Pressed plants reveal living genetic messages, decades later

Chicago's treasured Field Museum is home to nearly 3 million preserved plants, some collected centuries ago. Each specimen is pressed, dried and labeled, making a snapshot of biodiversity frozen in time.

But what else can scientists do with the specimens in museum collections besides display them?

In a new study, researchers from the University of Illinois Chicago extracted viable RNA, the essential messenger of genetic information, from plants from museum collections. This research breakthrough will make it possible for scientists to study plant evolution, gene regulation and adaptation using specimens that were long thought to hold only degraded genetic material.

A centuries-old resource

Scientists and scholars have been collecting and cataloging plants for centuries. "People have been preserving their plants for as long as we've been interested in botany," said Alexa Tyszka, a PhD candidate in biological sciences in the UIC College of Liberal Arts and Sciences.

In 1544, the Italian scientist Luca Ghini created the first known herbarium, a curated collection of plant samples for study. Today, herbaria housed in museums, universities and other institutions are rich sources of historical and biological data.

"If you can't obtain a sample from an area because you can't go there, or the plant doesn't exist anymore, or you might not have funding to go get fresh tissue, herbaria are very integral to the study of plant morphology," said Tyszka.

In recent decades, scientists have tapped herbaria as sources of plant DNA, which they extract and sequence for essential information about plant evolution and diversity. But for years, botanists assumed that RNA, the cousin of DNA that converts genetic information into proteins, couldn't be extracted from herbarium samples. While DNA dictates what a gene is, RNA dictates where, when and how a gene is expressed.

The method of preparing and preserving plant samples for herbaria has not changed much since the 16th century. Once collected in the field, specimens are typically flattened and dried between thin sheets of paper, then archived and stored. In recent decades, scientists have also taken to drying plants in desiccant silica beads, which dry the samples more quickly for DNA extraction. But common wisdom holds that uber-sensitive RNA will degrade in samples left out even for a few hours at room temperature.

"Unlike DNA, which is double-stranded, RNA is single-stranded," said Joe Walker, assistant professor of biology in the College of Liberal Arts and Sciences and senior author on the new study. "It's less stable and gets fragmented easily."

Missing on the map

The assumption has been that RNA must be immediately preserved in ultracold freezers to remain viable.

In their study, Tyszka, Walker and their collaborators found that this isn't necessarily the case.

Back when Tyszka started her PhD in 2021, during the COVID-19 pandemic, travel restrictions made it impossible to travel for fieldwork. Instead, he reached out to collaborators around the world for samples.

Collaborators in the Ivory Coast planned to send over plant material, but they did not have access to liquid nitrogen, a gold-standard technique for freezing samples and preserving RNA.

"We wondered how this influenced our sampling," Tyszka said. When she mapped the collection points of plant samples used in RNA studies, she noticed a pattern: Plants from countries with fewer financial resources were dramatically underrepresented in scientific sampling.

This sparked conversations with collaborators at UIC, including postdoctoral researcher Karolis Ramanauskas, PhD student Natalia Ruiz-Vargas and professor Roberta Mason-Gamer. The group wondered, could they extract RNA from plant samples dried in silica beads, or even samples from herbaria dried simply at room temperature?

They decided to try extracting RNA from silica-dried samples - some of which were three to six months old. To their surprise, it worked.

Remember "Jurassic Park?"

They decided to test their method further. For their study, published in the journal Genome Research, the researchers examined three samples from the University of Michigan herbarium, collected in 1950, 1956 and 1990. They compared RNA extracted from those samples with RNA from five-year-old silica-dried samples and freshly collected material from the same plant species to test the reliability of the data.

"A lot of this paper looks into how much we can trust the data, as well as what we can do with it," said Walker.

The plants they studied belong to the order Ericales, a diverse group that includes familiar foods like tea, kiwi and blueberries, as well as ornamentals and carnivorous plants. The group was particularly interested in plant immune genes known as NLRs, which help plants detect and respond to pathogens and evolve rapidly over time.

"If you can take a gene from a plant that's extinct in the wild and introduce it into an extant plant, then theoretically you're accessing immune strategies that modern pathogens haven't adapted to yet," Walker said.

It's somewhat like the 1993 blockbuster "Jurassic Park," in which scientists put extinct dinosaur genes into genomes from living reptile species.

To test whether RNA from herbarium samples could produce functional genes, the researchers synthesized an immune gene they identified from a plant pressed in 1956 and expressed it in a living tobacco plant. The gene triggered a classic immune response in the tobacco plant, a sign that it was working as intended.

This gene and others could be useful in fighting the plant diseases of today, Walker said.

"That's why we tested whether we could take an NLR gene from an herbarium plant and actually express it in a living plant," he said. "It gives access to the genetic diversity that exists within herbaria, instead of just the diversity that exists within living plants."

"It's not exactly 'Jurassic Park,'" Tyszka added, "but you can think of it that way."

What comes next

Tyszka, who completed her undergraduate degree at UIC, said the project reflects quality of training and encouragement to pursue research questions she received as an undergrad. "There's a reason I stuck around," she said.

Undergraduate researcher Linda Mansour also played a key role, joining Walker's lab to explore open-ended research questions and gain hands-on experience with real data. Mansour, in collaboration with UIC graduate student Eric Bretz, helped analyze the transcriptome data early in the project. "It's genuinely a breakthrough," she said of the research.

Beyond evolutionary biology, the findings carry implications for crop science, conservation and climate research. Storing tissue for RNA extraction traditionally requires costly ultracold freezers, which became famous for storing mRNA vaccines during COVID. But cheaper room-temperature preservation methods could expand who is able to participate in plant genetic research.

The approach opens the door to partnerships with researchers in regions that have historically been excluded from RNA-based studies, often the same regions that harbor the planet's greatest biodiversity.

"The blank spots on the map are actually where some of the most interesting plants grow," Tyszka said. "This lets us start filling those gaps."