Students Become Gene Detectives to Fight Citrus Greening

by | Jun 27, 2016

Psyllid Group

Researchers participate in a video conference to discuss their progress in annotating the Asian citrus psyllid genome.

Scientists nationwide and around the globe are working together to make sense of the genome of the Asian citrus psyllid—an insect that is spreading a bacterium that is devastating citrus crops—and they aren’t letting geography get in their way.

Each week, a group of students, postdocs and volunteer expert annotators from the insect research community gather on a video conference to review their progress in identifying and assigning a function to genes found in the psyllid genome. The group is coordinated by Surya Saha, a senior bioinformatics analyst at the Boyce Thompson Institute. They are gearing up to publish their first “release” of the official gene set as a collaborative paper, which will be a vital resource in finding a way to stop the psyllid from spreading the citrus greening pathogen.

“It’s a community annotation effort,” said Saha. “Annotation is important because everything is based on it. It’s the foundation for every experimental work.”

The annotators’ work is part of a 5-year USDA Specialty Crop Research Initiative grant worth $10 million to find a solution to citrus greening, a bacterial disease that causes trees to produce bitter, unripe fruits. But before they can figure out a way to disrupt the insect’s transmission of the bacterium, they need a starting point, namely, a list of potential genes to target on the psyllid genome. They will annotate immunity-related genes first, with the ultimate goal of controlling the psyllid by weakening its immune system.

Most genomes are annotated by experts, but the project’s lead, Susan Brown at Kansas State University, wanted to take an outreach approach. So they trained a small army of students to perform this high-level task. For many of these students, this is their first research experience and their first scientific article.

Chris Cordola, a senior at Indian River State College in Florida became involved through his professor Tom D’elia.

“I didn’t know what citrus greening was, I didn’t know, actually, that there was a problem with citrus,” said Cordola.  His research efforts have spun off into a separate project. He believes the work will be useful in his future plans to attain a degree in forensic science.

Though he can’t say exactly how many genes he has annotated so far, he said “I feel like I accomplished more than I expected when I started the internship.”

Psyllid Group

Bioinformatics analysts Prashant Hosmani and Surya Saha, and Danielle Dixon, a summer intern working in the Mueller and Cilia labs, participate in a weekly video conference.

David Hunter, a senior and biology major at Kansas State University, said that the experience has improved his teaching and presentation skills and taught him how to coordinate with other people.

“I’m planning on sticking with it for however long I really can—even past graduation.”  Hunter is planning to attend medical school but said that the project gave him a greater understanding of genetics and how organisms are related to each other.

Additionally, students at the University of Cincinnati are contributing through their professor, Joshua Benoit, and students at Cornell University are working with Lukas Mueller and Michele Cilia. Other faculty as far flung as Otago, New Zealand and Tennessee are contributing their annotation skills to the endeavor.

The group is planning to publish its annotation in the fall, but even after the data is made public, the annotators’ job won’t be finished. They expect to receive an improved version of the genome this summer. The psyllid has approximately 20,000 potential genes—an impossible number to complete—but the group will annotate as many as possible.

The students certainly have their work cut out for them.

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