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Background  Next-generation sequencing has provided a wealth of plastid genome sequence data from an increasingly diverse set of green plants ( Viridiplantae ). Although these data have helped resolve the phylogeny of numerous clades (e.g., green algae, angiosperms, and gymnosperms), their utility for inferring relationships across all green plants is uncertain.  Viridiplantae  originated 700-1500 million years ago and may comprise as many as 500,000 species. This clade represents a major source of photosynthetic carbon and contains an immense diversity of life forms, including some of the smallest and largest eukaryotes. Here we explore the limits and challenges of inferring a comprehensive green plant phylogeny from available complete or nearly complete plastid genome sequence data.    Results  We assembled protein-coding sequence data for 78 genes from 360 diverse green plant taxa with complete or nearly complete plastid genome sequences available from GenBank. Phylogenetic analyses of the plastid data recovered well-supported backbone relationships and strong support for relationships that were not observed in previous analyses of major subclades within  Viridiplantae . However, there also is evidence of systematic error in some analyses. In several instances we obtained strongly supported but conflicting topologies from analyses of nucleotides versus amino acid characters, and the considerable variation in GC content among lineages and within single genomes affected the phylogenetic placement of several taxa.    Conclusions  Analyses of the plastid sequence data recovered a strongly supported framework of relationships for green plants. This framework includes: i) the placement of  Zygnematophyceace  as sister to land plants ( Embryophyta ), ii) a clade of extant gymnosperms ( Acrogymnospermae ) with cycads +  Ginkgo  sister to remaining extant gymnosperms and with gnetophytes ( Gnetophyta ) sister to non- Pinaceae  conifers (Gnecup trees), and iii) within the monilophyte clade ( Monilophyta ),  Equisetales  +  Psilotales  are sister to  Marattiales  + leptosporangiate ferns. Our analyses also highlight the challenges of using plastid genome sequences in deep-level phylogenomic analyses, and we provide suggestions for future analyses that will likely incorporate plastid genome sequence data for thousands of species. We particularly emphasize the importance of exploring the effects of different partitioning and character coding strategies.

From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes