October 2, 2020 at 10:00 pm

Plant Biology Colloquium | Leveraging Global Gene Co-expression Networks for Specialized Metabolic Pathway Discovery, Oct. 9

Jennifer Wisecaver, portrait

Dr. Jennifer Wisecaver

The Environmental & Plant Biology Colloquium Series presents Dr. Jennifer H. Wisecaver discussing “Honor by association, leveraging global gene co-expression networks for specialized metabolic pathway discovery” on Oct. 9 at 11:50 a.m.

Wisecaver is Assistant Professor of Biochemistry at Purdue University.

Abstract: Specialized metabolites serve a myriad of biological functions that allow organisms to interact with and manage their environment (e.g., resist abiotic stress, combat negative ecological interactions and promote beneficial ones). These metabolites are synthesized in response to dynamic ecological pressures, and as a consequence, the pathways involved in metabolite biosynthesis are often fast-evolving, lineage-specific, and remain uncharacterized at the genetic level. This hampers our ability to understand metabolic gene innovation at the level of individual pathways. Critically, this also limits the potential utility of specialized metabolites in agriculture, pharma, and biotech applications. To address this challenge, we developed the mutual ranks to modules workflow, a method for identifying small, overlapping modules of co-expressed genes in global co-expression networks. These modules serve as the basis for high-throughput prediction of specialized metabolic pathways. Using the model plant Arabidopsis, modules accurately recovered the enzymatic genes of functionally characterized, specialized pathways as well as genes involved in pathway regulation and metabolite transport. Importantly, a co-expression network approach can straightforwardly be applied to any species, model and non-model, so long as the organism’s transcriptome can be sampled under a range of ecologically relevant conditions. Currently, we are utilizing Oxford Nanopore long-read sequencing technology to construct highly contiguous genome assemblies of eukaryotes with expanded metabolic repertoires to identify gene candidates for pathways of interest and characterize the genes’ location(s) within genomes. With these data, we aim to evaluate the degree to which specialized metabolic pathways form of biosynthetic gene clusters in different eukaryotic lineages. The utility of this approach is illustrated by ongoing work in our lab to characterize allelochemicals to algal phycotoxins.

Leave a Reply

Your email address will not be published. Required fields are marked *