Research project Polyploidy Uncovered: From Genome to Application through AI and Modelling

General introduction

Whole genome duplication (WGD) is a driving biological force. Nevertheless, there remain many questions about its roles and impact in biological processes and across the tree of life. Here, we want to apply a holistic approach using both wet-lab and computational approaches to study the mechanistic underpinnings of WGDs, as well as its applications. The project tackles the following questions: how does the increased complexity of duplicated gene regulatory networks affect polyploid organisms? Why is the polyploid state in ecological niches often transient, leading to the process of ‘diploidization’, and what is the contribution to polyploidy as well as to rediploidization of the different sub-genomes? What are the underlying mechanistic underpinnings that may confer an advantage for polyploids over diploids under stressful or changing environmental conditions?

Research approach

Replaying the ‘genome duplication’ tape of life with both populations of fast-growing cells or organisms or with artificial (digital) organisms in simulation should offer novel insights regarding when and how and under which circumstances WGD might confer a selective advantage. Spirodella and Chlamydomonas will be subjected to ‘evolve and resequence’ experiments, where genomes of natural and/or artificial polyploid cells or organisms are (re)sequenced or studied after many generations of selection. An AI framework will be built to study the effects of polyploidy through populations of digital organisms (DOs). Novel modeling approaches are developed to study the effects of polyploidy from an eco-evolutionary dynamics perspective, integrating population and quantitative genetics with ecological interactions. Interspecific Festulolium hybrids covering a range of genomic diversity and ploidy levels are used to unravel the genome and transcriptome response of allopolyploids to drought stress in an agronomic setting.

Relevance/Valorization

The Methusalem project investigates the role of WGD and polyploidy in generating biodiversity, adaptation to new environments, and improvements in agriculture and horticulture, cancer therapy, and other branches of medicine. Greater integration of research on WGD promises to identify commonalities across biological scales and phylogenetic distances while also clarifying which responses might be unique to a biological process or taxon, thus potentially revealing ‘rules’ to polyploidy. That is, predictable features (‘rules’) may allow polyploid organisms to solve environmental challenges.

Financing

UGent