Genome sequenced for annoying pathogenic pumpkins

Researchers at the University of Illinois, including Rikky Rai (pictured) and Sarah Hind, have sequenced the genome for the bacterium that causes bacterial spot disease in pumpkins, an economically devastating disease. Credits: Montgomery Flack

Pumpkin growers are afraid of the tiny tanned scales that form on their fruit, and each lesion is a hallmark of bacterial spot disease. Stains not only damage the flesh of the fruit, they provide entry points for fungi that cause rot and other pathogens that can destroy pumpkins and other zucchini inside. In any case, farmers pay the price, with the market yield reduced by as much as 90%.

Despite the severity of the disease, scientists do not know much about the genetics of the pathogen that causes it; almost all the molecular information needed for accurate diagnostic testing and targeted treatments is missing for this disease.

In a new study, scientists at the University of Illinois, with the help of two undergraduate students, put together the first complete genome for the disease-causing bacterium, Xanthomonas cucurbitae, and identified genes that are activated during infection.

“Compiling a complete circular genome means we now have the resources to better understand what is happening in the field. With this information, we can look at how the pathogen spreads, whether there are differences in host specificity between subgroups or strains, or how resistant it is to develop on chemical controls, ”says Sarah Hind, an assistant professor in the Department of Plant Sciences in Illinois and a senior author on Phytopathology study.

After genome sequencing, the Hind group compared it to the genomes of 12 other Xanthomonas species that cause disease in various plants such as tomatoes, rice, citrus and wheat. Surprisingly, given the propensity to create havoc in the field, Xanthomonas cucurbitae had the smallest genome and had fewer genes that other Xanthomonas species are known to be important in causing the disease.

“As this pathogen lacks many known virulence genes (ie pathogens), we do not know exactly which genes the pathogen needs to infect zucchini plants,” says Hind. “It could be something we’ve never seen before, like a new gene or mechanism that has evolved in this species that isn’t seen in the rest of the family. It could be very exciting.”

To approach the answer, the research team grew bacteria in liquid media that mimicked the host environment and identified more than 400 genes whose expression was altered when the pathogen interacted with its “host.” In particular, they noted increased gene expression for enzymes associated with the breakdown of plant tissues, which are crucial for the further development of the disease.

If Hind’s team can learn more about these factors and how zucchini respond to them, there may be a way to prevent bacteria from penetrating pumpkin fruits. “It would really save farmers,” she says. “They don’t care so much when it gets to the leaves, but if it infects the fruit, they’re in trouble.”

Hind adds: “This project would not have been possible without the contribution of some really talented undergraduate students. We love that students participate in our research. They bring a sense of enthusiasm and impatience to the lab – as well as really creative ideas.” “

Although both students have graduated, check out the new Crop Science students in this video who contribute to other Hindi pumpkin projects. High school students and transfer students can learn more about Crop Sciences courses online.

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More information:
Rikky Rai et al., Genome sequencing and functional characterization of Xanthomonas cucurbitae, the causative agent of the bacterial spotted disease cucurbita, Phytopathology (2021). DOI: 10.1094 / PHYTO-06-20-0228-R

Provided by the University of Illinois at Urbana-Champaign

Citation: Sequenced genome for annoying pumpkin pathogen (2021, March 25) retrieved March 25, 2021 from

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