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

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.