One thousand plant transcriptomes and the phylogenomics of green plants

These (gene-environment interactions) GEITP pages have a continued interest in evolution, because that process involves the genomes of all living organisms to “adapt” to changes in the environment in order better to survive (‘survival of the fittest’). Green plants comprise an estimated 450,000–500,000 species; they encompass incredible diversity and evolutionary timescales, and they play important roles in all terrestrial and most aquatic ecosystems.

This ecological diversity arises from developmental, morphological and physiological innovations that have continuously enabled plants to colonize and exploit any novel and emerging habitat. These innovations include: multicellularity and development of the plant cuticle, protected embryos, stomata (for ‘breathing’), vascular tissue, roots, ovules and seeds, and flowers and fruit. Hence, plant evolution ultimately influenced environments globally — and created a cascade of diversity in other lineages throughout the “tree of life.” Plant diversity has also driven innovations in agriculture and aided in the growth of human populations.

Phylogenomic approaches are now widely used to resolve species relationships, as well as the evolution of genomes, gene families (or groups), and gene functions. As part of the One Thousand Plant Transcriptomes Initiative, authors [see attached article] sequenced the transcriptomes (i.e. transcribed RNA from actively expressed genes) of 1,124 species that span the diversity of plants — including green plants (Viridiplantae), glaucophytes (freshwater unicellular algae), and red algae — together with 31 published genomes, to infer species relationships and characterize the relative timing of organism, molecular, and functional diversification across green plants.

Authors evaluated gene history discordance (i.e. inconsistencies) among single-copy genes; discordance is to be expected — in the face of rapid species diversification — owing to incomplete sorting of ancestral variation between events of speciation. Horizontal gene transfer,(i.e. movement of genetic material between unicellular and/or multicellular organisms — other than by the transmission of DNA from parent to offspring) hybridization, gene loss subsequent to gene and genome duplications, and estimation error — all these processes can also contribute to gene-tree discordance. Nevertheless, through rigorous gene- and species-tree analyses, authors carried out robust species-tree estimates (see the fantastic Fig. 2 of attached]. Gene-family expansions and genome duplications are recognized as causes of variation for the evolution of gene function and biological novelties. Authors also inferred the timing of ancient genome-duplications and large gene-family expansions.

This extensive analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported, across multiple species-tree and supermatrix analyses. However, discordance at a few important nodes — highlights the complexity of plant genome evolution (e.g. polyploidy, periods of rapid speciation, and extinction). Incomplete sorting of ancestral variation, polyploidization (i.e. creating more than the two sets of chromosomes, one from each parent), and massive expansions of gene families — punctuate the evolutionary history of green plants. Perhaps the most exciting finding is authors discovered that large expansions of gene families preceded the origins of green plants, land plants, and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of ferns and flowering plants. 😊


Nature 31 Oct 2019; 574: 679-685

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