Professor Li-Jun Ma, biochemistry and molecular biology, has received support from the U.S. Department of Energy’s Joint Genome Institute (JGI) Community Science Program (CSP) to conduct in-depth research on a group of soil fungi, Fusaria, that are economically important because they devastate crops – not only food but biofuel feedstocks. This is a collaborative project between principal investigator Ma and co-principal investigator Robert Proctor, a research microbiologist at the USDA Agricultural Research Service’s National Center for Agricultural Utilization.
Ma says that two of the top 10 plant pathogens are in the Fusariumfamily, based on a ranking by many molecular plant pathologists. For these new investigations, she will collaborate with Igor Grigoriev and his team at the Joint Genome Institute and Lawrence Berkeley National Laboratory. Other collaborators include evolutionary biologist David Geiser,director of the Fusarium Research Center at Penn State University; Kerry O’Donnell, an expert on taxonomy and biological diversity of Fusarium; and Daren Brown, who has more than 20 years of experience in Fusarium research.
She says of the honor and opportunity, “This is an exciting project. I’m honored by this award and I always appreciate the consistent and reliable support from JGI to the research community.”
The JGI CSP program provides the scientific community with access to high-throughput, high-quality sequencing, DNA synthesis, metabolomics and analysis capabilities that they might not otherwise have access to. For this project, JGI will allocate technical infrastructure support, such as characterizing 124 fungal samples via next-generation, long-read DNA and RNA sequencing techniques, according to the institute.
DOE also points out that “because of their associations with plants, Fusariumspecies (fusaria) can profoundly impact ‘bioenergy’ production and global ‘carbon cycling.’ The great genetic diversity of the genus is also reflected in their genomes and there is a great interest in understanding the dynamics of Fusariumgenomes and their impacts on the host-plant interactions.”
This funded project has two major components. One is to produce 50 high-quality genome assemblies that span the diversity in the genus. “I’m happy that the scope of the project covers the whole genus.” Further, the scientists will also explore the functional impact of genome dynamics on Fusarium-plant interactions by investigating 96 transcription factors identified in Fusarium oxysporum using DNA affinity purified sequencing (DAP-seq) and single cell RNAseq of three carefully selected samples. “I am excited by the opportunity to address some knowledge gaps using functional data to probe host-fungal interactions,” Ma says.
This project is based on a system developed at the Ma lab enabling the dissection of interaction between Fusarium and plants in both harmful and beneficent ways. Ma explains that another facet of this work will involve isolating individual plant cells and sequencing each cell separately, which is a cutting-edge and highly informative technique not easily used in non-human biology studies. Through network analysis, researchers will be able to “capture the action” and characterize patterns of temporal and spatial fungal-plant interactions. One goal of this research is to seek ways to intervene to prevent the plant’s death, specifically to prevent the loss of plant-based biofuel feedstocks.