Table 1 Differentially regulated transcripts in DRNL::GFP-positive protoplasts (fold change ≥ 1.5; p ≤ 0.01) compared to DRNL::GFP− protoplasts that have functions associated with meristem maintenance and identity, polarity, boundary formation, hormones, vasculature, epigenetic changes and that generate miRNAs

  ASYMMETRIC LEAVES2

AS2

At1g65620

+2.55

  FLOWERING PROMOTING FACTOR1

FPF1

At5g24860

+2.38

  SHORT VEGETATIVE PHASE

SVP

At2g22540

+2.16

  REPRODUCTIVE MERISTEM1

REM1

At3g19184

+2.10

  AINTEGMUMENTA

ANT

At4g37750

+2.08

  LEAFY

LFY

At5g61850

+1.98

  AINTEGUMENTA-LIKE6

AIL6

At5g10510

+1.96

  PISTILLATA

PI

At5g20240

+1.93

  REGULATOR OF AXILLARY MERISTEMS1/MYB37

RAX1

At5g23000

+1.86

  BASIC PENTACYSTEINE 3

BPC3

At1g68120

+1.85

  UNUSUAL FLORAL ORGANS

UFO

At1g30950

+1.85

  BRCA1-ASSOCIATED RING DOMAIN1

BARD1

At1g04020

+1.83

  CAULIFLOWER

CAL

At1g26310

+1.82

  REPRODUCTIVE MERISTEM3

REM3

At5g58280

+1.82

  LATERAL MERISTEM IDENTITY1

LMI1

At5g03790

+1.79

  ULTRAPETALA1

ULT1

At4g28190

+1.77

  APETALA1

AP1

At1g69120

+1.60

  LATERAL MERISTEM IDENTITY2

LMI2

At3g61250

+ 1.55

  TUBBY8

TUB8

At1g16070

+1.52

  SHOOTMERISTEMLESS

STM

At1g62360

−1.54

  BARELY ANY MERISTEM3

BAM3

At4g20270

−2.89

  BREVIPEDICELLUS/KNAT1

BP

At4g08150

−3.57

  YABBY5

YAB5

At2g26580

+14.01

  NUBBIN

NUB

At1g13400

+5.81

  BLADE-ON-PETIOLE2

BOP2

At2g41370

+ 5.44

  BLADE-ON-PETIOLE1

BOP1

At3g57130

+ 5.19

  FILAMENTOUS FLOWER (YABBY1)

FIL

At2g45190

+4.37

  JAGGED

JAG

At1g68480

+ 3.32

  PUCHI

PUCHI

At5g18560

+ 3.25

  KNOX ARABIDOPSIS THALIANA MEINOX

KNATM

At1g14760

+3.17

  HOMEOBOX GENE1

ATH1

At4g32980

+2.90

  PRESSED FLOWER

PRS

At2g28610

+2.40

  YABBY3

YAB3

At4g00180

+2.14

  ETTIN

ETT

At2g33860

+1.87

  KANADI3

KAN3

At4g17695

−3.52

  SUPERMAN

SUP

At3g23130

+3.07

  JAGGED LATERAL ORGANS (LBD30)

JLO

At4g00220

+2.38

  LATERAL BOUNDARY DOMAIN18

LBD18

At2g45420

+2.21

  GROWTH REGULATING FACTOR2

GRF2

At4g37740

+1.95

  GROWTH REGULATING FACTOR5

GRF5

At3g13960

+1.86

  LATERAL ORGAN JUNCTION

LOJ

At2g39230

+1.68

  GROWTH REGULATING FACTOR1

GRF1

At2g22840

+1.63

  CUP-SHAPED COTYLEDON1

CUC1

At3g15170

+1.54

  PETAL LOSS

PTL

At5g03680

−1.63

  LATERAL ORGAN BOUNDARY

LOB

At5g63090

−8.87

  MONOPTEROS

MP

At1g19850

+1.67

  IAA CARBOXYLMETHYLTRANSFERASE1

IAMT 1

At5g55250

−4.64

  BRI1-LIKE1

BRL1

At1g55610

+1.59

  BR ENHANCED EXPRESSION2

BEE2

At4g36540

−3.97

  BR ENHANCED EXPRESSION1

BEE1

At1g18400

−8.15

  HISTIDINE PHOSPHOTRANSFER PROTEIN6

AHP6

At1g80100

+18.08

  ISOPENTENYLTRANSFERASE7

IPT7

At3g23630

−7.25

  ISOPENTENYLTRANSFERASE3

IPT3

At3g63110

−13.47

  GIBBERELLIN OXIDASE3

GA3ox3

At4g21690

+4.13

  GIBBERELLIN 2-OXIDASE4

GA2ox4

At1g47990

+3.24

  GIBBERELLIN 20-OXIDASE2

GA20ox2

At5g51810

+2.16

  GIBBERELLIN 3-OXIDASE1

GA3ox1

At1g15550

+1.97

  GIBBERELLIN 2-OXIDASE2

GA2ox2

At1g30040

+1.58

  SHI-RELATED SEQUENCE4

SRS4

At2g18120

+3.61

  STYLISH1

STY1

At3g51060

+2.74

  SHI-RELATED SEQUENCE7

SRS7

At1g19790

+2.21

  INFLORESCENCE DEFICIENT IN ABSCISSION (IDA)-LIKE 2

IDL2

At5g64667

+1.93

  SHORT INTERNODES

SHI

At5g66350

+1.92

  TAS3A

At3g17185

−2.21

  MiR390A

At2g38325

−2.73

  MiR159/159B

At1g18075

−2.86

  MiR172D

At3g55512

−3.06

  MiR156E

At5g11977

−3.20

  MiR172/172B

At5g04275

−5.55

  MiR164/164B

At5g01747

−5.88

  MiR319/319B

At5g41663

−6.29

  MiR160/160C

At5g46845

−8.44

  MiR156C

At4g31877

−11.49

  MiR172/172A

At2g28056

−21.01

  EPIDERMALPATTERNING LIKE FACTOR-LIKE 6

EPFL6

At2g30370

−2.26

  REDUCED IN LATERAL GROWTH1

RUL1

At5g05160

−2.44

  TDIF-RECEPTOR/PHLOEM INTERCALATED WITH XYLEM

TDR/PXY

At5g61480

−2.81

  CLAVATA3/EMBRYO SURROUNDING REGION41

CLE41

At3g24770

−2.84

  XYLEM CYSTEINE PEPTIDASE1

XCP1

At4g35350

−3.02

  CLAVATA3/EMBRYO SURROUNDING REGION44

CLE44

At4g13195

−3.24

  HIGH CAMBIAL ACTIVITY2

HCA2

At5g62940

−6.05

  NAC SECONDARY WALL THICKENING PROMOTING FACTOR1

NST1

At2g46770

−6.45

  VASCULAR RELATED NAC DOMAIN6

VND6

At5g62380

−7.53

  VASCULAR RELATED NAC DOMAIN7

VND7

At1g71930

−7.76

  XYLEM CYSTEINE PEPTIDASE2

XCP2

At1g20850

−7.86

  WUSCHEL-RELATED HOMEOBOX4

WOX4

At1g46480

−23.91

  DECREASED DNA METHYLATION1

DDM1

At5g66750

+1.91

  SET DOMAIN GROUP4

SDG4

At4g30860

+1.82

  VARIANT IN METHYLATION2

VIM2

At1g66050

+1.78

  VARIANT IN METHYLATION6

VIM6

At4g08590

+1.77

  VARIANT IN METHYLATION1

VIM1

At1g57820

+1.75

  VARIANT IN METHYLATION3

VIM3

At5g39550

+1.73

  DNA METHYLTRANSFERASE1

MET1

At5g49160

+1.71

  CHROMOMETHYLASE3

CMT3

At1g69770

+1.63

  KRYPTONITE

KYP

At5g13960

+1.53

  SET DOMAIN PROTEIN35

SDG35

At1g26760

+1.52

  DEMETER-LIKE PROTEIN3

DML3

At4g34060

−4.58