We study polyploidy from various theoretical perspectives. Theory building and applying theoretical models from related field is a very valuable part of the cycle of scientific research, which complements our empirical research. By framing observations in a robust and transparent representation of the biological world, we can question our understanding in future research using our model systems.
Thousands of species are currently polyploid, possessing more than two complete sets of chromosomes. However, the long-term establishment of organisms that have undergone ancient whole genome duplications (WGDs) has been exceedingly rare and when we analyse the genomes of plants and animals, we can, at most, find evidence for a very limited number of WGDs that survived on the longer term. The paucity of (established) ancient genome duplications and the existence of so many species that are currently polyploid provides a fascinating paradox.
Constituting approximately 10% of flowering plant species, orchids (Orchidaceae) display unique flower morphologies, possess an extraordinary diversity in lifestyle, and have successfully colonized almost every habitat on Earth.
Because of our unique and long-standing expertise in genome annotation, as well as our expertise in documenting ancient whole genome duplication (WGD) events, our lab has been, and still is, involved in many international genome projects.
Early 2021, seven Ghent University research groups received funding so that they can develop projects throughout the next 7 years. Our research group was one of them. The Methusalem program offers the most prestigious and extensive funding from the Ghent University Special Research Fund. A total of 27.5 million euros have been allocated for a period of 7 years.
At present, knowledge about the (eco-)evolutionary effects of polyploidy is largely based on either the comparison of contemporary polyploids with their diploid ancestors' descendants, or based on signatures of Whole Genome Duplications (WGDs) in present-day plant genomes. These comparative methods, although informative, suffer from potential biases introduced by evolution of both the polyploid and the descendants of its ancestors after establishment.
Alongside studying the evolution of duplicated genomes through experimental evolution, we also investigate the evolution of polyploid genomes using computer-based in-silico simulations. These simulations involve tracking the evolution of (duplicated) artificial genomes that encode gene regulatory networks, providing valuable insights into the dynamics and adaptation of polyploid systems.
Seagrasses are unique flowering plants, adapted to a fully submerged existence in the highly saline environment of the ocean, where they must root in reducing sediments, endure chronic light limitation and withstand considerable hydrodynamic forces. In spite of these obstacles, the 80 or so species are among the most widely distributed flowering plants with recently measured estimates of coverage ranging from 600,000 km² to a modeled value of 1.6 million km².
The African Orphan Crops Consortium (AOCC) aims to sequence, assemble and annotate the genomes of more than 100 traditional neglected or under-utilized African crops, as well as to re-sequence hundred lines for each species.
These reference genomes are made available through our online genome annotation system ORCAE at http://bioinformatics.psb.ugent.be/orcae/aocc
Gene analyses revealing the capacity of marine flowering plants to exist under changing environmental conditions provide clues for the conservation and sustainable use of important ecosystems
