Pedro Pattyn

Phd Student (Group member from 2006 until 2012) + 32 (0) 9 33 13 692

Research

Plant evolutionary and comparative genomics

Arabidopsis thaliana is undoubtedly the most used plant model system in laboratories. However, fully sequenced genomes of close relatives until recently were not available, rendering extensive comparative genomics with this interesting species impossible. This changes with the genome sequencing of its closest relative, Arabidopis lyrata and of Capsella rubella, a species from the closest related genus. My interests mainly are:

• how fast do plant genomes evolve, at different levels. Despite the short evolutionary distances, chromosome numbers for instance have already changed. What is the frequency of chromosomal rearrangements and which mechanism are behind them?
• Secondly, three whole genome duplications have been shared. What has happened with these duplicates in the different species since their divergence? Have they been retained more or less in a similar way or did for instance A.thaliana with its smaller genome size loose more frequently large parts of duplicated regions? Do species-specific regions explain by GO-annotations in some way different lifestyles?
• Third, why is the genome of A.thaliana some remarkably smaller compared to its close relatives? How did the supposed genome reduction in A.thalianahappen?
• Forth, A.thaliana is a highly successful species nowadays occurring almost worldwide. Although part of this seems to be explained by the fact that A.thaliana is a self-fertilizer, not everything seems to be clarified by this fact.C.rubella is also highly inbreeding, yet has a much more limited areal compared to A.thaliana. Can we find additional explanations? Is genome size a factor? Are gene family expansions/contractions present? Also searching for rapidly evolving genes or regions is an important topic here. GO-annotation of the involved families/genes can lead us to more insight in this matter.

Papers

(2) * Hu, T.T., * Pattyn, P., Bakker, E.G., Cao, J., Cheng, Y.-Y., Clarck, R.M., Fahlgren, N., Fawcette, J., Grimwood, J., Gundlach, H., Haberer, G., Hollister, J.D., Ossowski, S., Ottilar, R.P., Salamov, A., Schneeberger, K., Spannagl, M., Wang, X., Yang, L., Nasrallah, M.E., Bergelson, J., Carrington, J.C., Gaut, B.S., Schmutz, J., Mayer, K., Van de Peer, Y., Grigoriev, I., Nordborg, M., Weigel, D., Guo, Y-L. (2011) The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat. Genet. 43(5):476-81. *contributed equally

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(1) Proost, S., Pattyn, P., Gerats, T., Van de Peer, Y. (2011) Journey through the past: 150 million years of plant genome evolution. Plant J. 66(1):58-65.

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