Wincker
Patrick
Wincker
Patrick
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ArticleGenome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita(Nature Publishing Group, 2008-07-27) Abad, Pierre ; Gouzy, Jerome ; Aury, Jean-Marc ; Castagnone-Sereno, Philippe ; Danchin, Etienne G. J. ; Deleury, Emeline ; Perfus-Barbeoch, Laetitia ; Anthouard, Veronique ; Artiguenave, Francois ; Blok, Vivian C. ; Caillaud, Marie-Cecile ; Coutinho, Pedro M. ; Da Silva, Corinne ; De Luca, Francesca ; Deau, Florence ; Esquibet, Magali ; Flutre, Timothe ; Goldstone, Jared V. ; Hamamouch, Noureddine ; Hewezi, Tarek ; Jaillon, Olivier ; Jubin, Claire ; Leonetti, Paola ; Magliano, Marc ; Maier, Tom R. ; Markov, Gabriel V. ; McVeigh, Paul ; Pesole, Graziano ; Poulain, Julie ; Robinson-Rechavi, Marc ; Sallet, Erika ; Segurens, Beatrice ; Steinbach, Delphine ; Tytgat, Tom ; Ugarte, Edgardo ; van Ghelder, Cyril ; Veronico, Pasqua ; Baum, Thomas J. ; Blaxter, Mark ; Bleve-Zacheo, Teresa ; Davis, Eric L ; Ewbank, Jonathan J. ; Favery, Bruno ; Grenier, Eric ; Henrissat, Bernard ; Jones, John T. ; Laudet, Vincent ; Maule, Aaron G. ; Quesneville, Hadi ; Rosso, Marie-Noelle ; Schiex, Thomas ; Smant, Geert ; Weissenbach, Jean ; Wincker, PatrickPlant-parasitic nematodes are major agricultural pests worldwide and novel approaches to control them are sorely needed. We report the draft genome sequence of the root-knot nematode Meloidogyne incognita, a biotrophic parasite of many crops, including tomato, cotton and coffee. Most of the assembled sequence of this asexually reproducing nematode, totaling 86 Mb, exists in pairs of homologous but divergent segments. This suggests that ancient allelic regions in M. incognita are evolving toward effective haploidy, permitting new mechanisms of adaptation. The number and diversity of plant cell wall–degrading enzymes in M. incognita is unprecedented in any animal for which a genome sequence is available, and may derive from multiple horizontal gene transfers from bacterial sources. Our results provide insights into the adaptations required by metazoans to successfully parasitize immunocompetent plants, and open the way for discovering new antiparasitic strategies.
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ArticleGenomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga(Nature Publishing Group, 2013-07-21) Flot, Jean-Francois ; Hespeels, Boris ; Li, Xiang ; Noel, Benjamin ; Arkhipova, Irina R. ; Danchin, Etienne G. J. ; Hejno, Andreas ; Henrissat, Bernard ; Koszul, Romain ; Aury, Jean-Marc ; Barbe, Valerie ; Barthelemy, Roxane-Marie ; Bast, Jens ; Bazykin, Georgii A. ; Chabrol, Olivier ; Couloux, Arnaud ; Da Rocha, Martine ; Da Silva, Corinne ; Gladyshev, Eugene A. ; Gouret, Philippe ; Hallatschek, Oskar ; Hecox-Lea, Bette ; Labadie, Karine ; Lejeune, Benjamin ; Piskurek, Oliver ; Poulain, Julie ; Rodriguez, Fernando ; Ryan, Joseph F. ; Vakhrusheva, Olga A. ; Wajnberg, Eric ; Wirth, Benedicte ; Yushenova, Irina A. ; Kellis, Manolis ; Kondrashov, Alexey S. ; Mark Welch, David B. ; Pontarotti, Pierre ; Weissenbach, Jean ; Wincker, Patrick ; Jaillon, Olivier ; Van Doninck, KarineLoss of sexual reproduction is considered an evolutionary dead end for metazoans, but bdelloid rotifers challenge this view as they appear to have persisted asexually for millions of years1. Neither male sex organs nor meiosis have ever been observed in these microscopic animals: oocytes are formed through mitotic divisions, with no reduction of chromosome number and no indication of chromosome pairing2. However, current evidence does not exclude that they may engage in sex on rare, cryptic occasions. Here we report the genome of a bdelloid rotifer, Adineta vaga (Davis, 1873)3, and show that its structure is incompatible with conventional meiosis. At gene scale, the genome of A. vaga is tetraploid and comprises both anciently duplicated segments and less divergent allelic regions. However, in contrast to sexual species, the allelic regions are rearranged and sometimes even found on the same chromosome. Such structure does not allow meiotic pairing; instead, we find abundant evidence of gene conversion, which may limit the accumulation of deleterious mutations in the absence of meiosis. Gene families involved in resistance to oxidation, carbohydrate metabolism and defence against transposons are significantly expanded, which may explain why transposable elements cover only 3% of the assembled sequence. Furthermore, 8% of the genes are likely to be of non-metazoan origin and were probably acquired horizontally. This apparent convergence between bdelloids and prokaryotes sheds new light on the evolutionary significance of sex.
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ArticleLife-cycle modification in open oceans accounts for genome variability in a cosmopolitan phytoplankton(Nature Publishing Group, 2014-12-02) von Dassow, Peter ; John, Uwe ; Ogata, Hiroyuki ; Probert, Ian ; Bendif, El Mahdi ; Kege, Jessica U. ; Audic, Stephane ; Wincker, Patrick ; Da Silva, Corinne ; Claverie, Jean-Michel ; Doney, Scott C. ; Glover, David M. ; Flores, Daniella Mella ; Herrera, Yeritza ; Lescot, Magali ; Garet-Delmas, Marie-Jose ; de Vargas, ColombanEmiliania huxleyi is the most abundant calcifying plankton in modern oceans with substantial intraspecific genome variability and a biphasic life cycle involving sexual alternation between calcified 2N and flagellated 1N cells. We show that high genome content variability in Emiliania relates to erosion of 1N-specific genes and loss of the ability to form flagellated cells. Analysis of 185 E. huxleyi strains isolated from world oceans suggests that loss of flagella occurred independently in lineages inhabiting oligotrophic open oceans over short evolutionary timescales. This environmentally linked physiogenomic change suggests life cycling is not advantageous in very large/diluted populations experiencing low biotic pressure and low ecological variability. Gene loss did not appear to reflect pressure for genome streamlining in oligotrophic oceans as previously observed in picoplankton. Life-cycle modifications might be common in plankton and cause major functional variability to be hidden from traditional taxonomic or molecular markers.