Skip to main content
ARS Home » Midwest Area » Ames, Iowa » Corn Insects and Crop Genetics Research » Research » Publications at this Location » Publication #347467

Research Project: SoyBase and the Legume Clade Database

Location: Corn Insects and Crop Genetics Research

Title: One thousand plant transcriptomes and the phylogenomics of green plants

item DEGIRONIMO, LISA - New York Botanical Garden
item JORDON-THADEN, INGRID - University Of Florida
item JOYA, STEVEN - University Of British Columbia
item MELKONIAN, BARBARA - University Of Cologne
item MILES, NICHOLAS - University Of North Texas
item POKORNY, LISA - Royal Botanical Gardens
item QUIGLEY, CHARLOTTE - University Of Maine
item Cannon, Steven
item LEEBENS-MACK, JIM - University Of Georgia
item WONG, GANE - Bgi Shenzhen

Submitted to: Nature
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/12/2019
Publication Date: 10/23/2019
Citation: Degironimo, L., Jordon-Thaden, I.E., Joya, S., Melkonian, B., Miles, N.W., Pokorny, L., Quigley, C.T., Cannon, S.B., Leebens-Mack, J., Wong, G.K. 2019. One thousand plant transcriptomes and the phylogenomics of green plants. Nature. 574:679-685.

Interpretive Summary: Plants are essential to every ecosystem on the planet, to all of our food systems, and even to the atmosphere that we breathe. Over more than a billion years, plants have evolved and diversified into roughly half a million species. Determining the evolutionary histories of the major groups of plants has been one of the major scientific efforts of the last three hundred years, going back to the taxonomist Carl Linnaeus. In the study "A phylogenomic view of evolutionary complexity in green plants," researchers selected more than 1000 species from key evolutionary branches. From each species, most gene sequences were determined (the "transcriptome") - and then all genes across all species were compared. Important conclusions can be drawn about key evolutionary innovations, including the origins of multicellularity, vascular systems (structures that carry water and nutrients through the plant), as well as roots, seeds, flowers, and fruits. The study identifies several hundred instances over the history of plant evolution in which genomes (the collection of DNA in the plant) have doubled, and also many cases where groups of genes have dramatically increased in number - often, apparently contributing to the evolution of new traits and capacities such as more complex vascular systems or flower or fruit structures. This information provides fundamental understanding about the genetic basis for traits important in all crop plants, and will aid plant biologists and breeders to more efficiently develop more resilient and productive crops.

Technical Abstract: With approximately 500,000 species, green plants (Viridiplantae) are a foundational ecological driver of life on Earth, and of enormous economic importance. Analyses of over 1,000 transcriptomes spanning green plant diversity yielded a robust phylogenomic framework for examining more than a billion years of green plant evolution. Most inferred species relationships were well supported across multiple species trees and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes reveals the complexity of plant genome evolution. Incomplete sorting of ancestral variation through rapid radiations, as well as polyploidization and massive gene family expansions, punctuate the evolutionary history of green plants. These events are associated with key evolutionary innovations, including the origins of multicellularity, vascular systems, roots, seeds, and flowers. Notably, large gene family expansions precede the origins of Viridiplantae, land plants, and vascular plants, whereas genome doubling is more common in flowering plants and ferns.