AUTHOR=Flores-Sandoval Eduardo , Romani Facundo , Bowman John L. 

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

JOURNAL=Frontiers in Plant Science

VOLUME=9

YEAR=2018

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2018.01345

DOI=10.3389/fpls.2018.01345

ISSN=1664-462X

ABSTRACT=<p>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 <italic>M. polymorpha</italic> 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<italic>ARF3</italic>, 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<italic>arf3</italic> and Mp<italic>miR160</italic> mutant transcriptomes in the context of coexpression to suggest that Mp<italic>ARF3</italic> may antagonize the reproductive transition via activating the Mp<italic>MIR11671</italic> and Mp<italic>MIR529c</italic> precursors whose encoded microRNAs target <italic>SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE</italic> (SPL) transcripts of Mp<italic>SPL1</italic> and Mp<italic>SPL2</italic>. Both Mp<italic>SPL</italic> genes are part of the Mp<italic>ARF3</italic> co-expression group corroborating their functional significance. We provide evidence of the independence of Mp<italic>ARF3</italic> 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.</p>