(Edmonton) The University of Alberta's 1000 Plants (1KP) initiative, led by Gane Ka-Shu Wong, has published its first findings in the Proceedings of the National Academy of Sciences, revealing important details about key events in plant evolution.
With contributions from scientists in North America, Europe and China, the work sheds new light on roughly a billion years of history for plant species, from strange and exotic algae to mosses, ferns, trees and flowers growing deep in steamy rainforests, to the grains and vegetables we eat and the ornamental plants adorning our homes.
Jim Leebens-Mack, associate professor of plant biology at the University of Georgia and co-ordinating author of the current paper, said, "Our study generated DNA sequences for a vast number of distantly related plants, and we developed new analysis tools to understand their relationships and the timing of key innovations in plant evolution."
The researchers are generating millions of gene sequences for plant species sampled across the green tree of life. By resolving these relationships, they are illuminating the complex processes that allowed ancient water-faring algae to evolve into land plants, with adaptations to competition for light, water and soil nutrients.
"This is like taking a time machine back to get a glimpse of how ancient algae transitioned into the diverse array of plants we depend on for our food, building materials and critical ecological services," said lead author Norm Wickett of the Chicago Botanic Garden.
"When plants colonized the land 450 million years ago, it changed the world forever," said Simon Malcomber, program director in the National Science Foundation's Division of Environmental Biology, which funded parts of the research. "The results of this study offer new insights into the relationships among living plants."
As plants grew and thrived across the plains, valleys and mountains of Earth's landscape, rapid changes in their structures gave rise to a multitude of new species. The researchers' data helps scientists better understand the ancestry of the most common plant lineages, including flowering plants and non-flowering, cone-bearing plants such as pine trees.
The investigation has also revealed a number of previously unknown molecular characteristics of some plant species that may have applications in medicine and industry.
"We are using this diverse set of plant sequences to make many exciting discoveries, with implications across the life sciences," said Wong, principal investigator for 1KP, professor in the Faculty of Science and the Faculty of Medicine & Dentistry at the University of Alberta, and associate director of BGI-Shenzhen. "As just one example, new algal proteins identified in our sequence data are being used to investigate how the mammalian brain works."
"Seeing the global impact that 1KP has had inspired us to launch a series of 1,000-species projects for organisms like insects, birds and fish," said Yong Zhang, director of the China National GeneBank (CNGB).
Teaming up to tame big data
The project required an extraordinary level of computing power to store and analyze the massive amounts of sequence data. This was provided by the iPlant Collaborative at the University of Arizona, the Texas Advanced Computing Center, Compute-Calcul Canada, and CNGB.
"This study demonstrates how life scientists are employing high-performance computing resources to analyze astronomically large data sets and answer fundamental questions that were previously thought to be intractable," said iPlant's Naim Matasci.
Computer scientist Tandy Warnow from the University of Illinois at Urbana-Champaign and her student Siavash Mirarab developed new methods for analyzing the massive data sets used for this project. "These data sets were too big and too challenging for existing statistical methods; hence we developed approaches with better accuracy," Warnow said.
Many organizations, including iPlant, CNGB and the Computational Analysis of Novel Drug Opportunities (CANDO) group at SUNY Buffalo have joined forces to provide web-based open access to these results. The resources and sequence repositories are described in a companion paper published in GigaScience.
Leebens-Mack says the researchers hope the project will not only help us understand the origins and development of plant life, but also provide other researchers with a new framework for the study of evolution.
"We believe this study will help settle some long-standing scientific debates concerning plant relationships, and that others will use these data to further elucidate the evolution of plant genes and genomes."