Characterizing conflict and congruence of molecular evolution across organellar genome sequences for phylogenetics in land plants

Frontiers in Plant Science

Plant Science

Karolis Ramanauskas¹  Joseph F. Walker¹  Alexa S. Tyszka¹  Miles D. Woodcock-Girard¹  Eric C. Bretz¹  Drew A. Larson²  Gregory W. Stull³  Holly M. Robertson⁴ 

[1] Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States;Department of Biology, Indiana University, Bloomington, IN, United States;Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China;Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States;Sainsbury Laboratory, School of Biological Sciences, University of Cambridge, Cambridge, England, United Kingdom;

关键词: phylogenetics;    plastome;    mitochondrial genome;    chloroplast genome;    phylogenomics;    combinability;    phylogenetic conflict;   

DOI  :  10.3389/fpls.2023.1125107

 received in 2022-12-15, accepted in 2023-03-13,  发布年份 2023

来源: Frontiers

【 摘 要 】

Chloroplasts and mitochondria each contain their own genomes, which have historically been and continue to be important sources of information for inferring the phylogenetic relationships among land plants. The organelles are predominantly inherited from the same parent, and therefore should exhibit phylogenetic concordance. In this study, we examine the mitochondrion and chloroplast genomes of 226 land plants to infer the degree of similarity between the organelles’ evolutionary histories. Our results show largely concordant topologies are inferred between the organelles, aside from four well-supported conflicting relationships that warrant further investigation. Despite broad patterns of topological concordance, our findings suggest that the chloroplast and mitochondrial genomes evolved with significant differences in molecular evolution. The differences result in the genes from the chloroplast and the mitochondrion preferentially clustering with other genes from their respective organelles by a program that automates selection of evolutionary model partitions for sequence alignments. Further investigation showed that changes in compositional heterogeneity are not always uniform across divergences in the land plant tree of life. These results indicate that although the chloroplast and mitochondrial genomes have coexisted for over 1 billion years, phylogenetically, they are still evolving sufficiently independently to warrant separate models of evolution. As genome sequencing becomes more accessible, research into these organelles’ evolution will continue revealing insight into the ancient cellular events that shaped not only their history, but the history of plants as a whole.

【 授权许可】

Unknown   
Copyright © 2023 Tyszka, Bretz, Robertson, Woodcock-Girard, Ramanauskas, Larson, Stull and Walker