Cindy Martens

Postdoc
(Group member from 2004 until 2013)


+ 32 (0) 9 33 13 542

VIB / Ghent University
Bioinformatics & Systems Biology
Technologiepark 927
B-9052 Gent
BELGIUM

Research

The chromalveolate supergroup represents a large fraction of known eukaryotic diversity, ranging from tiny obligate intracellular parasites to free-living algae. Many of these protist species are of great medical (e.g. Plasmodium spp., causative agent of malaria), veterinary and agricultural importance because of their pathogenicity to man, cattle and crops. Others are of ecological interest such as the diatoms, which are responsible for approximately 40% of the marine primary production. The goal of my research is to characterize chromalveolate genome dynamics and to unravel the molecular mechanisms responsible for the unique features of these species using comparative genomics.

Papers

(17) Schmidt, M., Van Bel, M., Woloszynska, M., Slabbinck, B., Martens, C., De Block, J., Coppens, F., Van Lijsebettens, M. (2017) Plant-RRBS, a bisulfite and next-generation sequencing-based methylome profiling method enriching for coverage of cytosine positions . BMC Plant Biology (In Press).

(16) Verkest, A., Byzova, M., Martens, C., Willems, A., Verwulgen, T., Slabbinck, B., Rombaut, D., Van de Velde, J., Vandepoele, K., Standaert, E., Peeters, M., Van Lijsebettens, M., Van Breusegem, F., De Block, J. (2015) Selection for Improved Energy Use Efficiency and Drought Tolerance in Canola Results in Distinct Transcriptome and Epigenome Changes. Plant Physiol. 168(4):1338-50.

(15) Cock, M., Sterck, L., Ahmed, S., Allen, A., Amoutzias, G., Anthouard, V., Artiguenave, F., Arun, A., Aury, J., Badger, J. H., Beszteri, B., Billiau, K., Bonnet, E., H. Bothwell, J., Bowler, C., Boyen, C., Brownlee, C., Carrano, C., Charrier, B., Youn Cho, G., Coelho, S.M., Collen, J., Le Corguille, G., Corre, E., Dartevelle, L., Da Silva, C., Delage, L., Delaroque, N., Dittami, S., Doulbeau, S., Elias, M., Farnham, G., Gachon, C., Godfroy, O., Gschloessl, B., Heesch, S., Jabbari, K., Jubin, C., Kawai, H., Kimura, K., Kloareg, B., Küpper, F.C., Lang, D., Le Bail, A., Luthringer, R., Leblanc, C., Lerouge, P., Lohr, M., Lopez, P., Macaisne, N., Martens, C., Maumus, F., Michel, G., Miranda-Saavedra, D., Morales, J., Moreau, H., Motomura, T., Nagasato, C., Napoli, C., Nelson, D.R., Nyvall-Collén, P., Peters, S., Pommier, C., Potin, P., Poulain, J., Quesneville, H., Read, B., Rensing, S.A., Ritter, A., Rousvoal, S., Samanta, M., Samson, G., Schroeder, D., Scornet, D., Ségurens, B., Strittmatter, M., Tonon, T., Tregear, J., Valentin, K., von Dassow, P., Yamagishi, T., Rouzé, P., Van de Peer, Y., Wincker, P. (2012) The Ectocarpus Genome and Brown Algal Genomics. Adv. Bot. Res. 64: 141-184.

(14) Grbic, M., Van Leeuwen, T., Clark, T. G., Rombauts, S., Rouzé, P., Grbic, V., Osborne, E., Dermauw, W., Thi Ngoc Cao, P., Ortego, F., Hernandez-Crespo, P., Diaz, I., Martinez, N.J., Navajas, M., Sucena, E., Magalhaes, S., Nagy, L., Pace, N.R., Djuranovic, S., Smagghe, G., Iga, M., Christiaens, M., Veenstra, J., Ewer, J., Mancilla Villalobos, R., Hutter, J., Hudson, A., Velez, M., Yi, S., Zeng, Q., Pires-daSilva, A., Roch, F., Cazaux, M., Navarro, M., Zhurov, V., Acevedo, G., Bjelica, A., Fawcett, J., Bonnet, E., Martens, C., Baele, G., Wissler, L., Sanchez-Rodriguez, A., Tirry, L., Blais, C., Demeestere, K., Henz, SR., Gregory, R., Mathieu, J., Verdon, L., Farinelli, L., Schmutz, J., Lindquist, E., Feyereisen, R., Van de Peer, Y. (2011) The genome of Tetranychus urticae reveals herbivorous pest adaptations. Nature 479,487-492.

(13) Coyne, R. S., Hannick, L., Shanmugam, D., Hostetler, J. B., Brami, D., Joardar, V. S., Johnson, P.J., Radune, D., Singh, N., Kumar, U., Saier, M., Wang, X., Cai, H., Gu, J., Mather, M. W., Vaidya, A. B., Wilkes, D. E., Rajagopalan, V., Asai, D. J., Pearson, C. G., Findly, R. C., Dickerson, H. W., Badger, J. H., Wu, M., Martens, C., Van de Peer, Y., Roos, D. S., Cassidy-Hanley, D. M., Clark, T. G. (2011) Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control. Genome Biol. 12(10):R100.

(12) Cock, M., Colle, J., Sterck, L., Rouzé, P., Scornet, D., Anthouard, V., Artiguenave, F., Aury, J., Billiau, K., Bonnet, E., H.F. Bothwell, J., Brillet, L., Carre, W., Coelho, S.M., Corre, E., Da Silva, C., Jubin, C., Martens, C., Maumus, F., Miranda-Saavedra, D., Peters, S., Porcel, B., Quesneville, H., Boyen, C., Van de Peer, Y., Wincker, P. (2011) Nature, nurture and the structure of macroalgal genomes. Eur. J. Phycol. 46,39-39.

(11) Mortier, V., Fenta, B.A., Martens, C., Rombauts, S., Holsters, M. & Ver, Kunert, K., Goormachtig, S. (2011) Search for nodulation-related CLE genes in the genome of Glycine max. J. Exp. Bot. 62(8):2571-83.

(10) Sanchez-Rodriguez, A., Martens, C., Engelen, K., Van de Peer, Y., Marchal, K. (2010) The Potential for Pathogenicity was Present in the Ancestor of the Ascomycete subphylum Pezizomycotina. BMC Evol. Biol. 10:318.

(9) Martens, C., Van de Peer, Y. (2010) The hidden duplication past of the plant pathogen phytophthora and its consequences for infection. BMC Genomics 11:353.

(8) Cock, M., Sterck, L., Rouzé, P., Scornet, D., Allen, A., Amoutzias, G., Anthouard, V., Artiguenave, F., Aury, J., Badger, J., Beszteri, B., Billiau, K., Bonnet, E., Bothwell, J., Bowler, C., Boyen, C., Brownlee, C., Carrano, C., Charrier, B., Youn Cho, G., Coelho, S.M., Colln, J., Corre, E., Da Silva, C., Delage, L., Delaroque, N., Dittami, S., Doulbeau, S., Elias, M., Farnham, G., Gachon, C., Gschloessl, B., Heesch, S., Jabbari, K., Jubin, C., Kawai, H., Kimura, K., Kloareg, B., Küpper, F.C., Lang, D., Le Bail, A., Leblanc, C., Lerouge, P., Lohr, M., Lopez, P., Martens, C., Maumus, F., Michel, G., Miranda-Saavedra, D., Morales, J., Moreau, H., Motomura, T., Nagasato, C., Napoli, C., Nelson, D., Nyvall-Collén, P., Peters, S., Pommier, C., Potin, P., Poulain, J., Quesneville, H., Read, B., Rensing, S.A., Ritter, A., Rousvoal, S., Samanta, M., Samson, G., Schroeder, D., Ségurens, B., Strittmatter, M., Tonon, T., Tregear, J., Valentin, K., von Dassow, P., Yamagishi, T., Van de Peer, Y., Wincker, P. (2010) The Ectocarpus genome and the independent evolution of multicellularity in brown algae. Nature 465(7298):617-21.

(7) Huysman, M., Martens, C., Vandepoele, K., Gillard, J., Rayko, E., Heijde, M., Bowler, C., Inzé, D., Van de Peer, Y., De Veylder, L., Vyverman, W. (2010) Genome-wide analysis of the diatom cell cycle unveils a novel type of cyclins involved in environmental signalling. Genome Biol. 11(2):R17.

(6) Bowler, C., * Allen, A., * Badger, J., * Grimwood, J., * Jabbari, K., * Kuo, Y.-C., * Maheswari, U., * Martens, C., * Maumus, F., * Otillar, R., * Rayko, E., * Salamov, A., * Vandepoele, K., Beszteri, B., Gruber, A., Heijde, M., Katinka, M., Mock, T., Valentin, K., Vérret, F., Berges, J., Brownlee, C., Cadoret, J., Chiovitti, A., Jae Choi, C., Coesel, S., Martino, A., Detter, J., Durkin, C., Falciatore, A., Fournet, J., Haruta, M., Huysman, M., Jenkins, B., Jiroutova, K., Jorgensen, R., Joubert, Y., Kaplan, A., Kroeger, N., Kroth, P., Roche, J., Lindquist, E., Lommer, M., Martin-Jézéquel, V., Lopez, P., Lucas, S., Mangogna, M., McGinnis, K., Medlin, L., Montsant, A., Oudot-Secq, M., Napoli, C., Obornik, M., Petit, J., Porcel, B., Poulsen, N., Robison, M., Rychlewski, L., Rynearson, T., Schmutz, J., Schnitzler Parker, M., Shapiro, H.J., Siaut, M., Stanley, M., J.Sussman, M., Taylor, J.S., Vardi, A., von Dassow, P., Vyverman, W., Willis, A., Wyrwicz, L., Rokhsar, D., Weissenbach, J., Armbrust, V., Green, P.J., Van de Peer, Y., Grigoriev, I. (2008) The Phaeodactylum genome reveals the dynamic nature and multi-lineage evolutionary history of diatom genomes. Nature 456(7219):239-44. *contributed equally

(5) Gillard, J., Devos, J, Huysman, M., De Veylder, L., D'Hondt, S., Martens, C., Vanormelingen, P., Vannerum, K., Sabbe, K., Chepurnov, V., Inzé, D., Vuylsteke, M., Vyverman, W. (2008) Physiological and transcriptomic evidence for a close coupling between chloroplast ontogeny and cell cycle progression in the pennate diatom Seminavis robusta. Plant Physiol. 148(3):1394-411.

(4) Van Daele, I., Van Bockstaele, E., Martens, C., Roldán-Ruiz, I. (2008) Identification of transcribed derived fragments involved in self-incompatibility in perennial ryegrass (Lolium perenne L.) using cDNA-AFLP. Euphytica 163(1):67-80.

(3) Martens, C., Vandepoele, K., Van de Peer, Y. (2008) Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species. Proc. Natl. Acad. Sci. USA 105(9):3427-32.

(2) Geurden, T., Geldhof, P., Levecke, B., Martens, C., Berkvens, D., Casaert, S., Vercruysse, S., Claerebout, E. (2008) Mixed Giardia duodenalis assemblage A and E infections in calves. Int. J. Parasit. 38(2):259-64.

(1) Geurden, T., Berkvens, D., Martens, C., Casaert, S., Vercruysse, S., Claerebout, E. (2007) Molecular epidemiology with subtype analysis of Cryptosporidium in calves in Belgium. Parasitology 134(Pt.14):1981-7.











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VIB / UGent
Bioinformatics & Evolutionary Genomics
Technologiepark 927
B-9052 Gent
BELGIUM
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