Genome-wide landscape of m 6 A regulatory genes in Marchantia polymorpha : conservation, diversification, and expression dynamics
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Background
N 6 -Methyladenosine (m 6 A) regulates RNA fate in flowering plants, but the repertoire and expression patterns of m 6 A-related genes remain incompletely characterized in liverworts. Here, we characterized these gene families in the liverwort Marchantia polymorpha within a comparative framework spanning diverse plant lineages.
Results
A comparative survey of 119 plant genomes using sequence similarity and conserved-domain criteria identified 18 candidate m 6 A-related loci in M. polymorpha , comprising seven writer-related genes, five AlkB homolog genes, and six YTH- or CPSF30-related genes. Across the surveyed genomes, canonical writer components generally had low copy numbers, whereas AlkB homolog and reader-related families showed greater copy-number variation. Phylogenetic and domain analyses supported the family assignments of the M. polymorpha candidates. Eight of the 18 candidate loci showed detectable collinearity with Marchantia quadrata . Putative promoter analysis identified motifs annotated as hormone-, light-, and stress-responsive, with hormone-responsive motifs accounting for the largest share of predicted sites. Public transcriptome analysis revealed variation in candidate gene expression across developmental stages and tissues. Quantitative reverse-transcription PCR showed higher transcript abundance for all six YTH- or CPSF30-related genes in thalli than in gemmae or gemma cups. Cold, heat, osmotic, salt, and dark treatments elicited gene-specific expression responses. Darkness increased transcript abundance of several candidates, including MpMTA , MpALKBH1A , and MpECT2 . A predicted protein-association network suggested links between subsets of the candidates and RNA-processing proteins.
Conclusions
These findings define a candidate m 6 A-related gene repertoire in M. polymorpha and identify tissue- and stress-responsive genes for targeted functional studies of RNA methylation in this liverwort.
