A Reference Genome Sequence Resource for the Sugar Beet Root Rot Pathogen Aphanomyces cochlioides

Annie Harvieux, UMN Plant Pathology Communications and Relations Coordinator

Jacob Botkin, graduate research assistant

From his undergraduate plant pathology internship to his work assembling and annotating the Aphanomyces cochlioides genome, Jacob Botkin's plant pathology career thus far has been a testament to versatility and embracing the unknown.

While interning in the University of Minnesota Plant Disease Clinic (PDC) during his bachelor's degree program, Botkin discovered a love for examining plant samples and studying plant–microbe interactions. This great fit led to a subsequent job at the Forest Service research lab in St. Paul, MN, that was doing similar diagnostic work.

Botkin points out that what surprised him most when transitioning from coursework to the PDC was how much is still left to discover about plant health and plant genetics in particular. This theme of discovery held true as he pursued his master's degree in plant pathology at the University of Minnesota under the guidance of Drs. Ashok Chanda and Cory Hirsch. During his master's program Botkin picked up more skills on genome assembly and annotation, optimizing soil DNA isolations and qPCR-based detection of soilborne pathogens.

Minnesota is number one in the nation for sugar beet production, and sugar beet production is consistently challenged by A. cochlioides, especially during wet years. To sequence and annotate the A. cochlioides genome, Botkin unlocked an entirely new skill set through on-the-go learning and collaboration: computation and coding. Despite his lack of experience in this side of the work, Botkin was encouraged not to worry about it and to take on the new challenge. Botkin credits Dr. Hirsch, assistant professor of plant pathology, with giving him regular, detailed, and ongoing lessons in coding skills, as well as Hirsch's plant genomics coursework. Spending summers at the Northwest Research and Outreach Center and pursuing opportunities to present this research to sugar beet stakeholders were also rewarding experiences for Botkin.

When the COVID-19 pandemic began and universities sent staff and students home, Botkin's work continued. With his DNA sequence data in hand, Botkin was able to work from home and do the computational portion of the project utilizing the Minnesota Supercomputing Institute's computing power. Botkin identifies this as the steepest part of the learning curve, particularly installing and configuring new software being used for plant pathogen genome assembly and annotation.

This growth has all paid off by adding versatility and adaptability to Botkin's skills and career options. Beyond going from being a mild technophobe to being his new lab's bioinformatic troubleshooter, Botkin now has a variety of skills that can take him from the computer desk to the lab to the greenhouse in a single project. This ability to work in a variety of environments and to pick up new skills and bring them into any subsequent environment has helped Botkin break the assumption that plant pathology is too niche of a career path and move into embracing the variety of skills, settings, and job options available for him.

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