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Geneticists Join Botanist to Barcode Orchids

orchid researchImagine in the future, a customs agent at border control doesn’t have to guess if a traveler’s plant is an endangered species. He could simply put a sample of the plant into a machine and read the genetic “barcode.”

“In the future we could have a machine and put in a piece of a plant,” said Dr. Alexandra D. Simmons, assistant professor of biology. “It could grind it up and analyze the DNA to compare the barcode to those in the database. The guard doesn’t have to do guesswork about endangered species.”

As the world-wide effort to classify and produce a “DNA barcode” for every living thing is underway, a team of UST biology researchers – including five undergraduate students – hope to contribute data for 32 species of orchid plants in the genus Gongora. Along with Dr. Albert Ribes-Zamora, assistant professor of biology, they expect to generate hypotheses on the phylogenetic relationship between the species and compare the results to current, morphology-based classifications.

“Everyone can help contribute to the barcode of life,” Simmons said. “We’re contributing new research. We will be making this information available for cross-examination.”

Students, Professors Collaborate on Orchid Research

Fr. Ted Baenziger and student researchersThe orchids were sourced by the Rev. Ted Baenziger, CSB, associate professor and chair of French, who is an orchid enthusiast and judge with the American Orchids Association. With a greenhouse behind the Basilian priests’ residence, he has raised about 800 orchids. Father Baenziger joined the research team last fall, sitting in on many genetics labs to participate in collaborative research on the DNA barcode of orchids.

“He can’t do DNA; we can’t do orchids, so it’s perfect,” she said. “We’re getting species from 53 samples he’s collected – by himself, through friends or through his network.”

The undergraduate researchers are biology majors: Olivia Di Rodriguez, junior; Clara Ribadeneyra, sophomore; Keagan Foss, sophomore; Daniela Angulo Ludovic, junior; and Cesar Trivino, junior. Simmons said the students are doing science as scientists do science.

“They are 100 percent leading this project,” she said. “The students do everything on their own. They report findings to us. They ask questions.”

In larger research programs, Simmons said only select students might have the opportunity to do research, and they would likely work with a post-doctoral research. “Here, undergrads are working with a principal investigator, which I think would be rare in a larger institution.”

Research Analyzes Relationships of the Orchid Species

Alex Simmons, Ted Baenziger and Albert Ribes-ZamoraThe students extracted DNA from samples of the orchid leaves, sequenced the DNA of specific parts of the plant genome, and used software called DNA Subway to generate phylogenetic trees: a branched structure that groups two species at a time that share a common ancestor in the past. It provides great insight and helps classify some of the plants that are among 25,000 species of orchids.

The analysis studies four pieces of the chloroplast DNA of each sample, each around 350 letters, or bases, of the millions of base pairs that make up the full genome of an individual, which reads like “ATGGCC…” The sequence becomes a fingerprint of the orchid, or in scientific terms, a barcode, which can be used to identify the species. The group hopes to submit the data to a genetic database and publish their findings, as part of a world-wide effort to record the genetics of every living thing.

A group of 25 students will present a poster at the UST Research Symposium on April 10 about teaching genetics through orchid barcoding. The team is also hoping to present their results in at the American Society of Human Genetics Meeting in San Diego in October and the World Orchid Conference in Johannesburg, South Africa, in September.

“It’s been an incredibly dynamic exchange,” Simmons said. “It has made us all better.”