The Komarov Botanical Institute gave a tour of the Peter the Great Botanical Garden to its Moscow colleagues. Credit: IITP RAS Press Center

From January 12 to April 20, the Komarov Botanical Institute of the Russian Academy of Sciences in St. Petersburg hosted the Plant Genomics School, which focused on high-throughput sequencing (HTS) technologies. For four months, 40 attendees from several Russian universities and research centers mastered bioinformatics methods used in plant biology to apply them in their research. 

The school, organized by the Skolkovo Institute of Science and Technology (Skoltech) and the Kharkevich Institute for Information Transmission Problems (IITP RAS), is a part of the Federal Research Program for Genetic Technologies Development. Skoltech Bio assistant professor Maria Logacheva and the IITP team headed by leading researcher Alexey Penin developed the training course. Anna Klepikova and Denis Omelchenko from IITP RAS, Mikhail Shchelkunov, Tagir Samigullin, and Lavrenty Danilov joined the school as instructors.

The attendees included PhD students, PhD graduates, and doctors of science from the Komarov Botanical Institute, Vavilov All-Russian Institute of Plant Genetic Resources (VIR) in St. Petersburg, St. Petersburg State Chemical and Pharmaceutical University (SPCPU), St. Petersburg State University (SPbU), and Grodno State Agrarian University in Belarus. 

Attendees in class. Credit: IITP RAS Press Center

The classes took place in the historical building of the Komarov Botanical Institute Herbarium of Higher Plants in the scenic Peter the Great Botanical Garden. During the training, participants mastered high-throughput sequencing data processing from experiment planning to data analysis. The instructors explained how to assemble genomes and transcriptomes, explore relationships between organisms (phylogeny), analyze gene expression profiles, search the genome for genes associated with a particular phenotype, and much more. Within the statistics track, attendees learned to apply various statistical analysis methods and visualize results by creating illustrations for research papers using the R language.

Students and organizers at the entrance to the BIN RAS Herbarium of Higher Plants. Credit: IITP RAS Press Center

“The idea of the school came up in our informal discussion with Alexey Penin and Maria Logacheva at a conference last year,” said Dmitry Geltman, the Komarov Botanical Institute director. He said that Maria and his team were researching the genetic diversity of Sosnowsky’s hogweed and related giant hogweed species. “Researchers from the Komarov Botanical Institute can always help with taxonomic expertise because no matter how much genome sequencing you do, you must be able to recognize the plant on sight. IITP and Skoltech, in turn, have advanced competencies that botanists can use in their work,” he said.

According to Penin, the school was to establish cross-disciplinary connections between geneticists, bioinformaticians, and botanists. “This symbiosis benefits everyone involved: botanists know plants like no one else, while geneticists offer methods that can take plant research to a whole new level. Also, this evokes a historical parallel: in Soviet times, the Komarov Botanical Institute took under its wing the geneticists who suffered persecution instigated by academician Lysenko. Symbolically, this school has seen geneticists come back to the Komarov Botanical Institute in an entirely different context,” he said.

Explaining their decision to attend the school, the students said that this training helps them look at their research from another perspective, expand their research toolset, network with experts, and better understand scientific literature. “I now have a much better understanding of modern research and find it easier to read scientific publications. Now I can see what methods researchers use, what I should focus on, and why,” said Irina Varganova from the VIR Herbarium Department.

The participants tour the Herbarium of Higher Plants to pick plant species for future genetic research. Credit: IITP RAS Press Center

Maria Povydysh, head of the SPCPU Biochemistry Department, plans to apply her new knowledge and skills to research and teaching. “We were especially thrilled about using mathematical statistics in biological data processing. Sadly enough, our university lacks expertise in this topic. Statistical data processing methods can come in handy in the metabolomics of medicinal plants that we are deeply involved in, especially because data this big is often hard to process. Also, these techniques would facilitate calculating and properly presenting data about preclinical studies of new drugs.”

Participants in the program appreciated the easily understandable and captivating presentation of the material and the readiness with which instructors were answering questions outside of class. The fact that attendees were willing to come from other cities and even travel from Grodno to St. Petersburg every week is a testament to the importance of the school for the community. Klepikova, one of the instructors, expressed pleasure in teaching an audience of highly motivated students.

In the greenhouses of the Peter the Great Botanical Garden. From left to right: Maria Logacheva, Alexey Penin, Anna Klepikova, Denis Omelchenko and Irina Varganova. Credit: IITP RAS Press Center

“It was a pleasure to teach an audience of highly motivated students who not only asked penetrating questions on the topic, but also offered comments that will help improve this course,” Klepikova commented.

The school is a part of the educational initiative of Skoltech and IITP. The program started last summer with a crash course on high-throughput sequencing in genetics and plant breeding organized in Moscow for students and young researchers from across Russia. (Read more on Skoltech and IITP websites).

“We hope that these events will continue, since they serve to encourage collaborations between researchers from different fields of biology and generate new knowledge about important and interesting objects, such as plants,” Logacheva said.

The school on high-throughput plant genome analysis is coming up this fall in Moscow.

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More photos here.