This Research Topic is part of the article collection series - Rise to the Challenges in Plastome Phylogenomics.

The plastome, with its quadripartite organization and encoding about 114 unique genes, earned its reputation in plant phylogenomics for the ease of obtaining and handling plastome data as well as its considerable phylogenetic information content. The power of plastome phylogenomics has been exemplified by reconstructing deep phylogenetic relationships, deducing reticulate evolutionary histories, or phylogenetically placing taxa.

Despite the upsurge in popularity, decades of studies have raised controversy on the advantages and shortcomings of plastome phylogenomics. Features such as the inheritance characteristics of plastomes, recombination, gene transfer, or specific evolutionary patterns may result in limited or, even worse, wrong inferences. Whereas tree discordances often are the primary indication for such problems, the underlying mechanisms need to be more extensively explored. The challenges and possible workarounds for such issues with plastome data have to be addressed clearly and it is essential to show in which situations plastome phylogenomics can contribute and to find explanations for situations where plastome phylogenomics fail to do so.

In this Research Topic, we would like to collect studies conducting solid and thorough plastome phylogenomics throughout the plant tree of life. Comprehensive evaluation of the plastome data includes, but is not limited to, tackling substitution rate heterogeneity within plastome or among plant lineages, comparing tree discordance with nuclear gene results, revealing biological and computational factors affecting tree topologies, or developing novel analytical approaches. Based on the thus solidly inferred phylogenetic relationships, evolutionary issues of plant groups may be further discussed.

We welcome submissions of all article types accepted in Frontiers in Plant Science. Themes of interest include the following but are not limited to:
• Development of new analysis methods to reconstruct the correct phylogenetic tree based on the plastome data.
• Identify and explore factors responsible for the discordance among plastome gene trees.
• New phylogenomic approaches to disentangle the plant tree of life, especially those parts involving complex evolutionary histories.
• Assessment of the discordance between nuclear gene trees and plastome trees.

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Frontiers in Plant Science

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