Sequencing whole plant genomes in the classroom

Project Title: Sequencing whole plant genomes in the classroom

Project Lead's Name: Richard Moore

Project Lead's Email:

Project Lead's Phone: 513-529-4278

Project Lead's Division: CAS

Primary Department: Biology

List Departments Benefiting or Affected by this proposal: Biology

Estimated Number of Under-Graduate students affected per year (should be number who will actually use solution, not just who is it available to): 24

Estimated Number of Graduate students affected per year (should be number who will actually use solution, not just who is it available to): 0

Describe the problem you are attempting to solve and your approach for solving that problem: There are over 450,000 species of land plants on this earth. This incredible diversity is a product of genetics that provide the variation that is the fuel that natural selection acts upon to drive evolutionary change and diversification. Fundamental to understanding the mechanisms driving plant diversification is knowing how changes at the level of DNA affect physical changes in plant structure and function. However, students in our Biology and Botany programs can graduate without ever having learned how to analyze DNA at the whole-genome level and relate that information to evolutionary change. Therefore, many lack the skills used in modern genetic and molecular evolutionary analysis that will contribute to their success post-graduation.

In my course, BIO204 Evolution of Plant biodiversity, we address this relationship between change in plant genes and genomes and evolutionary change giving rise to the diversity of plant species. While this course has a laboratory component, we have never formally introduced a lab where we practice modern molecular techniques in DNA analysis with the intent of understanding better the relationship between a plant’s DNA sequence and its physical appearance. The intent of this technology grant would be to fund the appropriation of a pocket-sized DNA sequencing device that is capable of sequencing entire plant genomes in real-time. This equipment will be form the basis of a lab exercise in BIO204, training students in using modern DNA sequencing technology and analysis.

How would you describe the innovation and/or the significance of your project: The tech fee would be used to purchase a MinION sequencing device, with four flow cells and materials each used for sequencing up to 10-20 Gb of DNA sequence (i.e. 10-20 billion base pairs, or more than 2 times the size of the human genome). This is more than enough sequencing capacity to sequence smaller plant genomes. Specifically, the students will learn to isolate and prepare DNA from the common duckweed in order to analyze the structure of its genome. The genome of duckweed (Lemna gibba) is approximately 150 Mbp (150 million base pairs, or about 3% the size of the human genome), and duckweed can be obtained readily from ponds or through biological supply companies. The small genome size of duckweed will mean that one MinION flow cell will sequence the genome 10 times over, facilitating downstream analysis. Furthermore, duckweed is a model organism for studying flowering plant evolution, as it is the smallest flowering plant species and has one of the smallest genomes of flowering plants. There is also much variation in the genome sequence of duckweed from its native range, and students will be able to compare their sequences to duckweed genomes from around the world (mainly North American and Europe).

Importantly, this project will be the first experience most students with using modern DNA sequencing technology and analysis. It is essential for today’s biologists to learn how to work with and analyze large DNA datasets, as this forms the basis of genetic and evolutionary analysis in today’s research environment. It will give students their first experience with generating and manipulating “big data”, and open their eyes to the secrets hidden in the genomes of ordinary organisms. To date, we have not attempted even single gene analysis in BIO204, which is a great disservice to our students. This project will help introduce students to the genomic era of evolutionary analysis. It will also provide us with the MinION sequencing equipment, which can be re-used in future semesters and/or be available for use by other Biology department classes.

How will you assess the success of the project: A successful project will result in a high-quality, fully sequenced duckweed genome that can be analyzed for various qualities, such as gene predictions and repetitive sequence composition. In order to assess student success, the students will write up a report the project, including an introduction relating the relevance of the activity to understanding plant genomes and evolution, a description of the methodology, a summary of their findings and how it relates to what others have found. They will address the question of quality of the genome sequence and genome composition (numbers and types of genes), and will compare this to sequences from previously sequenced strains of duckweed from world-wide populations.

Total Amount Requested: $4,979

Budget Details:

  • MinION starter kit $4,909 Nanopore [includes the MinION sequencing equipment, 4 flow cells, and materials for sequencing up to four genomes]
  • Duckweed $10 Carolina Biological
  • Pipette tips $60 Fisher Scientific

Is this a multi-year request: No