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Plant Phylogenomics

A thousand plants’ phylogeny

Nature Plants volume 5, pages 1106–1107 (2019)Cite this article

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The One Thousand Plant Initiative analysed an unprecedented collection of >1,000 plant vegetative transcriptomes from species spanning the green tree of life, resolved controversial phylogenetic placements and highlighted gene family expansions and whole genome duplications that occurred during different stages of evolution.

The high number of studies that have already used parts of the genomic data made publicly available before publication (http://bit.ly/2J00NhT) demonstrates the high relevance of this transcriptome collection4,5. However, some important evolutionary questions receive reliable answers only when the whole collection is used. A number of controversial issues received much stronger support with this extensive data set compared to its previous, more limited release1. For instance, the branching order of Viridiplantae with two basal lineages of algae, the Rhodophyta and the Glaucophyta, has been debated6. This study provides a robust support for the Glaucophyta as a sister lineage to green plants, implying a complex pattern for loss of peptidoglycan biosynthesis. Another controversial issue is the nature of the bryophytes (comprising liverworts, mosses and hornworts) and their relationships with other land plants (namely ferns, lycophytes and the large group of seed plants). The authors found strong support for the monophyly of the bryophytes, apparently resolving one main uncertainty in the origins of land conquest by the green lineage. Among gymnosperms, different results were obtained for the phylogenetic placement of the gnetales when using nuclear versus organellar phylogenomics7. With this extensive data set, the authors placed the gnetales as sisters to conifers and explained much of the previous discrepancies by suggesting the possibility of gene flow among lineages. Using divergence between paralogous copies of genes in the transcriptomes, inferences of many potential new whole genome duplications (WGDs) were also made across seed plants. Accordingly, one of the most interesting observations made in this work is the difficulty in inferring some phylogenetic relationships, apparently because of the variable histories of genes in the same genomes. How this difficulty relates to the high frequency of WGDs in plant evolution is an interesting topic to pursue.

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Fig. 1: Green plant diversity.

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  1. Génomique Métabolique, Genoscope, Institut de biologie François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France

    Patrick Wincker

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  1. Patrick Wincker
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Correspondence to Patrick Wincker.

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Wincker, P. A thousand plants’ phylogeny. Nat. Plants 5, 1106–1107 (2019). https://doi.org/10.1038/s41477-019-0555-0

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