Study Provides Framework for 1 Billion Years of Green Plant Evolution
“New algorithms were developed by software engineers at BGI to assemble the massive volume of gene sequence data generated for this project,” explained Wong.
Founder Professor of Computer Science Tandy Warnow, of the University of Illinois at Urbana-Champaign, and Siavash Mirarab, assistant professor of electrical and computer engineering at the University of California San Diego, developed new algorithms for inferring evolutionary relationships from hundreds of gene sequences for over one thousand species, addressing substantial heterogeneity in evolutionary histories across the genomes.
The timing of 244 whole genome duplications across the green plant tree of life was one of the interrelated research foci of the project.
“Perhaps the biggest surprise of our analyses was the near absence of whole genome duplications in the algae,” said Mike Barker, associate professor of ecology and evolutionary biology at the University of Arizona. “Building on nearly 20 years of research on plant genomes, we found that the average flowering plant genome has nearly 4 rounds of ancestral genome duplication dating as far back as the common ancestor of all seed plants more than 300 million years ago. We also find multiple rounds of genome duplication in fern lineages, but there is little evidence of genome doubling in algal lineages.”
In addition to genome duplications, the expansion of key gene families has contributed to the evolution of multicellularity and complexity in green plants.
“Gene family expansions through duplication events catalyzed diversification of plant form and function across the green tree of life,” said co-author Marcel Quint, professor of crop physiology, at Halle University, Germany. “Such expansions unleashed during terrestrialization or even before set the stage for evolutionary innovations including the origin of the seed and later the origin of the flower.”
“The view of evolutionary relationships provided by 1KP has led to new hypotheses about the origins of key structures and processes in green plants,” said coauthor Pam Soltis, of the Florida Museum of Natural History, University of Florida.
The paper, “One Thousand Plant Transcriptomes and Phylogenomics of Green Plants,” was published in Nature (doi: 10.1038/s41586-019-1693-2). Sequences, sequence alignments and tree data are available through the CyVerse Data Commons.
Feature photo caption: Green alga Lacunastrum gracillimum, female cones of gymnosperm, Gnetum gnemon, and cherry tree flower, Prunus domestica. Photo credits: Michael Melkonian and Walter S. Judd.