Extreme plastid RNA editing may confound phylogenetic reconstruction: A case study of Selaginella (lycophytes)

Abstract

Cytidine-to-uridine (C-to-U) RNA editing is common in coding regions of organellar genomes throughout land plants. In most cases RNA editing alters translated amino acids or creates new start codons, potentially confounds phylogenetic reconstructions. In this study, we used the spike moss genus Selaginella (lycophytes), which has the highest frequency of RNA editing, as a model to test the effects of extreme RNA editing on phylogenetic reconstruction. We predicted the C-to-U RNA editing sites in coding regions of 18 Selaginella plastomes, and reconstructed the phylogenetic relationships within Selaginella based on three data set pairs consisted of plastome or RNA-edited coding sequences, first and second codon positions, and translated amino acid sequences, respectively. We predicted between 400 and 3100 RNA editing sites of 18 Selaginella plastomes. The numbers of RNA editing sites in plastomes were highly correlated with the GC content of first and second codon positions, but not correlated with the GC content of plastomes as a whole. Contrast phylogenetic analyses showed that there were substantial differences (e.g., the placement of clade B in Selaginella ) between the phylogenies generated by the plastome and RNA-edited data sets. This empirical study provides evidence that extreme C-to-U RNA editing in the coding regions of organellar genomes alters the sequences used for phylogenetic reconstruction, and might even confound phylogenetic reconstruction. Therefore, RNA editing sites should be corrected when plastid or mitochondrial genes are used for phylogenetic studies, particularly in those lineages with abundant organellar RNA editing sites, such as hornworts, quillworts, spike mosses, and some seed plants.

Plastid Phylogenomics and Plastomic Diversity of the Extant Lycophytes

“…As suggested in Figure 4, different taxonomic groups have different RNA editing types and numbers. Selaginellaceae plastomes show high levels of C-to-U RNA editing, consistent with the high occurrence of C-to-U RNA editing reported in Selaginella plastomes [71,72]. By contrast, we found that Lycopodiaceae mainly shows U-to-C RNA editing, and two completely different clades are present in Isoëtaceae plastomes: one shows almost all C-to-U editing, and the other shows two types coexist.…”

“…Therefore, Isoëtaceae plastomes with slower base substitution rates are more likely to retain more RNA-editing sites than Lycopodiaceae plastomes ( Figure 3 and Figure 4 ). However, given the particularity of the high occurrence of RNA editing in both Selaginella plastid and mitochondrial genomes [ 66 , 71 , 72 ], this model cannot account for the RNA editing of Selaginellaceae. Instead, some site recognition factors for editing events in the Selaginella genome may be associated with the abundance of organelle RNA editing [ 74 ].…”

The Cycas genome and the early evolution of seed plants

“…This conflict arising from the mitochondrial data cannot be explained by the presence of extensive RNA editing sites in the mitochondrial data (Fig. 1c ), which in some cases has been reported to bias phylogenetic inferences 25 , 26 , and instead may be best explained by incomplete lineage sorting, which is supported by our PhyloNet 27 and coalescent analyses of nuclear genes (Supplementary Note 5 ).…”

Uncovering the hidden diversity of the rosette‐forming Selaginella tamariscina group based on morphological and molecular data

“…Spring (Oldenkott & al., 2014). Du & al. (2020) proposed that the extreme RNA editing frequency might confound phylogenetic reconstruction and recommended to restore RNA editing sites when using organellar genes with abundant RNA editing sites in phylogenetic studies.…”

“…RNA editing sites prediction. -Massive cytidine-touridine (C-to-U) RNA editing sites have been reported in the Selaginella chloroplast genomes (Oldenkott & al., 2014;Smith, 2020;Shim & al., 2021), which might confound phylogenetic reconstruction (Du & al., 2020). We extracted proteincoding sequences (CDS) of the chloroplast genomes using Geneious v.11.1.4 (Kearse & al., 2012) and then predicted the C-to-U RNA editing sites using the online tool PREPACT 3 (Lenz & al., 2018) under BLASTX mode with S. uncinata plastid protein database as reference.…”