PS Seminar Series - Gene regulatory dynamics of germinating seeds from bulk tissue to single-cell resolution

Abstract - Seeds provide 70% of global food resources, being the most valuable output from plant production. They also play a critical role in agriculture because the lifecycle of most crops begins from seed germination. Uniform germination enables growers to achieve optimal plant-spacing and harvesting time. Despite this importance, we do not have a complete understanding of how seed germination is regulated, which limits our ability to improve its properties. We have made much progress identifying regulators by traditional bulk-tissue 'omics approaches. Through these we have discovered transcription factors that control both gene expression and the progress of germination. However, the seed is a complex structure comprised of many tissues and cell-types, each of which have distinct properties. Changes in gene expression occur in these cell-types throughout germination and are expected to be context-dependent, to enable spatiotemporal control of cellular processes. To better understand how gene expression is controlled within individual seed cell-types we have carried out single-cell RNA-Seq in germinating Arabidopsis embryos. We analysed seeds at three time points after stratification: 12 hours (mucilage excretion), 24 hours (testa rupture) and 48 hours (radicle emergence). We then identified individual cell-types within the embryo, annotated their identities and studied how they changed over time. This study provides unprecedented insight into the transcriptome of the germinating Arabidopsis embryo and genome regulatory network during seed germination. It will help us to develop practical solutions to promote the seed-to-seedling transition and to ensure germination happens uniformly at the right time.

Biography - A/Prof Lewsey’s lab studies genome regulation. We are interested in how organisms control expression of tens of thousands of genes at systems-level. Our goal is to understand how organisms use genome regulation to interact with and respond to their environments. Cutting edge ‘omics technologies are key to our work and we have a keen interest in applying new laboratory and computational approaches. Some of our most recent achievements have been in applying single-cell genomics to understand the processes that occur in seeds during germination. Our research ranges from the fundamental to the industrially applied, encompassing Arabidopsis, barley, malaria, oats, cannabis, opium poppy and a variety of mammals.

A/Prof Lewsey studied his PhD in plant virology under the guidance of Prof JP. Carr at the University of Cambridge (2002-2006). Between 2006 and 2010 I continued to study plant-virus-vector interactions as a postdoc in Prof Carr’s lab. In 2010 he was awarded a highly competitive European Union Marie Curie International Outgoing Fellowship (three years’ salary and research expenses), which I took to the laboratories of Prof JR. Ecker and Prof R. Solano (Salk Institute, USA and Centro Nacional de Biotecnologia, Spain, respectively). Concurrent appointment in two laboratories is characteristic of this fellowship scheme. Between 2010 and 2016 my research applied genomic and systems biology approaches to study plant epigenetics/epigenomics and plant hormone biology. In 2016, I was recruited by as an Assistant Professor (Senior Lecturer) at La Trobe University to establish my independent laboratory. In 2017 I became Director of the La Trobe Genomics Platform. In 2019 I became Co-Deputy Director of the ARC Research Hub for Medicinal Agriculture and was promoted to Associate Professor. From 2020 to 2022 I served as Director of Research for the La Trobe School of Life Sciences.