MarpolBase - Co-expression and Transcriptome Analysis of Marchantia polymorpha Transcription Factors Supports Class C ARFs as Independent Actors of an Ancient Auxin Regulatory Module.

Co-expression and Transcriptome Analysis of Marchantia polymorpha Transcription Factors Supports Class C ARFs as Independent Actors of an Ancient Auxin Regulatory Module.

Flores-Sandoval, E., et al. · 2018b · Frontiers in Plant Science research

doi:10.3389/fpls.2018.01345 PMID:30327658 PMC6174852

Linked genes (20) 2 core 18 peripheral

Gene ID	Name	Evidence / Role	Function (this paper)
Mp1g07070	MpARF3	experimental subject	Central subject of the study as the class C ARF. DGE analysis (edgeR and DESeq2) was performed on Mparf3/Mpmir160 CRISPR gain- and loss-of-function mutant transcriptomes, supporting class C ARFs as independent actors of an ancient auxin regulatory module.
Mp1g26670	MpMIR160	experimental subject	miR160 precursor functionally manipulated via CRISPR (Mpmir160 mutants) and analyzed by DGE alongside Mparf3; targets the class C ARF MpARF3, defining the studied regulatory module.
Mp2g08260	MpB3-8	sequence comparator	B3-domain TF noted via Arabidopsis ortholog comparison (ABA response) and listed among enriched DEGs.
Mp2g03850	MpGRAS4	sequence comparator	Described as the LAS ortholog in cross-species comparison of meristem-related TFs.
Mp1g22880	MpGRAS8	sequence comparator	GRAS-family gene from an uncharacterized GRAS lineage noted via sequence/phylogenetic context and DEG values.
Mp1g10020	MpSPL1	sequence comparator	miRNA target (MpmiR11671) reported as orthologous to Arabidopsis SPL8 in cross-species comparison.
Mp1g10030	MpSPL2	sequence comparator	miRNA target (MpmiR529c) reported as orthologous to Arabidopsis SPL3-5 in cross-species comparison.
Mp3g23300	MpBNB	experimental tool	Used as a known marker gene to validate a co-expression group given its role in promoting gametangiophore formation irrespective of sex.
Mp1g12750	MpARF1	citation background	Cited as the class A ARF required to elicit physiological and transcriptional responses to exogenous auxin; not newly studied here.
Mp4g11820	MpARF2	citation background	Mentioned as the uncharacterized class B ARF regarded as a transcriptional repressor; only referenced as background.
Mp3g19670	MpBBX3	experimental background	B-box zinc finger gene listed among differentially expressed genes (logFC 8.4, logCPM 5.7) in co-expression analysis.
Mp2g24200	MpC2HDZ	experimental background	Auxin-inducible class II HD-ZIP gene reported with logFC/logCPM values in expression analysis; measured only, not functionally tested.
Mp8g16900	MpGRF	experimental background	Detected in expression/co-expression analysis as highly expressed early in sporeling germination; no functional experiment performed.
Mp3g05470	MpMIR529C	experimental background	miR precursor identified by DESeq2 as activated by MpARF3 in co-expression/DGE analysis; not functionally mutated.
Mp2g07720	MpNAC1	experimental background	CUP-SHAPED COTYLEDON ortholog enriched in the differentially expressed gene set.
Mp2g22250	MpRAV	experimental background	RAV-like B3-domain TF listed among enriched DEGs (logFC 1.71, logCPM 3.32) in co-expression analysis.
Mp1g19590	MpTCP2	experimental background	Class II TCP TF listed in DEG/co-expression tables (logFC 11.89, logCPM 5.02).
Mp1g09500	MpWIP	citation background	Cited as a characterized auxin-inducible IDDL-like zinc finger TF essential for air pore differentiation; background only.
Mp7g06550	MpWRKY10	experimental background	WRKY TF listed among DEGs (logFC 5.25, logCPM 4.32), up-regulated in apical cells.
Mp8g08780	MpYUC2	experimental background	Auxin biosynthetic gene appearing in co-expression and expression analyses; noted as up-regulated in sporelings, not functionally manipulated.