A co-ordinated international effort involving almost 200 plant scientists has revealed the history of how and when plants gained the ability to grow tall and make seeds, flowers and fruits, providing a framework for understanding plant diversity around the planet including annual crops and long-lived forest trees.
The One Thousand Plant Transcriptomes Initiative (1KP) examined the diversification of plant species, genes and genomes across the more than one-billion-year history of green plants dating back to the ancestors of flowering plants and green algae.
The study, published today in Nature, reveal the timing of whole genome duplications and the origins, expansions and contractions of gene families that contributed to the evolution of green algae, mosses, ferns, conifer trees, flowering plants and all other green plant lineages.
“In the tree of life, everything is interrelated. And if we want to understand how the tree of life works, we need to examine the relationships between species. That’s where genetic sequencing comes in,” said University of Alberta genomicist Gane Ka-Shu Wong, who was the lead investigator on the nine-year project.
The group sequenced the genes of more than 1,100 plant species.
Understanding the tree of life
James Leebens-Mack, a professor of plant biology at the University of Georgia Franklin College of Arts and Sciences and co-corresponding author on the study, said the research shows that over the last billion years, ancestral green algal species split into two separate evolutionary lineages. One included flowering plants, land plants and related algal groups, and the other lineage comprised a diverse array of green algae. He also noted plant evolution has been punctuated with innovations and periods of rapid diversification
“In order to link what we know about gene and genome evolution to a growing understanding of gene function in flowering plant, moss and algal organisms, we needed to generate new data to better reflect gene diversity among all green plant lineages,” he said.
By sequencing and analyzing genes from a broad sampling of plant species from around the world, the researchers were better able to reconstruct gene content in the ancestors of all crops and model plant species, and gain a more complete picture of the gene and genome duplications that enabled evolutionary innovations.
The massive scope of the project demanded development and refinement of new computational tools for sequence assembly and phylogenetic analysis.
“New algorithms were developed by software engineers at BGI to assemble the massive volume of gene sequence data generated for this project,” explained Wong.
Computing science and engineering professors in the U.S. developed new algorithms for inferring complex evolutionary relationships from hundreds of gene sequences for over 1,000 species.
“Perhaps the biggest surprise of our analyses was the near absence of whole genome duplications in the algae,” said Mike Barker, an ecologist and evolutionary biologist 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 four 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 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, a crop physiologist at Halle University in 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,” added co-author Pam Soltis, of the Florida Museum of Natural History at the University of Florida.
The study, “One Thousand Plant Transcriptomes and Phylogenomics of Green Plants,” was published in Nature. Sequences, sequence alignments and tree data are available through the CyVerse Data Commons.
—with contributions from Folio staff