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We performed differential gene expression (DGE) and co-expression analyses with genes encoding components of hormonal signaling pathways and the ∼400 annotated transcription factors (TFs) of  M. polymorpha  across multiple developmental stages of the life cycle. We identify a putative auxin-related co-expression module that has significant overlap with transcripts induced in auxin-treated tissues. Consistent with phylogenetic and functional studies, the class C ARF, Mp ARF3 , is not part of the auxin-related co-expression module and instead is associated with transcripts enriched in gamete-producing gametangiophores. We analyze the Mp arf3  and Mp miR160  mutant transcriptomes in the context of coexpression to suggest that Mp ARF3  may antagonize the reproductive transition via activating the Mp MIR11671  and Mp MIR529c  precursors whose encoded microRNAs target  SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE  (SPL) transcripts of Mp SPL1  and Mp SPL2 . Both Mp SPL  genes are part of the Mp ARF3  co-expression group corroborating their functional significance. We provide evidence of the independence of Mp ARF3  from the auxin-signaling module and provide new testable hypotheses on the role of auxin-related genes in patterning meristems and differentiation events in liverworts.

frontiers in plant science

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