Mitochondrial RNA editing sites affect the phylogenetic reconstruction of gymnosperms

Abstract

Plant RNA editing mainly occurs in organellar genomes, which restores evolutionarily conserved amino acids. The abundance of RNA editing sites is correlated with the diversity of PPR PLS genes, and heterogeneity of GC content and substitution rates among plant species. Since the latter two have been suggested to affect phylogenomic reconstructions, a similar scenario may also apply to the RNA editing factor. Phylogenetic relationships among gymnosperms have long been debated, especially on the position of gnetophytes. Here, we revisited the recently published RNA editing data of gymnosperms to further evaluate the impact of RNA editing sites on phylogenetic reconstruction of gymnosperms. Our results indicated that a complete exclusion of RNA editing sites recovered a sister relationship between gnetophytes and Pinaceae, which is congruent with the results based on nuclear and plastid data, but is in stark contrast to the sister relationship of gnetophytes and cupressophytes that was recovered by the original mitochondrial DNA dataset, the mitochondrial RNA editing site revised dataset, the mitochondrial degenerated codon dataset, and the mitochondrial 3 rd codon positions excluded dataset. Our findings are yet another reminder of the impact of RNA editing on mitochondrial phylogenetic reconstruction. Exclusion of RNA editing sites, rather than revision of them, should be necessary to fully mitigate the effects of RNA editing.

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