Nematodes, or roundworms, account for a large share of the planet's biodiversity, colonising all environments. Some 25,000 species have been described, and the total number of nematodes is estimated at over a million. With the exception of the species Caenorhabditis elegans, used as a research model for studies on the development and ageing of organisms, not much is known of the diversity within nematodes as a group.
Plant-parasitic nematodes, most of which are found in the ground, cause crop damage estimated to cost the planet several tens of billions of euros every year. Until very recently, chemical pest control was the most popular weapon. However, because of their toxicity to both human health and the environment, many of the chemicals used have been banned, and the development of alternatives is a major challenge in the immediate future.
The publication of the genome sequence for the root-knot nematode*, Meloidogyne incognita, represents a major step forward in several ways. It is the first genome sequence for a plant-parasitic animal and for a parthenogenetic (i.e., asexually-reproducing) metazoan. For Pierre Abad, director of the Joint Research Unit for Biotic Interactions in Plant Health (INRA-CNRS-Université de Nice Sophia-Antipolis) and project coordinator, "this study will give us an initial indication of the parasite arsenal found in these plant pests as well as the genetic mechanisms behind these asexual organisms' remarkable capacity for adaptation."
The Génoscope (Paris, France) produced over a million sequenced fragments in total, which were then used in a gene-prediction platform with the assistance of INRA Toulouse. The resources and skills of the international consortium's members (including INRA, CNRS and Génoscope, for France) were then mobilised to analyse the data.
A complex genome holds the key to extreme flexibility
As the genome analysis progressed, researchers were surprised to learned that the nematode's genome was in fact a juxtaposition of at least two genomes. The average sequence divergence between the different genomes was one of the highest ever recorded for living things. This genetic characteristic may be behind the ability of these asexual organisms to acquire new functions very rapidly, giving them a significant capacity for adaptation that has led to their global distribution.
An enzyme arsenal fit for plant parasitism
Another major result of the analysis was the identification of a large range of enzymes that allowed plant cell wall degradation. This wealth and diversity was unheard of in the animal kingdom. The type of genes involved was also surprising, because of their similarity to bacterial genes, thus suggesting the existence of multiple horizontal transfers of bacterial origin. The acquisition of new functions through gene transfer may be a key element to the adaptation of animal organisms to plant parasitism.
The comparative analysis of this nematode's genome with that of other nematodes, such as C. elegans and the human parasite Brugia Malayi, as well as that of drosophila (or fruit fly), also provided a first picture of the identifying features of animal parasites, thereby highlighting new potential and more specific targets to combat these organisms.
This first full genome sequence of a plant-parasitic animal organism thus provides the foundations for understanding host-pathogen relationships, and rounds off the vision of the adaptations made by plant pests to invade their hosts.
In the near future, the planned sequencing of other nematode genomes with different living behaviours will contribute to a greater understanding of these organisms' evolutionary success in the planet.
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• Meloidogyne incognita is a highly voracious parasite that can attack more than 3000 host plants. It is particularly damaging to garden produce (tomato, pepper, melon, etc.), coffee, cotton, etc.
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– Reference:
Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita
Nature Biotechnology, Advance Online Publication 27 juillet 2008, DOI : 10.1038/nbt.1482
http://www.nature.com/nbt/index.html
Pierre Abad1,2,3*, Jérôme Gouzy4, Jean-Marc Aury5,6,7, Philippe Castagnone-Sereno1,2,3, Etienne G.J. Danchin1,2,3, Emeline Deleury1,2,3, Laetitia Perfus-Barbeoch1,2,3, Véronique Anthouard5,6,7, François Artiguenave5,6,7, Vivian C. Blok8, Marie-Cécile Caillaud1,2,3, Pedro M. Coutinho9, Corinne Dasilva5,6,7, Francesca De Luca10, Florence Deau1,2,3, Magali Esquibet11, Timothé Flutre12, Jared V. Goldstone13, Noureddine Hamamouch14, Tarek Hewezi15, Olivier Jaillon5,6,7, Claire Jubin5,6,7, Paola Leonetti10, Marc Magliano1,2,3, Tom R. Maier15, Gabriel V. Markov16,17, Paul McVeigh18, Graziano Pesole19,20, Julie Poulain5,6,7, Marc Robinson-Rechavi21,22, Erika Sallet23,24, Béatrice Ségurens5,6,7, Delphine Steinbach12, Tom Tytgat25, Edgardo Ugarte5,6,7, Cyril van Ghelder 1,2,3, Pasqua Veronico10, Thomas J. Baum15, Mark Blaxter26, Teresa Bleve-Zacheo10, Eric L. Davis14, Jonathan J. Ewbank27, Bruno Favery1,2,3, Eric Grenier11, Bernard Henrissat9, John T. Jones8, Vincent Laudet16, Aaron G. Maule18, Hadi Quesneville12, Marie-Noëlle Rosso1,2,3, Thomas Schiex24, Geert Smant25, Jean Weissenbach5,6,7, Patrick Wincker5,6,7
1INRA, UMR 1301, F-06903 Sophia-Antipolis, France. 2CNRS, UMR 6243, F-06903 Sophia-Antipolis, France. 3UNSA, UMR 1301, F-06903 Sophia-Antipolis, France. 4Laboratoire Interactions Plantes Micro-organismes UMR441/2594, INRA/CNRS, F-31320 Castanet Tolosan. 5Genoscope (CEA), 2 rue Gaston Crémieux CP5706, 91057 Evry, France. 6CNRS, UMR 8030, 2 rue Gaston Crémieux CP5706, 91057 Evry, France. 7Université d'Evry, 91057 Evry, France. 8Plant Pathology Programme, SCRI, Invergowrie, Dundee, DD2 5DA, UK. 9CNRS, UMR 6098 CNRS and Universités d'Aix-Marseille I & II, Marseille, France. 10Istituto per la Protezione delle Piante, Consiglio Nazionale delle Ricerche, Via G. Amendola 165/a, 70126, Bari, Italy. 11INRA, Agrocampus Rennes, Univ Rennes I, UMR1099 BiO3P; F-35653 Le Rheu;France. 12INRA, UR1164 Unité de Recherche en Génomique et Informatique (URGI), 523 place des terrasses de l'Agora 91034 Evry, France. 13Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA. 14Department of Plant Pathology North Carolina State University 840 Method Road, Unit 4, Box 7903 Raleigh, NC 27607. 15Department of Plant Pathology, Iowa State University, 351 Bessey Hall, Ames, IA 50011, USA. 16Université de Lyon, Institut de Génomique Fonctionnelle de Lyon, Molecular Zoology team, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, INRA, Institut Fédératif 128 Biosciences Gerland Lyon Sud, France. 17USM 501 - Evolution des Régulations Endocriniennes. Muséum National d'Histoire Naturelle, Paris, France. 18Biomolecular Processes: Parasitology, School of Biological Sciences, Medical Biology Centre, 97 Lisburn Road, Queen's University Belfast, Belfast, BT9 7BL, UK. 19Dipartimento di Biochimica e Biologia Molecolare "E. Quagliariello", University of Bari, Italy. 20Istituto Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Bari, Italy. 21Department of Ecology and Evolution, University of Lausanne, Switzerland. 22Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland. 23Plateforme Bioinformatique du Génopole Toulouse Midi-Pyrénées, GIS Toulouse Genopole, F-31320 Castanet Tolosan. 24Unité de Biométrie et d'Intelligence Artificielle UR875, INRA, F-31320 Castanet Tolosan. 25Laboratory of Nematology, Wageningen University, Binnenhaven 5, 6709PD Wageningen, The Netherlands. 26Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK. 27INSERM/CNRS/Université de la Méditerranée, Centre d'Immunologie de Marseille-Luminy, F-13288, France.
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