Plastid phylogenomic analysis of green plants A billion years of evolutionary history

• Published in: American journal of botany Vol. 105; no. 3; pp. 291 - 301
• Main Authors: Gitzendanner, Matthew A., Soltis, Pamela S., Wong, Gane K.-S., Ruhfel, Brad R., Soltis, Douglas E.
• Format: Journal Article
• Language: English
• Published: United States John Wiley and Sons, Inc 01.03.2018; Botanical Society of America, Inc
• Subjects: Amborella; Amino Acid Sequence; Amino Acids; Angiosperms; Aquatic plants; Biological Evolution; Biology; Biometrics; Bryophyta; Bryophyta - genetics; Ceratophyllum; Chloranthales; chloroplast phylogeny; Classification; Conifers; Conjugatophyceae; Cycadopsida - genetics; data collection; Datasets as Topic; Dating techniques; Dilleniaceae; Divergence; DNA, Plant - analysis; Equisetum; Evolution; Evolution, Molecular; Evolutionary genetics; Ferns; Ferns - genetics; Floating plants; Flowers & plants; Gene sequencing; Genes, Plant; Genome, Plant; Genome, Plastid; Genomes; Genomics - methods; Ginkgo; Ginkgo biloba - genetics; Gnetophyta - genetics; green plants; Gymnosperms; INVITED SPECIAL ARTICLE: For the Special Issue: Using and Navigating the Plant Tree of Life; Liliopsida; Macroevolution; Magnoliopsida - genetics; Marattiales; Molecular chains; morphological innovations; Nymphaeales; Phylogenetics; Phylogeny; plant evolution; Plant Proteins - genetics; plastid genome; plastid phylogenomics; Plastids - genetics; Plastomes; Proteins; Psilotaceae; transcriptome; transcriptomes; Viridiplantae; Viridiplantae - genetics; morphological innovations; green plants; plastid phylogenomics; transcriptomes; chloroplast phylogeny; Viridiplantae; plant evolution
• ISSN: 0002-9122; 1537-2197; 1537-2197
• DOI: 10.1002/ajb2.1048

Premise of the Study For the past one billion years, green plants (Viridiplantae) have dominated global ecosystems, yet many key branches in their evolutionary history remain poorly resolved. Using the largest analysis of Viridiplantae based on plastid genome sequences to date, we examined the phylogeny and implications for morphological evolution at key nodes. Methods We analyzed amino acid sequences from protein‐coding genes from complete (or nearly complete) plastomes for 1879 taxa, including representatives across all major clades of Viridiplantae. Much of the data used was derived from transcriptomes from the One Thousand Plants Project (1KP); other data were taken from GenBank. Key Results Our results largely agree with previous plastid‐based analyses. Noteworthy results include (1) the position of Zygnematophyceae as sister to land plants (Embryophyta), (2) a bryophyte clade (hornworts, mosses + liverworts), (3) Equisetum + Psilotaceae as sister to Marattiales + leptosporangiate ferns, (4) cycads + Ginkgo as sister to the remaining extant gymnosperms, within which Gnetophyta are placed within conifers as sister to non‐Pinaceae (Gne‐Cup hypothesis), and (5) Amborella, followed by water lilies (Nymphaeales), as successive sisters to all other extant angiosperms. Within angiosperms, there is support for Mesangiospermae, a clade that comprises magnoliids, Chloranthales, monocots, Ceratophyllum, and eudicots. The placements of Ceratophyllum and Dilleniaceae remain problematic. Within Pentapetalae, two major clades (superasterids and superrosids) are recovered. Conclusions This plastid data set provides an important resource for elucidating morphological evolution, dating divergence times in Viridiplantae, comparisons with emerging nuclear phylogenies, and analyses of molecular evolutionary patterns and dynamics of the plastid genome.