REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and virus strains
Agrobacterium tumefaciens c58 GV3101 pMP90	Koncz and Schell34	N/A
Escherichia coli DH5α	N/A	N/A
Chemicals, peptides, and recombinant proteins
17-β-oestradiol (17-β)	Sigma-Aldrich	Cat# 3301
6-benzylaminopurine (BAP)	Sigma-Aldrich	Cat# B3408
Cycloheximide (CHX)	Sigma-Aldrich	Cat#C7698
DdeI (HpyF3I)	ThermoFisher	Cat# FD1884
Dimethyl Sulfoxide (DMSO)	Sigma-Aldrich	Cat# D8418
DL-Phosphinothricin (PPT)	Duchefa Biochemie	Cat# P0159.1000
Dream Taq DNA Polymerase	ThermoFisher	Cat# EP0713
DNase I	ThermoFisher	Cat# EN0521
FTA Classic Card	Sigma-Aldrich	Cat# WHAWB120206
Gateway LR Clonase II Plus enzyme	ThermoFisher	Cat# 12538120
Hygromycin B Gold	InvivoGen	Cat# ant-hg-1
Maxima H Minus Reverse Transcriptase	ThermoFisher	Cat# EP0752
Murashige & Skoog medium	Murashige and Skoog35 and Duchefa Biochemie	Cat# M 0222.0050
NotI	ThermoFisher	Cat# FD0595
Oligo(dT)18 Primer	ThermoFisher	Cat# SO132
Phusion High-Fidelity DNA Polymerase	ThermoFisher	Cat# F530L
RiboLock RNase Inhibitor	ThermoFisher	Cat# EO0382
Rifampicin	Duchefa Biochemie	Cat# R0146
Ruthenium red	Fluka	Cat# 84071
ScaI	ThermoFisher	Cat# FD0434
SCRI Renaissance 2200 Stain	Renaissance Chemicals	N/A
Sodium deoxycholate	Sigma-Aldrich	Cat# 30970
Solis Biodyne 5x HOT FIREPol EvaGreen qPCR Mix Plus	Solis Biodyne	Cat# 08-25-00001
Spectinomycin	Duchefa Biochemie	Cat# S0188
Toluidine blue O	Sigma-Aldrich	Cat# T3260
Urea	Sigma-Aldrich	Cat# U0631
Xylitol	Sigma-Aldrich	Cat# X3375
Critical commercial assays
GeneJET GEL Extraction Kit	ThermoFisher	Cat# K0692
GeneJET Plant RNA purification kit	ThermoFisher	Cat# K0802
GeneJET Plasmid Miniprep Kit	ThermoFisher	Cat# K0503
Heat & Run gDNA removal kit	ArticZymes	SKU# 80200-50
Plant Ribo-Zero rRNA Removal Kit	Illumina	Cat# MRZSR116
TruSeq Stranded Total RNA HT Sample Prep Kit (with Ribo-Zero Plant)	Illumina	Cat# RS-122-2403
Deposited data
RNA-seq data files	BioProject	PRJNA684618
Experimental models: Organisms/strains
Arabidopsis: Col-0	Nottingham Arabidopsis Stock Centre	N/A
Arabidopsis: TCSnpro:nYFP	Vatén et al.18	N/A
Arabidopsis: TCSnpro:erYFP	This manuscript	N/A
Arabidopsis: ARR5pro:erYFP	Siligato et al.36	N/A
Arabidopsis: LBD1pro:erYFP	This manuscript	N/A
Arabidopsis: LBD3pro:erYFP	This manuscript	N/A
Arabidopsis: LBD4pro:erYFP	This manuscript	N/A
Arabidopsis: LBD11pro:erYFP	This manuscript	N/A
Arabidopsis: ipt1;3;5;7	Miyawaki et al.23	N/A
Arabidopsis: arr1-3;arr10-5	Argyros et al.37	N/A
Arabidopsis: arr1-3;arr12-1	Argyros et al.37	N/A
Arabidopsis: lbd1c	This manuscript	N/A
Arabidopsis: lbd3c	This manuscript	N/A
Arabidopsis: lbd4c	This manuscript	N/A
Arabidopsis: lbd11c	This manuscript	N/A
Arabidopsis: lbd3c;lbd4c	This manuscript	N/A
Arabidopsis: lbd1c;lbd11c	This manuscript	N/A
Arabidopsis: lbd1c;lbd3c;lbd4c	This manuscript	N/A
Arabidopsis: lbd3c;lbd4c;lbd11c	This manuscript	N/A
Arabidopsis: lbd1c;lbd3c;lbd4c;lbd11c	This manuscript	N/A
Arabidopsis: tdr	Hirakawa et al.24	N/A
Arabidopsis: wox4	Hirakawa et al.24	N/A
Arabidopsis: tdr;wox4	Hirakawa et al.24	N/A
Arabidopsis: lbd3c;lbd4c;wox4	This manuscript	N/A
Arabidopsis: lbd3c;lbd4c;lbd11c;tdr	This manuscript	N/A
Arabidopsis: 35S:XVE≫cLBD1	This manuscript	N/A
Arabidopsis: 35S:XVE≫cLBD3	This manuscript	N/A
Arabidopsis: 35S:XVE≫cLBD4	This manuscript	N/A
Arabidopsis: 35S:XVE≫cLBD11	This manuscript	N/A
Arabidopsis: 35S:XVE≫CKX7-RFP	This manuscript	N/A
Arabidopsis: TCSnpro:nYFP;35S:XVE≫CKX7-RFP	This manuscript	N/A
Arabidopsis: LBD3pro:erYFP;35S:XVE≫CKX7-RFP	This manuscript	N/A
Arabidopsis: LBD4pro:erYFP;35S:XVE≫CKX7-RFP	This manuscript	N/A
Arabidopsis: LBD3pro:gLBD3-YFP;lbd3c;lbd4c	This manuscript	N/A
Arabidopsis: LBD4pro:gLBD4-YFP;lbd3c;lbd4c	This manuscript	N/A
Arabidopsis: LBD11pro:gLBD11-YFP;lbd1c;lbd3c;lbd4c;lbd11c	This manuscript	N/A
Arabidopsis: ARR5pro:erYFP;35S:XVE≫cLBD3	This manuscript	N/A
Arabidopsis: TCSnpro:nYFP;35S:XVE≫cLBD3	This manuscript	N/A
Oligonucleotides
See Table S1	N/A	N/A
Recombinant DNA
pDONRP41R	ThermoFisher	N/A
p1R4z-LBD1pro	This manuscript	N/A
p1R4z-LBD3pro	This manuscript	N/A
p1R4z-LBD4pro	This manuscript	N/A
p1R4z-LBD11pro	This manuscript	N/A
p221z-erYFP	Siligato et al.36	N/A
p2R3a-nosT	Siligato et al.36	N/A
pBm43GW	Siligato et al.36	N/A
pHm43GW	Siligato et al.36	N/A
pDONR221	ThermoFisher	N/A
p1R4-35S:XVE	Siligato et al.36	N/A
p1R4z-TCSnpro	This manuscript	N/A
pHm43GW-pTCSn:erYFP	This manuscript	N/A
p221z-cLBD1	This manuscript	N/A
p221z-cLBD11	This manuscript	N/A
pBm43GW-35S:XVE≫cLBD3	Zhang et al.10	N/A
pBm43GW-35S:XVE≫cLBD4	Zhang et al.10	N/A
pBm43GW-35S:XVE≫cLBD1	This manuscript	N/A
pBm43GW-35S:XVE≫cLBD11	This manuscript	N/A
p221z-CKX7	This manuscript	N/A
2R3z-tagRFP	Siligato et al.36	N/A
pCAM-kan-R4R3	Siligato et al.36	N/A
pCAM-kan-R4R3-35S:XVE≫CKX7-RFP	This manuscript	N/A
pHEE2E-TRI	Wang et al.38	N/A
2R3z-Bsa I-ccdB-Bsa I	Wang et al.39	N/A
p221z-zCas9- rbcS-E9t	This manuscript	N/A
p1R4- pEC1.2en EC1.1p	This manuscript	N/A
p2R3z-AtU3b-sgRNALBD1+AtU3d-sgRNALBD3+ AtU6-1-sgRNALBD4+AtU6-29-sgRNALBD4	This manuscript	N/A
pEC1.2en EC1.1p:zCas9- rbcS-E9t-AtU3b-sgRNALBD1+AtU3d-sgRNALBD3+ AtU6-1-sgRNALBD4+AtU6-29-sgRNALBD4	This manuscript	N/A
pHEE2E-TRI-LBD4	This manuscript	N/A
p221z-gLBD3	This manuscript	N/A
p221z-gLBD4	This manuscript	N/A
p221z-gLBD11	This manuscript	N/A
pBm43GW-LBD3pro:gLBD3-YFP	This manuscript	N/A
pBm43GW-LBD4pro:gLBD4-YFP	This manuscript	N/A
pBm43GW-LBD11pro:gLBD11-YFP	This manuscript	N/A
Software and algorithms
Chipster v3.11- v3.16	Kallio et al.40	https://chipster.csc.fi/; RRID: SCR_010939
Clustal X 2.1	Larkin et al.41	http://www.clustal.org/clustal2/; RRID: SCR_017055
clusterProfiler v3.16.1	Yu et al.42	http://bioconductor.org/packages/release/bioc/html/clusterProfiler.html; RRID: SCR_016884
CorelDRAW Graphics Suite 2020	CorelDRAW	http://www.coreldraw.com/en/product/graphic-design-software/; RRID: SCR_014235
dCAPs Finder v2.0	Neff et al.43	http://helix.wustl.edu/dcaps/
DESeq2	Love et al.44	https://bioconductor.org/packages/release/bioc/html/DESeq2.html; RRID: SCR_015687
FastQC v0.11.3	Andrews45	https://www.bioinformatics.babraham.ac.uk/projects/fastqc/; RRID: SCR_014583
FIJI ImageJ v1.52	Schindelin et al.46	https://fiji.sc/; RRID: SCR_002285
ggplot2 v3.3.2	Wickham47	https://cran.r-project.org/web/packages/ggplot2/index.html; RRID: SCR_014601
gplots v3.1.0	Warnes et al.48	https://cran.r-project.org/web/packages/gplots/index.html
HTSeq	Anders et al.49	https://htseq.readthedocs.io/en/release_0.9.1/; RRID: SCR_005514
Leica Application Suite X	Leica Microsystems	https://www.leica-microsystems.com/products/microscope-software/p/leica-las-x-ls/; RRID: SCR_013673
Leica LAS AF Lite 2.6.x	Leica Microsystems	https://leica-las-af-lite.software.informer.com/2.6/
MEGA7	Kumar et al.50	https://megasoftware.net/; RRID: SCR_000667
R v4.0.2	The R Development Core Team51	https://www.r-project.org/
RStudio v1.4.1106	Racine52	https://www.rstudio.com/; RRID: SCR_000432
SPSS Statistics 26	IBM	https://www.ibm.com/products/spss-statistics; RRID: SCR_019096
TopHat2	Kim et al.53	http://ccb.jhu.edu/software/tophat/index.shtml; RRID: SCR_013035
Venny v2.1.0	Oliveros54	https://bioinfogp.cnb.csic.es/tools/venny/; RRID: SCR_016561
Other
GENEWIZ	GENEWIZ	https://www.genewiz.com/
Bioanalyzer 2100	Agilent Technologies	https://www.agilent.com/cs/library/posters/Public/BioAnalyzer.PDF; RRID: SCR_019715
Leica DM2500 microscope	Leica Microsystems	https://www.leica-microsystems.com/products/light-microscopes/p/leica-dm2500/; RRID: SCR_020224
Leica M165 FC fluorescent stereo microscope	Leica Microsystems	https://www.leica-microsystems.com/products/stereo-microscopes-macroscopes/p/leica-m165-fc/
Leica Stellaris 8 confocal microscope	Leica Microsystems	https://www.leica-microsystems.com/products/confocal-microscopes/p/stellaris-8/
Leica TCS SP5 II confocal microscope	Leica Microsystems	https://downloads.leica-microsystems.com/Leica%20TCS%20SP5%20II/Brochures/Leica%20TCS_SP5_II-Brochure_Technical_Data.EN.pdf; RRID: SCR_018714
NanoDrop 1000 Spectrophotometer	ThermoFisher	http://tools.thermofisher.com/content/sfs/manuals/nd-1000-v3.8-users-manual-8%205x11.pdf; RRID: SCR_016517