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1. Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen

Author

Olson, Ake, Aerts, Andrea, Asiegbu, Fred, Belbahri, Lassaad, Bouzid, Ourdia, Broberg, Anders, Canback, Bjorn, Coutinho, Pedro M., Cullen, Dan, Dalman, Kerstin, Deflorio, Giuliana, Diepen, Linda T. A. van, Dunand, Christophe, Duplessis, Sebastien, Durling, Mikael, Gonthier, Paolo, Grimwood, Jane, Fossdal, Carl Gunnar, Hansson, David, Henrissat, Bernard, Hietala, Ari, Himmelstrand, Kajsa, Hoffmeister, Dirk, Hogberg, Nils, James, Timothy Y., Karlsson, Magnus, Kohler, Annegret, Lucas, Susan, Lunden, Karl, Morin, Emmanuelle, Murat, Claude, Park, Jongsun, Raffaello, Tommaso, Rouze, Pierre, Salamov, Asaf, Schmutz, Jeremy, Solheim, Halvor, Stahlberg, Jerry, Velez, Heriberto, Vries, Ronald P. de, Wiebenga, Ad, Woodward, Steve, Yakovlev, Igor, Garbelotto, Matteo, Martin, Francis, Grigoriev, Igor V., and Stenlid, Jan

Subjects
genome, Heterobasidion, parasitism, pathology, saprotrophy, trade-off, wood decay
Abstract

Parasitism and saprotrophic wood decay are two fungal strategies fundamental for succession and nutrient cycling in forest ecosystems. An opportunity to assess the trade-off between these strategies is provided by the forest pathogen and wood decayer Heterobasidion annosum sensu lato.We report the annotated genome sequence and transcript profiling, as well as the quantitative trait loci mapping, of one member of the species complex: H. irregulare. Quantitative trait loci critical for pathogenicity, and rich in transposable elements, orphan and secreted genes, were identified.A wide range of cellulose-degrading enzymes are expressed during wood decay. By contrast, pathogenic interaction between H. irregulare and pine engages fewer carbohydrate-active enzymes, but involves an increase in pectinolytic enzymes, transcription modules for oxidative stress and secondary metabolite production.Our results show a trade-off in terms of constrained carbohydrate decomposition and membrane transport capacity during interaction with living hosts. Our findings establish that saprotrophic wood decay and necrotrophic parasitism involve two distinct, yet overlapping, processes.

Published
2012

7. The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea

Author

Olsen, Jeanine L., Rouze, Pierre, Verhelst, Bram, Lin, Yao-Cheng, Bayer, Till, Collen, Jonas, Dattolo, Emanuela, De Paoli, Emanuele, Dittami, Simon, Maumus, Florian, Michel, Gurvan, Kersting, Anna, Lauritano, Chiara, Lohaus, Rolf, Topel, Mats, Tonon, Thierry, Vanneste, Kevin, Amirebrahimi, Mojgan, Brakel, Janina, Bostrom, Christoffer, Chovatia, Mansi, Grimwood, Jane, Jenkins, Jerry W., Jueterbock, Alexander, Mraz, Amy, Stam, Wytze T., Tice, Hope, Bornberg-Bauer, Erich, Green, Pamela J., Pearson, Gareth A., Procaccini, Gabriele, Duarte, Carlos M., Schmutz, Jeremy, Reusch, Thorsten B.H., and Van de Peer, Yves

Subjects
Adaptation (Biology) -- Analysis, Angiosperms -- Research -- Physiological aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Seagrasses colonized the sea (1) on at least three independent occasions to form the basis of one of the most productive and widespread coastal ecosystems on the planet (2). Here [...]

Published
2016

11. Obligate biotrophy features unraveled by the genomic analysis of rust fungi

Author

Duplessis, Sébastien, Cuomo, Christina A., Lin, Yao-Cheng, Aerts, Andrea, Tisserant, Emilie, Veneault-Fourrey, Claire, Joly, David L., Hacquard, Stéphane, Amselem, Joëlle, Cantarel, Brandi L., Chiu, Readman, Coutinho, Pedro M., Feau, Nicolas, Field, Matthew, Frey, Pascal, Gelhaye, Eric, Goldberg, Jonathan, Grabherr, Manfred G., Kodira, Chinnappa D., Kohler, Annegret, Kües, Ursula, Lindquist, Erika A., Lucas, Susan M., Mago, Rohit, Mauceli, Evan, Morin, Emmanuelle, Murat, Claude, Pangilinan, Jasmyn L., Park, Robert, Pearson, Matthew, Quesneville, Hadi, Rouhier, Nicolas, Sakthikumar, Sharadha, Salamov, Asaf A., Schmutz, Jeremy, Selles, Benjamin, Shapiro, Harris, Tanguay, Philippe, Tuskan, Gerald A., Henrissat, Bernard, Van de Peer, Yves, Rouzé, Pierre, Ellis, Jeffrey G., Dodds, Peter N., Schein, Jacqueline E., Zhong, Shaobin, Hamelin, Richard C., Grigoriev, Igor V., Szabo, Les J., and Martin, Francis

Published
2011

12. Green Evolution and Dynamic Adaptations Revealed by Genomes of the Marine Picoeukaryotes Micromonas

Author

Worden, Alexandra Z., Lee, Jae-Hyeok, Mock, Thomas, Rouzé, Pierre, Simmons, Melinda P., Aerts, Andrea L., Allen, Andrew E., Cuvelier, Marie L., Derelle, Evelyne, Everett, Meredith V., Foulon, Elodie, Grimwood, Jane, Gundlach, Heidrun, Henrissat, Bernard, Napoli, Carolyn, McDonald, Sarah M., Parker, Micaela S., Rombauts, Stephane, Salamov, Aasf, Von Dassow, Peter, Badger, Jonathan H., Coutinho, Pedro M., Demir, Elif, Dubchak, Inna, Gentemann, Chelle, Eikrem, Wenche, Gready, Jill E., John, Uwe, Lanier, William, Lindquist, Erika A., Lucas, Susan, Mayer, Klaus F. X., Moreau, Herve, Not, Fabrice, Otillar, Robert, Panaud, Olivier, Pangilinan, Jasmyn, Paulsen, Ian, Piegu, Benoit, Poliakov, Aaron, Robbens, Steven, Schmutz, Jeremy, Toulza, Eve, Wyss, Tania, Zelensky, Alexander, Zhou, Kemin, Armbrust, E. Virginia, Bhattacharya, Debashish, Goodenough, Ursula W., Van de Peer, Yves, and Grigoriev, Igor V.

Published
2009
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13. The Tiny Eukaryote Ostreococcus Provides Genomic Insights into the Paradox of Plankton Speciation

Author

Palenik, Brian, Grimwood, Jane, Aerts, Andrea, Rouzé, Pierre, Salamov, Asaf, Putnam, Nicholas, Dupont, Chris, Jorgensen, Richard, Derelle, Evelyne, Rombauts, Stephane, Zhou, Kemin, Otillar, Robert, Merchant, Sabeeha S., Podell, Sheila, Gaasterland, Terry, Napoli, Carolyn, Gendler, Karla, Manuell, Andrea, Tai, Vera, Vallon, Olivier, Piganeau, Gwenael, Jancek, Séverine, Heijde, Marc, Jabbari, Kamel, Bowler, Chris, Lohr, Martin, Robbens, Steven, Werner, Gregory, Dubchak, Inna, Pazour, Gregory J., Ren, Qinghu, Paulsen, Ian, Delwiche, Chuck, Schmutz, Jeremy, Rokhsar, Daniel, Van de Peer, Yves, Moreau, Hervé, and Grigoriev, Igor V.

Published
2007
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14. Genome Analysis of the Smallest Free-Living Eukaryote Ostreococcus tauri Unveils Many Unique Features

Author

Derelle, Evelyne, Ferraz, Conchita, Rombauts, Stephane, Rouzé, Pierre, Worden, Alexandra Z., Robbens, Steven, Partensky, Frédéric, Degroeve, Sven, Echeynié, Sophie, Cooke, Richard, Saeys, Yvan, Wuyts, Jan, Jabbari, Kamel, Bowler, Chris, Panaud, Olivier, Piégu, Benoît, Ball, Steven G., Ral, Jean-Philippe, Bouget, François-Yves, Piganeau, Gwenael, De Baets, Bernard, Picard, André, Delseny, Michel, Demaille, Jacques, Van de Peer, Yves, and Moreau, Hervé

Published
2006
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26. Evidence for an ancient chromosomal duplication in Arabidopsis thaliana by sequencing and analyzing a 400-kb contig at the APETALA2 locus on chromosome 4

Author

Terryn, Nancy, Heijnen, Leo, De Keyser, Annick, Van Asseldonck, Martien, De Clercq, Rebecca, Verbakel, Henk, Gielen, Jan, Zabeau, Marc, Villarroel, Raimundo, Jesse, Taco, Neyt, Pia, Hogers, René, Van Den Daele, Hilde, Ardiles, Wilson, Schueller, Christine, Mayer, Klaus, Déhais, Patrice, Rombauts, Stephane, Van Montagu, Marc, Rouzé, Pierre, and Vos, Pieter

Published
1999
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27. Higher intron loss rate in Arabidopsis thaliana than A. lyrata is consistent with stronger selection for a smaller genome

Author

FAWCETT, Jeffrey A, ROUZE, Pierre, VAN DE PEER, Yves, and Jeffrey A, FAWCETT

Subjects
Genetics, Mutation rate, DNA Repair, Models, Genetic, Arabidopsis, Intron, Biology, Genome, Genomic Instability, Introns, Evolution, Molecular, Non-homologous end joining, Genome Size, Mutation Rate, Mutation, DNA Breaks, Double-Stranded, splice, Selection, Genetic, Molecular Biology, Genome, Plant, Ecology, Evolution, Behavior and Systematics, Loss rate
Abstract

The number of introns varies considerably among different organisms. This can be explained by the differences in the rates of intron gain and loss. Two factors that are likely to influence these rates are selection for or against introns and the mutation rate that generates the novel intron or the intronless copy. Although it has been speculated that stronger selection for a compact genome might result in a higher rate of intron loss and a lower rate of intron gain, clear evidence is lacking, and the role of selection in determining these rates has not been established. Here, we studied the gain and loss of introns in the two closely related species Arabidopsis thaliana and A. lyrata as it was recently shown that A. thaliana has been undergoing a faster genome reduction driven by selection. We found that A. thaliana has lost six times more introns than A. lyrata since the divergence of the two species but gained very few introns. We suggest that stronger selection for genome reduction probably resulted in the much higher intron loss rate in A. thaliana, although further analysis is required as we could not find evidence that the loss rate increased in A. thaliana as opposed to having decreased in A. lyrata compared with the rate in the common ancestor. We also examined the pattern of the intron gains and losses to better understand the mechanisms by which they occur. Microsimilarity was detected between the splice sites of several gained and lost introns, suggesting that nonhomologous end joining repair of double-strand breaks might be a common pathway not only for intron gain but also for intron loss.

Published
2011
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28. Generic eukaryotic core promoter prediction using structural features of DNA

Author

Abeel, Thomas, Saeys, Yvan, Bonnet, Eric, Rouze, Pierre, and Peer, Yves Van de

Subjects
DNA -- Structure, DNA -- Research, Genomics -- Research, Promoters (Genetics) -- Research, Health
Abstract

An approach of using large-scale structural properties of DNA is presented to predict the core region of promoters in whole-genome sequences. This method is applicable to many eukaryotic genomes and performs well in comparison with the other promoter prediction programs.

Published
2008

29. Chapter Five - The Ectocarpus Genome and Brown Algal Genomics: The Ectocarpus Genome Consortium

Author

Cock, J. Mark, Sterck, Lieven, Ahmed, Sophia, Allen, Andrew E., Amoutzias, Grigoris, Anthouard, Veronique, Artiguenave, François, Arun, Alok, Aury, Jean-Marc, Badger, Jonathan H., Beszteri, Bank, Billiau, Kenny, Bonnet, Eric, Bothwell, John H., Bowler, Chris, Boyen, Catherine, Brownlee, Colin, Carrano, Carl J., Charrier, Bénédicte, Cho, Ga Youn, Coelho, Susana M., Collén, Jonas, Le Corguillé, Gildas, Corre, Erwan, Dartevelle, Laurence, Da Silva, Corinne, Delage, Ludovic, Delaroque, Nicolas, Dittami, Simon M., Doulbeau, Sylvie, Elias, Marek, Farnham, Garry, Gachon, Claire M.M., Godfroy, Olivier, Gschloessl, Bernhard, Heesch, Svenja, Jabbari, Kamel, Jubin, Claire, Kawai, Hiroshi, Kimura, Kei, Kloareg, Bernard, Küpper, Frithjof C., Lang, Daniel, Le Bail, Aude, Luthringer, Rémy, Leblanc, Catherine, Lerouge, Patrice, Lohr, Martin, Lopez, Pascal J., Macaisne, Nicolas, Martens, Cindy, Maumus, Florian, Michel, Gurvan, Miranda-Saavedra, Diego, Morales, Julia, Moreau, Hervé, Motomura, Taizo, Nagasato, Chikako, Napoli, Carolyn A., Nelson, David R., Nyvall-Collén, Pi, Peters, Akira F., Pommier, Cyril, Potin, Philippe, Poulain, Julie, Quesneville, Hadi, Read, Betsy, Rensing, Stefan A., Ritter, Andrés, Rousvoal, Sylvie, Samanta, Manoj, Samson, Gaelle, Schroeder, Declan C., Scornet, Delphine, Ségurens, Béatrice, Strittmatter, Martina, Tonon, Thierry, Tregear, James W., Valentin, Klaus, Von Dassow, Peter, Yamagishi, Takahiro, Rouzé, Pierre, Van de Peer, Yves, and Wincker, Patrick

Published
2012
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31. Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas

Author

Worden, Alexandra, Lee, Jae-Hyeok, Mock, Thomas, Rouze, Pierre, Simmons, Melinda P., Aerts, Andrea L., Allen, Andrew E., Cuvelier, Marie L., Derelle, Evelyne, Everett, Meredith V., Gready, Jill, Worden, Alexandra, Lee, Jae-Hyeok, Mock, Thomas, Rouze, Pierre, Simmons, Melinda P., Aerts, Andrea L., Allen, Andrew E., Cuvelier, Marie L., Derelle, Evelyne, Everett, Meredith V., and Gready, Jill

Abstract

Picoeukaryotes are a taxonomically diverse group of organism less than 2 micrometers in diameter. Photosynthetic marine picoeukaryotes in the genus Micromonas thrive in ecosystems ranging from tropical to polar and could serve as sentinel organisms for biogeochemical fluxes of modern oceans during climate change. These broadly distributed primary producers belong to an anciently diverged sister clade to land plants. Although Micromonas isolates have high 18S ribosomal RNA gene identity, we found that genomes from two isolates shared only 90% of their predicted genes. Their independent evolutionary paths were emphasized by distinct riboswitch arrangements as well as the discovery of intronic repeat elements in one isolate, and in metagenomic data, but not in other genomes. Divergence appears to have been facilitated by selection and acquisition processes that actively shape the repertoire of genes that are mutually exclusive between the two isolates differently than the core genes. Analyses of the Micromonas genomes offer valuable insights into ecological differentiation and the dynamic nature of early plant evolution.

Published
2009

33. Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information

Author

Hebsgaard, Stefan M., Korning, Peter G., Tolstrup, Niels, Engelbrecht, Jacob, Rouze, Pierre, Brunak, Søren, Hebsgaard, Stefan M., Korning, Peter G., Tolstrup, Niels, Engelbrecht, Jacob, Rouze, Pierre, and Brunak, Søren

Abstract

Artificial neural networks have been combined with a rule based system to predict intron splice sites in the dicot plant Arabidopsis thaliana. A two step prediction scheme, where a global prediction of the coding potential regulates a cutoff level for a local predicition of splice sites, is refined by rules based on splice site confidence values, prediction scores, coding context and distances between potential splice sites. In this approach, the prediction of splice sites mutually affect each other in a non-local manner. The combined approach drastically reduces the large amount of false positive splice sites normally haunting splice site prediction. An analysis of the errors made by the networks in the first step of the method revealed a previously unknown feature, a frequent T-tract prolongation containing cryptic acceptor sites in the 5'end of exons. The method presented here has been compared with three other approaches, GeneFinder, GeneMark and Grail. Overall the method presented here is an order of magnitude better. We show that the new method is able to find a donor site in the coding sequence for the jelly fish Green Fluorescent Protein, exactly at the position that was experimentally observed in A.thaliana transformants. Predictions for alternatively spliced genes are also presented, together with examples of genes from other dicots, monocots and algae. The method has been made available through electronic mail (NetPlantGene@cbs.dtu.dk), or the WWW at http://www.cbs.dtu.dk/NetPlantGene.html

Published
1996

34. Use of a proteome strategy for tagging proteins present at the plasma membrane

Author

Santoni, Veronique, primary, Rouquie, David, additional, Doumas, Patrick, additional, Mansion, Monique, additional, Boutry, Marc, additional, Degand, Herve, additional, Dupree, Paul, additional, Packman, Len, additional, Sherrier, Janine, additional, Prime, Tracy, additional, Bauw, Guy, additional, Posada, Esmeralda, additional, Rouze, Pierre, additional, Dehais, Patrice, additional, Sahnoun, Ilhem, additional, Barlier, Isabelle, additional, and Rossignol, Michel, additional

Published
1998
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35. The Ectocarpus genome and the independent evolution of multicellularity in brown algae.

Author

Cock, J. Mark, Sterck, Lieven, Rouze, Pierre, Scornet, Delphine, Allen, Andrew E., Amoutzias, Grigoris, Anthouard, Veronique, Artiguenave, François, Aury, Jean-Marc, Badger, Jonathan H., Beszteri, Bank, Billiau, Kenny, Bonnet, Eric, Bothwell, John H., Bowler, Chris, Boyen, Catherine, Brownlee, Colin, Carrano, Carl J., Charrier, Bénédicte, and Cho, Ga Youn

Subjects
BROWN algae, MARINE algae, BIOSYNTHESIS, METABOLISM, GENETIC transduction, PLANT genomes, GENOMICS, GENETIC research, PLANT genetics, ALGAE & the environment
Abstract

Brown algae (Phaeophyceae) are complex photosynthetic organisms with a very different evolutionary history to green plants, to which they are only distantly related. These seaweeds are the dominant species in rocky coastal ecosystems and they exhibit many interesting adaptations to these, often harsh, environments. Brown algae are also one of only a small number of eukaryotic lineages that have evolved complex multicellularity (Fig. 1). We report the 214 million base pair (Mbp) genome sequence of the filamentous seaweed Ectocarpus siliculosus (Dillwyn) Lyngbye, a model organism for brown algae, closely related to the kelps (Fig. 1). Genome features such as the presence of an extended set of light-harvesting and pigment biosynthesis genes and new metabolic processes such as halide metabolism help explain the ability of this organism to cope with the highly variable tidal environment. The evolution of multicellularity in this lineage is correlated with the presence of a rich array of signal transduction genes. Of particular interest is the presence of a family of receptor kinases, as the independent evolution of related molecules has been linked with the emergence of multicellularity in both the animal and green plant lineages. The Ectocarpus genome sequence represents an important step towards developing this organism as a model species, providing the possibility to combine genomic and genetic approaches to explore these and other aspects of brown algal biology further. [ABSTRACT FROM AUTHOR]

Published
2010
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37. NATURE, NURTURE AND THE STRUCTURE OF MACROALGAL GENOMES

Author

Cock, J. Mark, Collen, Jonas, Lieven Sterck, Rouze, Pierre, Scornet, Delphine, Anthouard, Veronique, Artiguenave, Francois, Aury, Jean-Marc, Billiau, Kenny, Bonnet, Eric, Bothwell, John H. F., Brillet, Loraine, Carre, Wilfrid, Coelho, Susana M., Corre, Erwan, Da Silva, Corinne, Jubin, Claire, Martens, Cindy, Maumus, Florian, Miranda-Saavedra, Diego, Peters, Akira F., Porcel, Betina, Quesneville, Hadi, Boyen, Catherine, Peer, Yves, Wincker, Patrick, Signaux oligosaccharidiques et lipidiques (SOL), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-GOEMAR-Centre National de la Recherche Scientifique (CNRS), Universiteit Gent = Ghent University [Belgium] (UGENT), Flanders Institute for Biotechnology, Institut de Génomique, Queen's University [Belfast] (QUB), Marine Biological Association of the UK, Centre National de la Recherche Scientifique (CNRS), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL), University of Cambridge [UK] (CAM), Universiteit Gent = Ghent University (UGENT), École normale supérieure - Paris (ENS-PSL), GOEMAR-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV]Life Sciences [q-bio], Biology and Life Sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, nature, structure, ComputingMilieux_MISCELLANEOUS, macroalgal genomes
Abstract

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