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Identification of miRNAs and Their Targets in the Liverwort Marchantia polymorpha by Integrating RNA-Seq and Degradome Analyses.

Lin, P. C., et al. · 2016 · Plant and Cell Physiology   research

doi:10.1093/pcp/pcw020   PMID:26861787   PMC4788410

Linked genes (13)  0 core 13 peripheral

Gene ID	Name	Evidence / Role	Function (this paper)
Mp1g07070	MpARF3	sequence comparator	Auxin response factor (AB981319/LW1641) identified as the predicted target of conserved Mpo-miR160.
—	MpC3HDZ1 missing	sequence comparator	CLASS III HD-ZIP gene (LW6010) identified as the predicted target of conserved Mpo-miR166a.
Mp4g12490	MpMADS1	experimental comparator	MADS-box gene (LW2328) identified as a target of Mpo-miR11687.1; cleavage supported by degradome evidence.
Mp4g11760	MpMADS2	experimental comparator	MADS-box gene (LW14289) identified as a target of Mpo-miR11681.1; cleavage supported by degradome evidence.
Mp5g03810	MpPHOT	sequence comparator	Phototropin blue-light photoreceptor gene (LW771) predicted to be targeted by Mpo-miR171-5p.2.
Mp6g03240	MpPPR_66	experimental comparator	Pentatricopeptide-repeat gene (LW9825) that generates Mpo-miR11692.1 to autoregulate its own mRNA; dual precursor/target.
Mp1g18110	MpAGO1	sequence background	Argonaute family member (LW1759) identified by homology as a core RISC/silencing-pathway component. Also reported as a miRNA target: Mpo-miR11707.1/.2 target MpAGO1.
—	MpAGO4 missing	sequence background	Second Argonaute protein (LW8524) identified by sequence homology alongside MpAGO1 as part of the gene-silencing machinery.
—	MpDCL1 missing	sequence background	DICER-LIKE homolog (LW6271) with high similarity to AtDCL1, identified as the pri-miRNA processing component of the pathway.
—	MpDRB2 missing	sequence background	dsRNA-binding protein ortholog (LW1470) identified by homology as a miRNA-pathway silencing component.
—	MpNRPD2A missing	sequence background	RNA polymerase subunit ortholog (LW8690) identified by homology within the silencing-pathway gene survey.
—	MpRDR6 missing	sequence background	RNA-dependent RNA polymerase ortholog (LW8437) identified by homology, implicated in secondary siRNA production.
—	MpSGS3 missing	sequence background	SGS3 ortholog (LW4624) found among flowering-plant gene-silencing components, implicated in phased siRNA biogenesis.