Archives For plant genetics

It’s like having a time machine—supercomputers and gene sequencing allow scientists to study early events in plant evolution. 

One of our conservation scientists, Norman Wickett, Ph.D., is co-leader of a global initiative involving some 40 researchers on four continents. The team has spent the past five years analyzing 852 genes from 103 types of land plants to tease out early events in plant evolution. The results, published recently in the Proceedings of the National Academy of Sciences, expand our knowledge of relationships among the earliest plants on land.

An Infographic About Plant Evolution

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Illustration by Maria Ciaccio
©2014 Chicago Botanic Garden and my.chicagobotanic.org

There’s less mystery in the natural history of aquatic green algae and its relationship to land plants, thanks to research co-led by Chicago Botanic Garden scientist Norm Wickett, Ph.D., published this week in the Proceedings of the National Academy of Sciences and GigaScience.

The study examined how major forms of land plants are related to each other and to aquatic green algae, casting some uncertainty on prior theories while developing tools to make use of advanced DNA sequencing technologies in biodiversity research.

“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,” explained Dr. Wickett, conservation scientist in genomics and bioinformatics.

Over the past four years, he has collaborated with an international team of researchers on the study that gathered an enormous amount of genetic data on 103 plants and developed the computer-based tools needed to process all of that information.

The study is the first piece of the One Thousand Plants (1KP) research partnership initiated by researchers at the University of Alberta and BGI-Shenzhen, with funding provided by many organizations including the iPlant Collaborative at the University of Arizona (through the National Science Foundation), the Texas Advanced Computing Center, Compute-Calcul Canada, and the China National GeneBank. The results released this week were based on an examination of a strategically selected group of the more than 1,000 plants in the initiative.

Researchers dove into the genetic data at a fine level of detail, looking deeply at each plant’s transcriptome (the type of data generated for this study), which represents those pieces of DNA that are responsible for essential biological functions at the cellular level. In all, they selected 852 genes to identify patterns that reflect how species are related.

The study is consistent with ideas and motivations that parallel research Wickett is pursuing in work funded by the National Science Foundation program called “Assembling the Tree of Life.” Both studies seek to better understand how the earliest land plants that first appeared more than 460 million years ago evolved from green algae to yield the diversity of plants we know today.

DIAGRAM: Land plant tree of life.

The “land plant tree of life”

Understanding those lineages, Wickett explained, allows scientists to make better-informed decisions in their research pursuits, and illuminates historical environmental conditions that may have impacted evolution. “Knowing that set of relationships offers a foundation for all evolutionary studies about land plants,” he said.

Using Bioinformatics to Better Understand Our World

Wickett’s expertise in a field of science called bioinformatics allowed him to serve as one of the leaders in the data analysis process, which relied on a set of tools developed by the research team. Using those tools, Wickett helped develop the workflow for a large part of the 1KP study. “The tools we have developed through this project are able to scale up to bigger data sets,” he said. This is significant because “the more data you have, the more power you have to correctly identify those close relatives or relationships.”

By working with a large amount of data, explained Wickett, the team was able to resolve patterns that were previously unsupported. Until recently, the scientific community has largely believed that land plants are more closely related one of two different lineages of algae—the order Charales or the order Coleochaetales, which share complex structures and life cycle characteristics with land plants. However, the study reinforced, with strong statistical support, recent work that has shown that land plants are actually more closely related to a much less complex group of freshwater algae classified as Zygnematophyceae.

A Simpler Ancestor

It may mean that the ancestor of all land plants was an alga with a relatively simple growth form, like the Zygnematophycean algae, according to Wickett. More than 500 million years ago, that ancestral species split into two new species; one became a more complex version that colonized the land, and the other continued on to become the Zygnematophyceae we know today. The unique direction of both species was likely influenced by environmental conditions at the time, and this study may suggest that evolution could have reduced complexity in the ancient group that formed what we now recognize as Zygnematophyceae.

“Our new paper suggests that the order of events of early land plant evolution may have been different than what we thought previously,” said Wickett. “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.”

Wickett can’t help but feel encouraged by the wave of enthusiasm around the release of the publication. “When you get involved in these kinds of projects, it never seems as big as it is—you just get used to the scale. It’s been really great to get the public reaction and to see that people are really excited about it,” he said.

PHOTO: Norman Wickett, Ph.D.

Norman Wickett, Ph.D.

Where We Go from Here

Wickett will convene with the research team in January in San Diego to discuss next steps for 1KP, which will lead to the analysis of some 1,300 species. The team will likely break into subgroups to focus on sets of plants that share characteristics such as whether they produce flowers or cones, or have a high level of drought tolerance.

With the publication of this research, a door to the past has been cast wide open, offering untold access to natural events spanning some 500 million years. After such significant discovery it’s hard to imagine that there could be more in the wings. But with the volume of data generated by the 1KP project, there are certainly exciting results yet to come.


©2014 Chicago Botanic Garden and my.chicagobotanic.org

Using Genetics to Rescue a Rare Desert Shrub

Undercover Science

Julianne Beck —  December 5, 2013 — Leave a comment

Huddled on a sand dune, the small community of bristly Lepidospartum burgessii plants would be easy for most of us to overlook. But to scientists from the Chicago Botanic Garden, the rare shrubs shine like a flare in the night sky. This is one of two known locations of the species worldwide—both in New Mexico—and the center of a rather dazzling rescue mission.

Evelyn Williams, Ph.D., a Garden postdoctoral research associate, is pulling out all the stops to save the sensitive species. Commonly called Burgess’ scale broom, it has suffered from a mysterious lack of seed production since the late 1980s.

PHOTO: Burgess' scale broom (Lepidospartum burgessii).

Burgess’ scale broom (Lepidospartum burgessii) are among the tallest plants in their New Mexico location.

Standing about five feet tall, the silvery-green plants only grow on gypsum dunes. They possess unique characteristics that allow them to help stabilize sand dunes in the desert conditions where they live.

“I’m interested in how we can use genetics broadly to address conservation and ecological restoration questions,” said Dr. Williams. Her curiosity led her to the Garden in 2011 to join a team of genetic experts for this formidable undertaking.

The team suspects that, because the two populations of Lepidospartum burgessii are relatively small, the existing plants have interbred and are now too closely related to pollinate one another—which means they cannot produce seeds and create new plants.

Williams set out to confirm this theory, gathering plant cuttings during summer fieldwork in 2013. She hoped to grow the cuttings into full plants that she could cross-pollinate and study at the Garden. She also took samples from 320 plants back to the Garden. There, using a microsatellite technique, she recorded the genetic pattern of each plant, noting similarities and differences.

“When we have all of these different shrubs from a population, we want to use a fine genetic tool to tease apart genetic variations,” she explained. The microsatellite approach allowed her to identify genetic markers occurring in multiple plants down to the finest level of detail.

The results were encouraging. Williams found enough genetic diversity within the two populations that they should be able to cross pollen, or DNA material, and produce seeds. “Because there is diversity in these populations, we’re really hopeful that if we do a genetic rescue we can get some seeds in these two different populations,” said Williams. A genetic rescue, she explained, is when a species is revived with the addition of new genes, which normally occurs during pollination.

That day didn’t come right away, as the cuttings failed to grow in the Garden greenhouses. Accustomed to the trial and error process of scientific discovery, Williams moved on to her backup plan.

PHOTO: Dr. Williams hand-pollinating a specimen.

Evelyn Williams, Ph.D., delivers pollen to a plant.

She returned to the field in October, where she personally carried pollen-filled flowers from one population of plants to another, brushing the fluffy yellow blooms against other plants that may accept their genetic material. With plants as much as one mile apart, it was a process of patience and precision.

She will soon look for seeds in the resulting buds from that pilot study with an x-ray machine in the Garden’s Harris Family Foundation Plant Genetics Laboratory.

Williams is poised for the challenge of whatever she may, or may not, find. Ultimately, she hopes to convey a successful technique to land managers who carry out the daily work of furthering the species and enriching the biodiversity of the southwestern landscape.

“I really like that as part of the Garden we can help these public agencies and use our knowledge of genetics and conservation to stabilize and increase some of these rare populations. That’s really important to me,” said Williams.

PHOTO: Lepidospartum burgessii, framed by the sunset.

Lepidospartum burgessii, framed by the sunset. Photo: Mike Howard

She has been intent on advancing conservation science since childhood, inspired by her aunt, an ecologist. Her interest grew into expertise as she studied the genetics of ferns while earning her Ph.D. in botany at the University of Wisconsin.

In winter at the Garden, Williams takes every opportunity to walk through the Elizabeth Hubert Malott Japanese Garden. “I like being here in the winter and seeing a side of the Garden that’s unexpected: the snow and the beautiful structures in the Malott Japanese Garden,” she said.

Perhaps it is that perspective, of looking for the unexpected, that will unlock the mystery of Lepidospartum burgessii one day soon.


©2013 Chicago Botanic Garden and my.chicagobotanic.org

Coloring Between the Lines

Undercover Science

Julianne Beck —  March 4, 2013 — 1 Comment

As dusk fell over Illinois State Beach Park, Jeremie Fant, Ph.D., perched silently beside the rare downy Indian paintbrush. He watched as the white-blooming Castilleja plant opened its tubular flower and emitted a sweet scent. The clock ticked past 6 p.m. Cautiously, a moth appeared out of the night sky, and fluttered over to sip the plant’s nectar. Bingo.

That moment, and subsequent research in Illinois and Colorado, led Dr. Fant, a molecular ecologist with the Chicago Botanic Garden, to become the first to document the moth as a pollinator of Castilleja with Krissa Skogen, Ph.D., his research partner and a conservation scientist at the Garden.

Dr. Fant in the field

Dr. Fant conducts fieldwork in the Comanche National Grasslands in Colorado.

Fant studies the importance of how flowers are designed to attract specific pollinators, and what a plant’s pollinator means for its survival as a species. “I am fascinated by the way these events can lead to permanent impacts on a plant population,” he said.

He recently explained the intricacies of the process to me, and why the palette of colors we see in the Garden and elsewhere is not only beautiful, but also functional.

The Palette of Pollinators
Pollinators—such as bees, birds, flies, and moths—offer specific benefits to plants, according to Fant. Birds travel expansive geographic areas, and can spread the pollen of a single plant over a large area. Bees, on the other hand, are more localized in their foraging, covering more plants in a condensed area. Where moths fall in this spectrum is not known: they may diversify the genes in a plant population by carrying pollen further than bees, but they may not travel as far as birds.

“The imprint left behind from genealogy is stamped on the landscape, and it’s my job to figure out how that pattern got there,” said Dr. Fant.

Plants Spin the Color Wheel
A flowering plant puts a lot of energy into producing a flower. Why? The purpose of flowers is to attract pollinators who will spread the plant’s genes— promoting the continuation of the species, said Fant. When a plant is red, it attracts birds as pollinators, but if it is yellow, it attracts bees. White flowers are particularly appealing to moths—especially those that bloom after sunset when moths are out and about. The color, combined with the scent, allows a plant to lure in a specific pollinator.

Connecting the Dots
This information led to a hunch when Fant considered the white flowers on the downy Indian paintbrush in Colorado and at Illinois State Beach Park, where he conducts much of his fieldwork. Most species of Castilleja plants produce red flowers and are known to be pollinated by birds. But here in Illinois, in the furthest east population of such plants, they chose a different color, and as he confirmed, a different pollinator. It is the question of why, and what that choice means for the plant, that Fant is now preparing to study when he returns to his field research this spring.

prairie aug-2574

Charismatic red flowers bloom on the gravel hill in the Dixon Prairie, Fant’s favorite area at the Garden.

Ultimately, Fant tracks how genes move within plant populations, which largely hinges on how they are carried by pollinators. He examines plant DNA to determine if they share one or more genes, and are therefore related. Then, he maps the location of related plants, tracking the movement of specific genes and inferring how and why they got there. “There’s always some reason for the movement,” he said.

This spring and summer, look for red flowers on the gravel hill in the Dixon Prairie, where Dr. Fant is growing unique bird-pollinated plants such as the royal catchfly, with the goal of increasing the plants’ genetic diversity.

Fant noted that moths are often overlooked as pollinators, and along with Dr. Skogen he is especially interested in studying their relationship with many kinds of plants. In addition to the Castilleja, he also studies rare species of the gravel hill in the Garden’s Dixon Prairie.

At the end of our conversation, Fant, dressed in a bright-yellow sweater, jumped up from his desk and headed toward his lab in the Daniel F. and Ada L. Rice Plant Conservation Science Center, where he is always moving forward to catch up with the past.


©2013 Chicago Botanic Garden and my.chicagobotanic.org