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Study uses DNA sequences to track plant evolution

Posted November 3, 2014

From strange and exotic algae, mosses, ferns, trees and flowers growing deep in steamy rainforests to the common plants adorning people’s homes, all plant life on Earth shares over a billion years of history. An international collaboration of researchers, including scientists from North America, Europe and Asia, has generated DNA sequences from a vast number of distantly related plants, and has developed new analysis tools to understand their relationships and the timing of key innovations in plant evolution.

As part of the One Thousand Plants (1KP) initiative, the research team is generating millions of gene sequences from plant species sampled from across the green tree of life. By resolving these relationships, the international research team is 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.

“The datasets we were analyzing in this study were too big and too challenging for existing statistical methods to handle, and so my student, Siavash Mirarab, and I developed a new method to produce the species trees described in the paper,” explained Tandy Warnow, a Founder professor in the departments of computer science and bioengineering at Illinois. Warnow recently came to Illinois from the University of Texas at Austin, where she and her and her students were involved in the project. The results of these analyses are helping to settle many longstanding controversies about relationships among major plant groups and sharpen our understanding of the “green tree of life,” she added.As lead author of the PNAS paper, Norm Wickett of the Chicago Botanic Garden, described the study as “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.”

As plants grew and thrived across the plains, valleys and mountains of Earth’s landscape, rapid changes in their structures gave rise to a myriad of new species, and the group’s data also helps scientists better understand the ancestry of the most common plant linages, including flowering plants and non-flowering cone-bearing plants such 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 sequences to make many exciting discoveries with implications across the life sciences,” said Gane Ka-Shu Wong, principal investigator for 1KP, professor at the University of Alberta and associate director of BGI-Shenzhen. “For example, new algal proteins identified in our sequence data are being used to investigate how the mammalian brain works.”

“One of our exciting findings illustrates that evolution does not always favor increased complexity. Whereas the origin of land plants was facilitated by evolutionary innovations including new cell types and parental care of an embryo, the most closely related group of algae actually evolved simpler body plans [reduced complexity] relative to the ancestors they shared with land plants more than 500 million years ago,” said Jim Leebens-Mack, associate professor of plant biology at The University of Georgia and corresponding author of paper.

As part of the One Thousand Plants (1KP) initiative, the research team is generating millions of gene sequences derived from plant species sampled from across the green tree of life.

“One of our goals was to expand genomics from the study of model organisms and species of economic importance to the study of biological diversity across the planet; this particular study highlights one use of these data, but we have also published discoveries in fields as unexpected and distant as mammalian neurosciences,” said Gane Ka-Shu Wong, principal investigator for 1KP, professor at the University of Alberta, and associate director of BGI-Shenzhen. For the published study, a subset of the sequences was used to reconstruct the evolutionary developments that gave rise to defining characteristics of the plants we see all around us today.

The project required an extraordinary level of computing power to store and analyze the massive libraries of genetic data, which was provided by the iPlant Collaborative at the University of Arizona, the Texas Advanced Computing Center (TACC), Compute-Calcul Canada, and CNGB.

“This study demonstrates how life scientists are using high performance computing resources to analyze astronomically large datasets to answer fundamental questions that were previously thought to be intractable,” said iPlant’s Naim Matasci.

Ultimately the researchers hope that their project will not only shed new light on the origins and development of plant life, but also provide researchers with a new framework for the study of evolution.

“We hope that this study will help settle some longstanding scientific debates concerning plant relationships, and others will use our data to further elucidate the molecular evolution of plant genes and genomes,” Leebens-Mack said.

Source: University of Illinois at Urbana-Champaign

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