J Syst Evol

• Research Articles •    

Exploring the impact of RNA editing on mitochondrial phylogenetic analyses in liverworts, an early land plant lineage

Shan-Shan Dong1, Hong-Lei Li2, Bernard Goffinet3, and Yang Liu1*   

  1. 1Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen 518004, China

    2Chongqing Key Laboratory of Economic Plant Biotechnology/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing 402160, China

    3Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA

  • Received:2020-06-04 Accepted:2020-11-05

Abstract:

Plant mitochondrial protein-coding genes are slow-evolving, and thus are less subjected to substitution saturation, and therefore perhaps more suitable for resolving deep relationships of high taxonomic categories. Plant mitochondrial genes hold, however, hundreds of RNA editing sites, involving mostly non-synonymous substitutions in the 1st and 2nd codon positions, which has been reported to affect phylogenetic reconstructions. We have previously identified ca. 4,700 mitochondrial RNA editing sites within a group of liverworts representing the ordinal diversity of liverworts, allowing us to critically evaluate the impacts of RNA editing sites on phylogenetic reconstructions in liverworts. Our phylogenetic inferences are mostly congruent on topology inferred from the original mitochondrial gene dataset, dataset with RNA editing sites corrected, and dataset with RNA editing sites excluded. RNA editing site excluded dataset recovered a topology identical to that of the RNA editing site corrected dataset, supporting the sister relationship of Ptilidium and Jungermanniales, whereas the original dataset supported the sister relationship of Ptilidium and Jungermanniidae. The controversial placements of Ptilidium could be explained by site-wise log-likelihood analysis as the majority of liverwort RNA editing sites support the sister relationship of Ptilidium and Jungermanniidae, hence the correction or exclusion of the RNA editing sites changed the tree topology and supported the sister relationship of Ptilidium and Jungermanniales. Our study shows that RNA editing sites potentially impact phylogenetic analyses, suggesting either genome or transcriptome derived data should be used with caution for phylogenetic reconstruction with genes hosting vast numbers of RNA editing sites like plant organellar genes.

Key words: Phylogenetic inferences, Site likelihood, Jungermanniales, Jungermanniidae, Ptilidium