Jeroen Raes

Postdoc
(Group member from 2000 until 2005)


+49 6221 387- 8372
Personal homepage

EMBL Heidelberg
Meyerhofstraße 1
69117 Heidelberg
Germany

Research

Gene family evolution - functional divergence of duplicated genes

A large fraction of genes can be grouped into families. Although the biochemical function is generally the same within a family, the biological function varies greatly. My interest lies in the reason for this functional diversification. To do this, annotation is an important issue: find all the members of a family and predict a correct gene model. In plants, this is not as easy as it seems: gene prediction software is still lagging behind and sequence data is far from as abundant as in the animal world. I worked for two years in the Genoplante Arabidopsis thaliana annotation project and have (co-)analysed (mining, annotation, phylogeny,...) many gene families since then. Some examples are genes involved in cell cycle regulation, monolignol biosynthesis and flower development (MADS). My current goal is to investigate the mechanisms behind the functional divergence within these and other gene families.

Genome evolution

The expansion and functional diversification of gene families is thightly linked to the genome evolution. From duplications of large chromosome segments over chromosomal duplications to poly-and alloploidy events, all have their impact on the availability and redundancy of genes and their interactors, and, by consequence, on the functional diversification within a gene family. In this respect, we investigated ancient duplications in the evolutionary history of the Arabidopsis thaliana genome, and made a critical assessment of the reliability of different methodologies that can be used for this.

Papers

(20) Casneuf, T., De Bodt, S., Raes, J., Maere, S., Van de Peer, Y. (2006) Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana. Genome Biol. 7(2):R13.

(19) Baele, G., Raes, J., Van de Peer, Y., Vansteelandt, S. (2006) An improved statistical method for detecting heterotachy in nucleotidesequences. . Mol. Biol. Evol. 23(7):1397-405.

(18) * Maere, S., * De Bodt, S., Raes, J., Casneuf, T., Van Montagu, M., Kuiper, M., Van de Peer, Y. (2005) Modeling gene and genome duplications in eukaryotes. Proc. Natl. Acad. Sci. USA 102(15):5454-9. *contributed equally

(17) Aubourg, S., Brunaud, V., Bruyere, C., Cooke, R., Cottet, A., Couloux, A., Dehais, P., Deleage, G., Duclert, A., Echeverria, M., Eschbach, A., Falconet, D., Filippi, G., Gaspin, C., Geourjon, C., Grienenberger, J.M., Houlne, G., Jamet, E., Lechauve, F., Leleu, O. L., Leroy, P., Mache, R., Meyer, C., Nedjari, H., Negrutiu, I., Orsini, V., Peyretaillade, E., Raes, J., Risler, J.L., Riviere, S., Rombauts, S., Rouzé, P., Schneider, M., Schwob, P., Small, I., Soumayet-Kampetenga, G., Stankovski, D., Toffano, C., Tognolli, M., Caboche, M., Lecharny, A. (2005) GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts. Nucleic Acids Res. 33(Database issue):D641-6.

(16) Raes, J., Van de Peer, Y. (2005) Functional divergence of proteins through frameshift mutations. Trends Genet. 21(8):428-31.

(15) Beysen, D., Raes, J., Leroy, B.P., Lucassen, A., Yates, J.R., Clayton-Smith, J., Ilyina, H., Sklower Brooks, S., Christin-Maitre, S., Fellous, M., Fryns, J.P., Kim, J.R., Lapunzina, P., Lemyre, E., Meire, F., Messiaen, L.M., Oley, C., Splitt, M., Thomson, J., Van de Peer, Y., Veitia, R.A., De Paepe, A., De Baere, E. (2005) Deletions involving long-range conserved non-genic sequences (CNGs) upstream and downstream of FOXL2 as novel disease-causing mechanism in bpes. Am. J. Hum. Genet. 77(2):205-18.

(14) Vercruysse, S., Gelman, D., Van De Velde, S., Raes, J., Hooghe, B., Vermeirssen, V., Van Camp, J., Smagghe, G. (2005) ACE inhibitor captopril reduces ecdysteroids and oviposition in moths. Ann. NY. Acad. Sci. 1040:498-500.

(13) Torres Acosta, J.A., de Almeida Engler, J., Raes, J., Magyar, Z., De Groodt, R., Inzé, D., De Veylder, L. (2004) Molecular characterization of Arabidopsis PHO80-like proteins, a novelclass of CDKA;1-interacting cyclins. Cell. Mol. Life Sci. 61(12):1485-97.

(12) Taylor, J.S., Raes, J. (2004) Duplication and Divergence: The Evolution of New Genes and Old Ideas. Annu. Rev. Genet. 38:615-43.

(11) Vercruysse, S., Gelman, D., Raes, J., Hooghe, B., Vermeirssen, V., Van Camp, J., Smagghe, G. (2004) The angiotensin converting enzyme inhibitor captopril reduces oviposition and ecdysteroid levels in Lepidoptera. Arch. Insect Biochem. Physiol. 57(3):123-32.

(10) Raes, J., Rohde, A., Holst-Christensen, J., Boerjan, W. (2003) Genome-wide characterization of the lignification toolbox in Arabidopsis. Plant Physiol. 133(3):1051-71.

(9) De Bodt, S., Raes, J., Van de Peer, Y., Theissen, G. (2003) And then there were many: MADS goes genomic. Trends Plant Science 8(10):475-83.

(8) Raes, J., Van de Peer, Y. (2003) Gene duplications, the evolution of novel gene functions, and detecting functional divergence of duplicates in silico. Applied Bioinformatics 2(2):91-101.

(7) Raes, J., Vandepoele, K., Saeys, Y., Simillion, C., Van de Peer, Y. (2003) Investigating ancient duplication events in the Arabidopsis genome. J. Struct. Func. Genomics. 3(1-4):117-29.

(6) De Bodt, S., Raes, J., Florquin, K., Rombauts, S., Rouzé, P., Theissen, G., Van de Peer, Y. (2003) Genomewide structural annotation and evolutionary analysis of the type I MADS-box genes in plants. J. Mol. Evol. 56(5):573-86.

(5) Breyne, P., Dreesen, R., Vandepoele, K., De Veylder, L., Van Breusegem, F., Callewaert, L., Rombauts, S., Raes, J., Cannoot, B., Engler, G., Inzé, D., Zabeau, M. (2002) Analysis of the transcriptome during cell division in plants. Proc. Natl. Acad. Sci. USA 99(23):14825-30.

(4) Vandepoele, K., Saeys, Y., Simillion, C., Raes, J., Van de Peer, Y. (2002) The Automatic Detection of Homologous Regions (ADHoRe) and its application to microcolinearity between Arabidopsis and Rice. Genome Res. 12(11):1792-801.

(3) Vandepoele, K., Raes, J., De Veylder, L., Rouzé, P., Rombauts, S., Inzé, D. (2002) Genome-wide analysis of core cell cycle genes in Arabidopsis. The Plant Cell 14(4):903-16.

(2) Taylor, J.S., Raes, J. (2002) Small-scale gene duplications. 31, 205-9.

(1) Raes, J., Van de Peer, Y. (1999) ForCon : a software tool for the conversion of sequence alignments. Embnet. News 6, 10-12..











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