ViPS Invited Seminar April 2023

Matias Kirst, University of Florida, USA

Date: 19th April 2023

Time: 13:00

Title: Tracing cell lineages and the regulators giving rise to exceptional plant traits

Location: Lecture room B6, Forest Sciences Building, Latokartanonkaari 7-9 and remotely via Zoom

Host: Ykä Helariutta

Abstract: Certain plant species acquired unique traits that provide adaptive advantages under biotic and abiotic stress conditions. These characteristics include obtaining atmospheric nitrogen through a symbiotic relationship with N-fixing bacteria in root nodules and photosynthetic adaptation to water deprivation through crassulacean acid metabolism (CAM). The discovery of the genetic elements that contribute to the emergence of these traits could lead to their introduction into crops to increase agricultural sustainability and productivity. Identifying cell lineages that lead to the emergence of these traits was challenging until the recent creation of single-cell genomics and cell lineage trajectories inference methods.

We recently developed methods to characterize single-cell transcriptomes by isolating and analyzing the ensemble of expressed genes from solid plant tissues, including wood. In parallel, we created a web application that simplifies and integrates bioinformatics tools for analyzing and mining single-cell genomics data. We are now applying these approaches to understand plant development, including nodule formation in the roots of Medicago truncatula and in facultative plants that perform Crassulacean Acid Metabolism photosynthesis. Here I will review our studies to reconstruct the developmental trajectories of cells undergoing differentiation during these processes and discover the genes that regulate them. I will also briefly touch on our work to uncover cell lineage trajectories and regulators involved in wood formation in poplar.

Matias is a Professor in Quantitative Genetics and Genomics at the Institute of Food and Agricultural Sciences at the University of Florida and a Fellow of the American Association for the Advancement of Science. After completing his early education in Brazil, he received his Ph.D. from the North Carolina State University in 2003, working under Dr. Ron Sederoff. After a short period at Dr. Ed Buckler’s lab at Cornell, he joined the faculty of the University of Florida in 2004. His research is focused on high-risk, high-reward approaches to address climate change and bioenergy demand with plant-based and synthetic biology approaches, primarily funded by the National Science Foundation and the US Department of Energy. He is the co-founder of several startups, which deploy genomic technologies to characterize and improve crops. He also assists and develops training opportunities for faculty engaging in entrepreneurship to accelerate the development of new ventures and translation of research into real-world applications.

Read more about Matias' work

Related publications:

Kelly M. Balmant, Jerald D. Noble, Filipe C. Alves, Christopher Dervinis, Daniel Conde, Henry W. Schmidt, Ana I. Vazquez, William B. Barbazuk, Gustavo de los Campos, Marcio F.R. Resende Jr., and Matias Kirst (2023) Xylem systems genetics analysis reveals a key regulator of lignin biosynthesis in Populus deltoides.

Paolo M. Triozzi , Thomas B. Irving, Henry W. Schmidt, Zachary P. Keyser, Sanhita Chakraborty, Kelly Balmant, Wendell J. Pereira, Christopher Dervinis, Kirankumar S. Mysore, Jiangqi Wen, Jean-Michel Ane, Matias Kirst and Daniel Conde (2022) Spatiotemporal cytokinin response imaging and  ISOPENTENYLTRANSFERASE 3 function in Medicago nodule development. doi:10.1093/plphys/kiab447

Daniel Conde, Paolo M. Triozzi, Wendell J. Pereira, Henry W. Schmidt, Kelly M. Balmant, Sara A. Knaack, Arturo Redondo-López, Sushmita Roy,  Christopher Dervinis and Matias Kirst (2022) Single-nuclei transcriptome analysis of the shoot apex vascular system differentiation in Populus. doi:10.1242/dev.200632

Daniel Conde and Matias Kirst (2022) Decoding exceptional plant traits by comparative single-cell genomics. Trends in Plant Science, November 2022, Vol. 27, No. 11

W. J. Pereira, F. M. Almeida, D. Conde, K. M. Balmant, P. M. Triozzi, H. W. Schmidt, C. Dervinis, G. J. Pappas Jr and M. Kirst (2021) Asc‑Seurat: analytical single‑cell Seurat‑based web application.‑021‑04472‑2