Table 1.

Description of differentially expressed and methylated transcription factors co-expressed with MIA genes. Expression LogFC and methylation differences are given for the most contrasting comparison.

Locus Tag	Best Hit in Uniprot Database (blastx)	% id	e-Value	Comparison	LogFC	Methylation Difference
Community 1 (GES, IS, IO, and DL7GT, T16H2, 16OMT, T3R, NMT, D4H, and DAT, vindoline-related community)
CRO_T102172	DOF56_ARATH, Dof zinc finger protein DOF5.6 (AtDOF5.6)	71.77	4 $\times {10}^{-43}$	Distal vs. Aroot	2.54	0.31
CRO_T109632	BH048_ARATH, Transcription factor bHLH48 (AtbHLH48)	40.55	3 $\times {10}^{-49}$	Root vs. Basal	−2.27	0.29
CRO_T110203	WOX1_ARATH, WUSCHEL-related homeobox 1	56.95	4 $\times {10}^{-43}$	Root vs. Yleafcat	−9.16	0.22
Community 2 (DXS1, DXS2, HDS, HDR, MECS, G10H, and 8HGO; terpene precursor community)
CRO_T107249	UNE10_ARATH, Transcription factor UNE10 (AtbHLH16) (bHLH 16)	52.71	5 $\times {10}^{-25}$	Root vs. Mleaf	−8.76	0.19
CRO_T107392	MYB06_ANTMA, Myb-related protein 306	61.43	3 $\times {10}^{-85}$	Root vs. Flower	−6.72	−0.29
CRO_T110065	UNE10_ARATH, Transcription factor UNE10 (AtbHLH16) (bHLH 16)	46.13	2 $\times {10}^{-51}$	Yleafcat vs. Aroot	2.44	0.24
Community 3 (GS1, GS2, THAS1, THAS3, and THAS4, strictosidine aglycone acting enzymes)
CRO_T110954	BH113_ARATH, Transcription factor bHLH113 (AtbHLH113)	42.74	1 $\times {10}^{-39}$	Yleafcat vs. Aroot	−1.85	0.18
Community 4 (ORCA3 and STR; control of strictosidine accumulation)
CRO_T101111	BH030_ARATH, Transcription factor bHLH30 (AtbHLH30)	40.18	5 $\times {10}^{-30}$	Root vs. Basal	2.92	−0.28
CRO_T108223	PTI6_SOLLC, Pathogenesis-related genes transcriptional activator PTI6	59.51	3 $\times {10}^{-39}$	Root vs. Yleafcat	5.66	0.26
Community 5 (SLS2 and IDI1)
CRO_T101037	PCF5_ORYSJ, Transcription factor PCF5	85.92	4 $\times {10}^{-35}$	Flower vs. Yleafcat	3.72	−0.29
CRO_T102366	BH079_ARATH, Transcription factor bHLH79 (AtbHLH79) (bHLH 79)	57.19	2 $\times {10}^{-80}$	Flower vs. Aroot	5.46	−0.24
CRO_T110108	YAB1_ARATH, Axial regulator YABBY 1 (Fl-54)	65.12	3 $\times {10}^{-82}$	Mleafcat vs. Yleafcat	−2.41	−0.32
CRO_T110248	ICE1_ARATH, Transcription factor ICE1 (AtbHLH116)	60.62	2 $\times {10}^{-102}$	Flower vs. Mleafcat	1.74	−0.26