ZfE0K2JpF-KJ_8X6yncKqiYguNRH8LB9uLSP0OIs7XP03f8C6L5_Nk
  priority: 102
  providerName: ProQuest
– databaseName: Scholars Portal Journals: Open Access
  dbid: M48
  link: http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwfV1Lb9QwELZQERIXxJuUgoyEuAXWsePYB1SVx2pB6p66Um-R7diw0MZld1ux_54ZJ1kIVEg5JLEtjcYezzd-fEPIy0ngrjTc5V7qMhfggtCkJrlxTmtXqElIC27HczlbiM-n5elvSqFegetrQzvMJ7VYnb3--WN7CAb_FiNOCNnfLL-drxEYAHjBfMM3C8EFDvZjsdtQgOKUN42BO8plqWVHt_lv85F7Siz-10HPv09Q_uGSpnfJnR5L0qOu8--RG769T2512SW3D8j37hJu6FflaAw0eaZhnoCm8-4Q-Jp-amGauvINXbb0g6fzeBVpuqZJp8PtRiw6ifAe6Wx7EV3cbM8oHuHDkzQPyWL68eT9LO9zK-ROKLbJPdht0QB6MZKzxoKnhrimkmGiGlkYq1lgnpkGghlTBNNwj6wy0igPM0DjnOOPyF4bW_-EUGeV0iZYVXkvPCuVg2miErqw3sOnyMirQaX1RUehUUPogbqvR7rPyDtU-K4SMl-nH3H1pe4NqW4Ul0oYAzIjlOMWpFehCsYIW1pXZeRg6K56GE01ctxXHMCOzsiLXTEYEu6OmNbHy1RHMQRMPCOPu97dScJlWQKulRmpRv0-EnVc0i6_JrJujXz9ku__X6yn5HaB9yoYPNUB2dusLv0zQDsb-zyN41-MjP-u
  priority: 102
  providerName: Scholars Portal
Title Identification of Transcriptional Networks Involved in De Novo Organ Formation in Tomato Hypocotyl Explants
URI https://www.ncbi.nlm.nih.gov/pubmed/36555756
https://www.proquest.com/docview/2756738209
https://www.proquest.com/docview/2758107823/abstract/
https://pubmed.ncbi.nlm.nih.gov/PMC9788163
https://doaj.org/article/d83684aadb064413b1db8f7faa4b5bc7
Volume 23
hasFullText 1
inHoldings 1
isFullTextHit
isPrint
link http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV3da9swED_ajsFexr7nrTMajL25iS1bkh_Xrlk2SCijhbwZSZa6bI0VmrSQ_34n2Q7z2NPACNuy4NDd6X4n350APowt1YWkOjGsLJIcTZBXqXEitS5LnYmxDRtuszmbXuXfFsXiAIo-FyYE7Wu1PGluVifN8keIrVyv9KiPExtdzM5KXwOd0dEhHHJKexe987IoAvq2mCZFf360_LnaeNSAyCb1R9dQVhQIUdjADoVy_f_CmH-HSv5heyZP4HEHGsmnlrincGCaZ_CwPUZy9xx-tdm2ttt-I86SYIL6BQGHztto7w352uB6dG9qsmzIZ0Pm7t6RkI9JJn0ao--6dHjvyHS3dtptdzfEx-r5kJkXcDU5vzybJt0hConORbpNDCpoViNMkYymtUKTjA4MZ3YsapZJVaY2Nams0WuRmZU1Nb58DJPCoKrXWmv6Eo4a15jXQLQSopRWCW5MbtJCaFwPeF5myhh8zCP42E9ptW5rZVToY3g2VAM2RHDqJ3z_kS9xHV642-uqY3RVC8pELiXS7DEbVUi9sNxKmatCaR7Bcc-uqtO7TeWL2XOKqKaM4P2-GzXG_waRjXF34RuRemREI3jVcndPSS8dEfAB3wekDntQSENV7k4o3_z3yLfwKPO5FSle_BiOtrd35h0inq2KUc4XHFsx-RLDg9Pz-cX3OOwexN4SFdjOchEHPfgNxdYKJg
link.rule.ids 230,315,733,786,790,870,891,2115,2236,12083,12792,21416,24346,27955,27956,31752,31753,33406,33407,33777,33778,43343,43633,43838,53825,53827,74100,74390,74657
linkProvider National Library of Medicine
linkToHtml http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwfV1Lb9QwEB7BVoheKt4NLWAkxC3qOk4c51RR6GoLbYTQVuotchy7LI946W4r7b_vTB4LQQgphyROpJHtmfnGHn8D8GbshEm0MKGVWRLG6IJIpcahNibLTKTGrllwO8vl9Dz-eJFcdAtuyy6tsreJjaGuvKE18gOiKU8F-qvscPErpKpRtLvaldC4C1tEualGsHV0nH_-sgm5RNSUS-PohUKZZLJl2RQY6B_Mv_1cEpxAyMOjgVdqyPv_hTj_Tpz8wxNNHsBOByHZu3bMH8IdWz-Ce21RyfVj-N6evXXdYhzzjjUOqTcP-Gve5n4v2UmN1unGVmxesw-W5f7Gs-Z0Jpv0hxqpaebx3rPpeuGNX61_MMrcowSaJ3A-OZ69n4ZdSYXQxIqvQovqGlUIWrQUvCrRQWM4k0o3VpWMdJlxxy3XFcYwOnK6EpbIZKRWFhW_MsaIpzCqfW13gZlSqUy7UqXWxpYnyqB1SOMsKq3FxziAt32XFouWOaPAiIP6vhj0fQBH1OGbj4jwunnhry6LTn-KSgmpYq1RZkJwokTplUud1nGZlCYNYL8frqLTwmXxe84E8HrTjPpDmyK6tv66-UZxwkkigGft6G4kETJJEM7KANLBuA9EHbbU868NR3dGNP1SPP-_WK_g_nR2dlqcnuSf9mA7oqMVHK90H0arq2v7AgHPqnzZzepb97MBPw
linkToPdf http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwfV1Lb9QwEB5BEYhLxZvQAkZC3KJdx4njnKpCCVseKw6t1FvkOHZZHvHS3Vbaf8-MkywEIaQcktiRRjOemc_OPABeTp0wmRYmtrLI4hRdEKnUNNbGFIVJ1NSFA7dPczk7Td-fZWd9_NOqD6scbGIw1I03dEY-oTLluUB_VUxcHxbx-ag8WP6MqYMU_Wnt22lchxsEsqmNgyrfbTdfIgmN0zj6o1hmhezqbQqcOFl8_bEiYIHghycj_xTK-P8Le_4dQvmHTyrvwG4PJtlhJ_27cM229-Bm115ycx--dVm4rj-WY96x4JoGQ4Gfzrso8BU7btFOXdmGLVp2ZNncX3kW8jRZOaQ30tCJx3vPZpulN369-c4oho9CaR7Aafn25M0s7psrxCZVfB1bVNykQfiipeBNja4aNza5dFPVyETXBXfcct3gbkYnTjfCUlkZqZVFE9AYY8RD2Gl9ax8DM7VShXa1yq1NLc-UQTuRp0VSW4uPaQSvBpZWy66GRoV7D-J9NeJ9BK-J4dtJVPo6vPAX51WvSVWjhFSp1kgzYTlRI_XK5U7rtM5qk0ewP4ir6vVxVf1ePRG82A6jJtHvEd1afxnmKE6ISUTwqJPulhIhswyBrYwgH8l9ROp4pF18CdW6CyrYL8WT_5P1HG7hcq4-Hs8_7MHthHIsOF75PuysLy7tU0Q-6_pZWNK_AHYXBAU
openUrl ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Identification+of+Transcriptional+Networks+Involved+in+De+Novo+Organ+Formation+in+Tomato+Hypocotyl+Explants&rft.jtitle=International+journal+of+molecular+sciences&rft.au=Larriba%2C+Eduardo&rft.au=Nicol%C3%A1s-Albujer%2C+M%C3%ADriam&rft.au=S%C3%A1nchez-Garc%C3%ADa%2C+Ana+Bel%C3%A9n&rft.au=P%C3%A9rez-P%C3%A9rez%2C+Jos%C3%A9+Manuel&rft.date=2022-12-17&rft.pub=MDPI+AG&rft.issn=1661-6596&rft.eissn=1422-0067&rft.volume=23&rft.issue=24&rft.spage=16112&rft_id=info:doi/10.3390%2Fijms232416112&rft.externalDBID=HAS_PDF_LINK
thumbnail_l http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1422-0067&client=summon
thumbnail_m http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1422-0067&client=summon
thumbnail_s http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1422-0067&client=summon