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Dec 20
InterConnections: Get to Know Danielle Stevens

​​A Genetic Toolkit for Investigating Clavibacter Species: Markerless Deletion, Permissive Site Identification, and an Integrative Plasmid

Name: Danielle Stevens

Current Position: Integrative genetics and genomics Ph.D. candidate and USDA NIFA predoctoral fellow, University of California Davis, California, USA

Education: B.S. degree in biochemistry and biophysics at Oregon State University, OR, USA

Non-scientific Interest: Traveling, tech, hiking

Brief Bio: Often we hear of scientists who were driven by their passions as children. Growing up, I enjoyed science but nothing in particular perked my interests. At Oregon State University, I worked toward a B.S. degree in biochemistry and biophysics thinking I would work in the medical field to make a difference in people's lives. However, an accidental introduction to gram-positive actinobacterial plant pathogens and molecular plant–microbe interactions thanks to Dr. Jeff Chang changed much of my perspective and goals.

As an undergraduate student in his lab, I investigated the contribution of bacterial virulence loci to disease in plant-associated Rhodococcus and worked collaboratively in a team that elucidated the misdiagnosis of beneficial Rhodococcus bacteria as a pathogen in pistachio. During those formative years, I learned and loved what it meant to do science. I also witnessed the economic implications of the misdiagnosis on both pistachio growers and in the loss of time for many research groups as we tried to repeat incorrect findings. Since then, I have been committed to making my research, both data and code, accessible to others.

Now, I am fortunate to continue studying actinobacterial pathogens, focusing on important crop pathogens of the Clavibacter genus under the mentorship of Dr. Gitta Coaker. Using large-scale genomics and functional biology, I am investigating effector-driven host range, which has been a question in Clavibacter biology for over a decade. Additionally, I am investigating how these bacteria interact with the plant immune system, an area which has been relatively unexplored in the context of pattern-triggered immunity.

Compared to their gram-negative peers, actinobacterial pathogens are greatly understudied, in part, due to the limited number of genetic and biochemical tools. Thus, I wanted to first generate a genetic toolkit for Clavibacter during my Ph.D. studies, which could expand the type of questions that could be investigated. The work I published in MPMI highlights new genetic tools we have adapted and developed for Clavibacter with potential application in orphan systems. We have a vector designed for markerless deletion and another that can be combined with an R package, permissR, which aids in targeted integrated expression. These vectors build on tools designed for other actinobacterial pathogens, while taking advantage of the growing genomics-focused era of plant–microbe research today.

In the long run, I hope to continue combining computational and functional approaches to unravel how actinobacterial pathogens evolve and adapt to their hosts. In turn, this can help us develop long-term, sustainable solutions to managing actinobacterial pathogens.

Twitter: @Dani_M_Stevens

Personal website:

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