Yves Van de Peer Lab

Research focus

​Yves Van de Peer leads the Bioinformatics and Evolutionary Genomics (BEG) Division. The BEG division is a center of excellence in the field of gene and genome annotation and in the field of comparative and evolutionary genomics.

Nowadays, BEG is considered a genome analysis powerhouse specialized in the study of the structure and evolution of plant genomes. Because of our unique expertise and experience in gene prediction, genome annotation, and genome analysis, our research group has been, and still is, involved in many international genome projects and works closely together with international genome sequencing centers such as the DOE Joint Genome Institute (USA), Genoscope (France), and BGI (China). In the past years, BEG has been heavily involved in analyzing and studying the genomes of the poplar tree, grape, apple, tomato, potato, Arabodopsis lyrata, Eucalyptus grandis, Medicago, the orchids Phalaenopsis equestris and Dendrobium catenatum, the sea grass Zostera marina, several green and brown algae, several fungi that are associated with plants, and different kinds of mites and other arthropods that are pests to plants. In total, our contribution to these important genome projects describing analyses of complete genomes that serve a very wide community of scientists has already led to more than 25 highly cited papers in the highest impact journals such as PNAS, Nature, Nature Genetics, and Science.

Also in the field of genome evolution and gene and genome duplications, we have obtained a world-renowned reputation. We have been the first to link whole genome duplications with the origin of the angiosperms, coined ‘an abominable mystery’ by Charles Darwin, and more recently we have provided exciting evidence that whole genome duplications probably play a role in avoiding extinctions. Most flowering plants have been shown to be ancient polyploids that have undergone one or more whole genome duplications early in their evolution. Furthermore, many different plant lineages seem to have experienced an additional, more recent genome duplication.  Starting from paralogous genes lying in duplicated segments or identified in large expressed sequence tag collections, we recently dated these youngest duplication events through penalized likelihood phylogenetic tree inference and could show that a majority of these independent genome duplications are clustered in time and seem to coincide with the Cretaceous–Paleogene (K/Pg) boundary. Therefore, we proposed that polyploidization may have contributed to the survival and propagation of several plant lineages during or following the K/Pg extinction event.  Although we published a first study on the possible correlation between WGDs and periods of environmental upheaval in 2009, we recently revisited this hypothesis and confirmed our previous results, based on more than 40 genomes and using the most sophisticated evolutionary models available. We are now planning to use both evolutionary experiments with unicellular green algae as well as evolutionary robotics to get more insights into the mechanisms and adaptive capabilities of polyploid organisms in dynamically changing environments.

 

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Publications

The genome of the seagrass Zostera marina reveals angiosperm adaptation to the seaOlsen J* Rouzé P Verhelst B Lin Y Bayer T Collen J Dattolo E De Paoli E Dittami S Maumus F Michel G Kersting A Lauritano C Lohaus R Töpel M Tonon T Vanneste K Amirebrahimi M Brakel J Boström C Chovatia M Grimwood J Jenkins J Jueterbock A Mraz A Stam W Tice H Bornberg-Bauer E Green P Pearson G Procaccini G Duarte C Schmutz J Reusch T* Van De Peer Y*NATURE, 530, 331-5, 2016* These authors contributed equally
The genome sequence of the orchid Phalaenopsis equestrisCai J* Liu X* Vanneste K* Proost S* Tsai W* Liu K* Chen L He Y Xu Q Bian C Zheng Z Sun F Liu W Hsiao Y Pan Z Hsu C Yang Y Hsu Y Chuang Y Dievart A Dufayard J Xu X Wang Y Wang J Xiao X Zhao X Du R Zhang G Wang M Su Y Xie G Liu G Li L Huang L Luo Y Chen H Van De Peer Y Liu ZNATURE GENETICS, 47, 65-72, 2015* These authors contributed equally
The genome of Eucalyptus grandisMyburg A, Grattapaglia D, Tuskan G, Hellsten U, Hayes R, Grimwood J, Jenkins J, Lindquist E, Tice H, Bauer D, Goodstein D, Dubchak I, Poliakov A, Mizrachi E, Kullan A, Hussey S, Pinard D, Van Der Merwe K, Singh P, Van Jaarsveld I, Silva-Junior O, Togawa R, Pappas M, Faria D, Sansaloni C, Petroli C, Yang X, Ranjan P, Tschaplinski T, Ye C, Li T, Sterck L, Vanneste K, Murat F, Soler M, Clemente H, Saidi N, Cassan-Wang H, Dunand C, Hefer C, Bornberg-Bauer E, Kersting A, Vining K, Amarasinghe V, Ranik M, Naithani S, Elser J, Boyd A, Liston A, Spatafora J, Dharmwardhana P, Raja R, Sullivan C, Romanel E, Alves-Ferreira M, Kulheim C, Foley W, Carocha V, Paiva J, Kudrna D, Brommonschenkel S, Pasquali G, Byrne M, Rigault P, Tibbits J, Spokevicius A, Jones R, Steane D, Vaillancourt R, Potts B, Joubert F, Barry K, Pappas G, Strauss S, Jaiswal P, Grima-Pettenati J, Salse J, Van de Peer Y, Rokhsar D, Schmutz JNATURE, 509, 356-62, 2014
Genome dynamics of the human embryonic kidney 293 lineage in response to cell biology manipulationsLin Y, Boone M, Meuris L, Lemmens I, Van Roy N, Soete A, Reumers J, Moisse M, Plaisance S, Drmanac R, Chen J, Speleman F, Lambrechts D, Van de Peer Y, Tavernier J, Callewaert NNature Communications, 5, 4767, 2014
The Norway spruce genome sequence and conifer genome evolutionNystedt B, Street N, Wetterbom A, Zuccolo A, Lin Y, Scofield D, Vezzi F, Delhomme N, Giacomello S, Alexeyenko A, Vicedomini R, Sahlin K, Sherwood E, Elfstrand M, Gramzow L, Holmberg K, Hallman J, Keech O, Klasson L, Koriabine M, Kucukoglu M, Kaller M, Luthman J, Lysholm F, Niittyla T, Olson A, Rilakovic N, Ritland C, Rossello J, Sena J, Svensson T, Talavera-Lopez C, Theissen G, Tuominen H, Vanneste K, Wu Z, Zhang B, Zerbe P, Arvestad L, Bhalerao R, Bohlmann J, Bousquet J, Garcia Gil R, Hvidsten T, De Jong P, Mackay j, Morgante M, Ritland K, Sundberg B, Thompson S, Van de Peer Y, Andersson B, Nilsson O, Ingvarsson P, Lundeberg J, Jansson SNATURE, 497, 579-84, 2013

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News

How flowering plants colonized the sea

13/05/2016 - A recent genome study of the seagrass Zostera marina, published by an international team of 35 researchers in early 2016, may prove to lay the foundations for a range of functional ecological studies. Yves Van de Peer is happy to give a full account.

Seagrass genome study to boost ecological insight in marine ecosystems

18/02/2016 - This study reveals unique insights into the genomic losses and gains involved in achieving the structural and physiological adaptations required for its marine lifestyle, arguably the most severe habitat shift ever accomplished by flowering plants.

The genome sequence of the orchid Phalaenopsis equestris

20/04/2015 - The lab of Yves Van de Peer (VIB Department of Plant Systems Biology) can add an extra genome paper to its long list.

ERC awards €2.22 million to Yves Van de Peer for his innovative Advanced Grant proposal DOUBLE-UP

27/06/2013 - ”This exceptional grant will allow me to think out of the box (ERC projects have to be high risk-high gain) and explore less obvious ways of addressing major questions in evolutionary biology.

Looking for data in the Arabidopsis mine, no canary needed

27/06/2013 - Sofie Van Landeghem from the group of Yves Van de Peer at the VIB Department of Plant Systems Biology, UGent together with the group of Dirk Inzé, director of PSB, digged into the wealth of information hidden in the biomolecular literature mine.

An international consortium sequences tomato genome

30/05/2012 - The Tomato Genome Consortium (TGC), a group of over 300 scientists from thirteen countries, has sequenced the genomes of the domesticated tomato and its wild ancestor, Solanum pimpinellifolium.

Genome of first arachnid cracked

24/11/2011 - An international team of scientists - including VIB-UGent - has succeeded in deciphering the genome of the spider mite.

GenomeView wins 'Most Creative Visualization' Award

15/09/2011 - Thomas Abeel, VIB Department of Plant Systems Biology, UGent, is one of the winners in the first iDEA (Illumina’s Data Excellence Award) Challenge

VIB scientists win DREAM-5 for systems biology

18/03/2011 - The DREAM is the most important benchmark for the comparison of computational models used in systems biology. Among all the top labs, their test was unanimously rated the overall best performer based on a number of gold standard data sets.

Genetic code of ‘Golden Delicious’ apple cracked

30/08/2010 - An international team of scientists – including Yves Van de Peer of VIB (Vlaams Instituut voor Biotechnologie) and Ghent University – have cracked the genetic code of the apple.

DNA duplication - a mechanism for 'survival of the fittest'

20/03/2010 - 150 years after Darwin published his theory of evolution, VIB researchers connected to Ghent University have discovered that DNA duplications have given plants an evolutionary advantage.

Secrets of cooperation between trees and fungi revealed

03/03/2008 - VIB researchers have succeeded in unravelling the genetic code of Laccaria bicolor. This new information will lead to a better understanding of how fungi help trees to grow and how together they can be indicators of climate change.

Poplar DNA code cracked − new possibilities for sustainable energy

15/09/2006 - Scientists has succeeded in unraveling the first tree genome − that of the poplar. Moreover, their research indicates that the poplar has about 45,000 genes

DNA duplications found to have been essential for the evolution man and fish

10/02/2004 - The genes that people and fish have in common are the result of duplications of the entire DNA sometime in the distant past, VIB research has shown.

Yves Van de Peer

Yves Van de Peer

Research area(s)

Bio

​​PhD: Univ. of Antwerp, Antwerp, Belgium, 1995
VIB Group leader since 2002
VIB Division Coordinator since 2003

Contact Info

VIB-UGent Center for Plant Systems BiologyUGent-VIB Research Building FSVMTechnologiepark 927 9052 GENTRoute description