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Evolution of mitochondrial RNA editing sites and stop codon-lacking transcripts in angiosperms.

Runxian Yu1,2,3, Lumei Liu1,2,3, Matthias Jost4

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Communications Biology
|July 2, 2025
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Angiosperm mitochondrial RNA editing sites were analyzed, revealing magnoliids retain ancestral sites. Researchers also found novel motifs linked to stop codon-lacking transcripts, predating angiosperm divergence.

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Area of Science:

  • Plant Molecular Biology
  • Genomics
  • Evolutionary Biology

Background:

  • Mitochondrial protein-coding gene evolution in angiosperms is well-studied.
  • Post-transcriptional RNA processing in angiosperm mitochondria is underexplored.

Purpose of the Study:

  • To systematically infer RNA editing site gain-and-loss dynamics in angiosperm mitochondrial protein-coding genes.
  • To investigate the prevalence and mechanisms of stop codon-lacking transcripts.

Main Methods:

  • Analysis of newly generated and public RNA-sequencing data from 20 angiosperm species.
  • Inference of RNA editing site dynamics.
  • Identification of RNA sequence motifs associated with RNA processing.

Main Results:

  • Magnoliids exhibit a higher retention of ancestral RNA editing sites compared to monocots and eudicots.
  • Contrasting correlations between gene expression and RNA editing density were observed (negative for core genes, positive for variable genes).
  • Widespread occurrence of stop codon-lacking transcripts for ccmC, nad6, sdh3, and sdh4 genes across angiosperms was identified, with novel motifs implicated in their processing.

Conclusions:

  • The study illuminates ancestral RNA editing characteristics in angiosperm mitochondrial genes.
  • Evidence suggests that processing-derived stop codon-lacking transcripts existed before angiosperm divergence.