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Genomic Discovery Unearths New Theories on Plant Evolution

Norm Wickett, Ph.D.
Conservation Scientist, Genomics and Bioinformatics
Chicago Botanic Garden

I have always been fascinated by natural history and evolution. As a conservation scientist in genomics and bioinformatics at the Chicago Botanic Garden, I work to understand how plants – aquatic and terrestrial – all fit together in the biological tree of life. We have known for quite some time that all plants on land share a common ancestor with green algae, but there has been some debate as to what form of algae is the closest relative, and how some of the major groups of land plants are related to each other.

Over the past four years, I collaborated with an international team of researchers on a study examining how major forms of land plants are related to each other and to aquatic green algae. Together, we gathered an enormous amount of genetic data on 103 plants and developed computer-based tools that allow us to apply advanced DNA sequencing technologies to biodiversity research. These tools helped us understand our own data and uncover some exciting results – and we believe our analysis techniques can be scaled up to help scientists make sense of even larger data sets.

Last week, our results – the first piece of the One Thousand Plants (1KP) research partnership – were published in the Proceedings of the National Academy of Sciences (PNAS) and GigaScience. With the publication of this research, we’ve thrown open a door to the past, giving us unprecedented access to natural events spanning some 500 million years.

A Simpler Ancestor
Until recently, the scientific community has largely believed that land plants are more closely related to one of two different lineages of algae which share complex structures and life cycle characteristics with land plants. We dove into plant genetic data at a fine level of detail, looking deeply at each plant’s transcriptome, which represents those pieces of DNA that are responsible for essential biological functions at the cellular level. In all, we selected 852 genes to identify patterns that reflect how species are related.

Despite earlier theories, our research reinforced, with strong statistical support, recent work showing that land plants are actually more closely related to a much less complex group of freshwater algae classified as Zygnematophyceae. This may mean that the ancestor of all land plants was actually an alga with a relatively simple growth form. Our new paper suggests that the order of events of early land plant evolution may have been different than what we thought previously. That order of events informs how scientists interpret when and how certain characteristics or processes, like desiccation tolerance, came to be; our results may lead to subtle differences in how scientists group mosses, liverworts and hornworts, the lineage of plants (bryophytes) that descended from the earliest land plants.

Using Bioinformatics to Better Understand Our World
The study is consistent with the ideas and motivations in another study I am pursuing, funded by the National Science Foundation’s “Assembling the Tree of Life” program. Both studies seek to better understand how the earliest land plants evolved from green algae to yield the diversity of plants we know today. Understanding how those lineages are related allows scientists to make better informed decisions in our research pursuits, and illuminates historical environmental conditions that may have affected evolution. Knowing these relationships offers a foundation for all evolutionary studies about land plants.

My experience in bioinformatics – a field of science dedicated to the organization and analysis of complex biological data – allowed me to serve as one of the leaders in the data analysis process, which relied on a set of tools we developed as a research team. Using those tools, we developed a workflow for a large part of the 1KP study, creating a toolkit that we believe can be scaled up to even bigger data sets. This is significant, because the more data we have, the more power we have to correctly identify relationships between plants.

By working with a large amount of data, we were able to resolve patterns that were previously unsupported.

Where We Go From Here
In January, the 1KP research team will reconvene in San Diego to tackle our next challenge – expanding our approach to some 1,300 species. After such a significant discovery following the analysis of only 103 plants, it’s hard to imagine what results could be waiting for us in the future – and I can’t wait to see them.

 

Norm Wickett, Ph.D. is Conservation Scientist in Genomics and Bioinformatics at the Chicago Botanic Garden and a Lecturer for the Program in Biological Sciences at Northwestern University.

About Chicago Botanic Garden: The Chicago Botanic Garden is one of the world’s great living museums and conservation science centers. In 2013, one million people visited the Garden’s 26 gardens and four natural areas, uniquely situated on 385 acres on and around nine islands, with six miles of lake shoreline. Within the nine laboratories of the Garden’s Daniel F. and Ada L. Rice Plant Conservation Science Center, scientists and graduate students conduct a wide array of plant research. The Garden is one of only 17 public gardens accredited by the American Association of Museums. Its Lenhardt Library contains 110,000 volumes — including one of the nation’s best collections of rare botanical books.

About One Thousand Plants: The 1000 plants (oneKP or 1KP) initiative is an international multi-disciplinary consortium generating large-scale gene sequencing data for over 1000 species of plants. Major supporters include Alberta Enterprise and Advanced Education, Musea Ventures (Somekh Family Foundation), Beijing Genomics Institute in Shenzhen (BGI-Shenzhen), Alberta Innovates Technology Futures (AITF-iCORE Strategic Chair), iPlant Tree-of-Life (iPToL) Grand Challenge, and WestGrid Compute-Calcul. The results released in PNAS and GigaScience were based on an examination of a strategically selected group of the more than 1,000 plants in the initiative.