Yves Van de Peer - DOUBLE UP

Onderstaande beschrijving is in het Engels:

Yves Van de Peer is full Professor at Ghent University, adjunct Research Professor at the department of Computer Science and the department of Biology, Faculty of Science, University of Western Ontario, Canada and part-time Professor at the Genomics Research Institute, Department of Genetics, University of Pretoria, South Africa.
He leads the The Bioinformatics and Evolutionary Genomics (BEG) group at VIB-PSB and is widely regarded as a world-leader for bioinformatics, with unique expertise in algal and plant genomics. His group is a centre of excellence for gene and genome annotation, comparative and evolutionary genomics, evolutionary systems biology. Currently, his research focuses on two major themes, namely plant and algal genomes and evolutionary analyses, with an emphasis on gene and genome duplication. A substantial amount of work is devoted to the development of novel gene prediction and modelling tools, and on improving machine learning algorithms and comparative approaches using sequence information from other genomes. His team has also extensive expertise in the development of (online) resources, both in the field of genome annotation and comparative evolutionary genomics.
Yves Van de Peer co-authored over 330 publications in peer-reviewed journals, (>26.000 citations, H-index: 80). He is currently the 2nd most cited plant scientist in Europe. Associate editor for 8 peer-reviewed journals. Within his recently acquired Advanced ERC grant he wants to study the significance of whole genome duplications for the evolution of natural and artificial organism populations.

Contact: Yves.VandePeer@UGent.be

Publications: publication list

DOUBLE-UP- The importance of gene and genome duplications for natural and artificial organism populations

The long-term establishment of ancient organisms that have undergone whole genome duplications (paleopolyploids) has been exceedingly rare. On the other hand, tens of thousands of now-living species, both plants and animals, are polyploid, and contain multiple copies of their genome (neopolyploids). The apparent paucity of ancient genome duplications and the existence of so many species that are currently polyploid provide an interesting and fascinating enigma. A question that remains to be answered is whether these older genome duplications have survived by coincidence or whether they could survive only because they did occur, or were selected for, at very specific times, for instance during major ecological upheavals and periods of extinction. It has indeed been proposed that chromosome doubling conveys greater stress tolerance by, for instance, fostering slower development, delayed reproduction, longer life span, and greater defence against pathogens and herbivores.  Furthermore, polyploids have also been considered to have greater ability to colonize new or disturbed habitats. If polyploidy allowed many plant lineages to survive and adapt during global changes, as previously suggested, we might wonder whether polyploidy will confer a similar advantage in the current period of global warming and general ecological pressure caused by the human race. Given predictions that species extinction is now occurring at as high rates as during previous mass extinctions, does the presumed extra adaptability of polyploid plants mean they will become the dominant species? In the current research proposal, we hope to address these questions at different levels through 1) the analysis of whole plant genome sequence data and 2) the in silico modelling and evolution of artificial gene regulatory networks to mimic the genomic consequences of genome doubling and how this may affect network structure, redundancy, rewiring, and dosage balance. Furthermore, we aim at using simulated robotic models running on artificial gene regulatory networks in complex and challenging environments to evaluate how both natural and artificial organism populations can potentially benefit from gene and genome duplications for adaptation, survival, and evolution in general.  

DOUBLE-UP will explain how organisms - through the evolution of their duplicated genomes - have been able to diversify, compete for niches, and survive ecological turmoil.  DOUBLE-UP should also allow prediction of future species evolution.  DOUBLE-UP is a truly interdisciplinary proposal that will open up new horizons and perspectives for different fields of research, from bioinformatics and systems biology over comparative and evolutionary biology, to network modelling and evolutionary robotics.