Researchers Generate Gene Sequences for 1,124 Plant Species, Illuminate One Billion Years of Evolution

As part of the One Thousand Plant Transcriptomes (1KP) Initiative, an international consortium of scientists has sequenced transcriptomes — the set of genes that is actively expressed — of 1,124 plant species to shine a light on one-billion-year history of green plants.

Diversity within the family Viridiplantae: (a-e) green algae — (a) Acetabularia sp.; (b) Stephanosphaera pluvialis; (c) Botryococcus sp.; (d) Chara sp.; (e) Spirotaenia sp; (f-p) land plants — (f) Notothylas orbicularis; (g) Conocephalum conicum; (h) Sphagnum sp.; (i) Dendrolycopodium obscurum; (j) Equisetum telmateia; (k) Parablechnum schiedeanum; (l) Ginkgo biloba; (m) Pseudotsuga menziesii; (n) Welwitschia mirabilis; (o) Bulnesia arborea; (p) Paphiopedilum lowii. Image credit: Leebens-Mack et al, doi: 10.1038/s41586-019-1693-2.

The family Viridiplantae (green plants) include around 450,000-500,000 species of great diversity and have important roles in terrestrial and aquatic ecosystems.

This ecological diversity derives from developmental, morphological and physiological innovations that enabled the colonization and exploitation of new and emergent habitats. These innovations include multicellularity and the development of the plant cuticle, protected embryos, stomata, vascular tissue, roots, ovules and seeds, and flowers and fruit.

Plant evolution influenced environments globally and created a cascade of diversity in other lineages that span the tree of life. Plant diversity also fuelled agricultural innovations and growth in the human population.

Much of plant research has focused on crops and a few model species, obscuring the evolutionary backstory of a clade that is nearly half a million species strong.

To get a bird’s-eye view of plant evolution, the 1KP researchers sequenced transcriptomes to illuminate the genetic underpinnings of green algae, mosses, ferns, conifers, flowering plants and all other lineages of green plants.

“This gives a much broader perspective than what you could get by just looking at crops, which are all concentrated in one little part of the evolutionary tree,” said University of Florida’s Professor Pamela Soltis.

“By having this bigger picture, you can understand how changes occurred in the genome, which then allows you to investigate changes in physical characteristics, chemistry or any other feature you’re interested in.”

“Plants have evolved to produce numerous useful chemicals. This study provides insight into that evolutionary process,” added Dr. Toni Kutchan, a scientist at the Donald Danforth Plant Science Center.

The massive scope of the 1KP project demanded development and refinement of new computational tools for sequence assembly and phylogenetic analysis.

New algorithms were developed for inferring evolutionary relationships from hundreds of gene sequences for 1,124 plant species, addressing substantial heterogeneity in evolutionary histories across the genomes.

One hallmark of plant evolution is the frequency of genome duplication. Over and over again, lineages doubled, tripled or even quadrupled their entire set of genes, resulting in massive genome sizes. While the purpose of whole genome duplication is still unclear, scientists suspect that it may drive evolutionary innovation.

“Addressing the frequency of whole genome duplication in plants was one of 1KP’s goals,” said University of Florida’s Professor Douglas Soltis.

While flowering plants and ferns were already famous for genome duplication, the scientists uncovered a number of previously unknown duplication events in these groups, as well as in the gymnosperms, the group of plants that includes conifers.

Other plant lineages took a different route, expanding certain gene families rather than copying their entire genome. This, too, is thought to provide new avenues for evolutionary development, and not surprisingly, the team uncovered a major expansion of genes just before the appearance of vascular plants, land plants with xylem and phloem — special cells for transporting water and nutrients.

But gene expansions did not always correspond to major plant evolutionary milestones.

“There’s not much of an expansion before seed plants appear or for flowering plants,” Professor Douglas Soltis said.

“In fact, flowering plants actually shrank certain gene families, which may be a sign that they just co-opted existing genes for new functions.”

Another surprise finding was that mosses, liverworts and hornworts form a single related group, confirming a centuries-old hypothesis that had been reversed in recent decades.

“In the tree of life, everything is interrelate,” said University of Alberta’s Professor Gane Ka-Shu Wong.

“Our inferred relationships among living plant species inform us that over the billion years since an ancestral green algal species split into two separate evolutionary lineages, one including flowering plants, land plants and related algal groups and the other comprising a diverse array of green algae, plant evolution has been punctuated with innovations and periods of rapid diversification,” added University of Georgia’s Professor James Leebens-Mack.

The findings were published in the journal Nature.

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James H. Leebens-Mack et al (One Thousand Plant Transcriptomes Initiative). One thousand plant transcriptomes and the phylogenomics of green plants. Nature, published online October 23, 2019; doi: 10.1038/s41586-019-1693-2