Selfish DNA: the ultimate parasite, Nature, vol.284, pp.604-607, 1980. ,
The ecology of the genome -mobile DNA elements and their hosts, 2005. ,
, Nature Reviews Genetics, vol.6, pp.128-136
The origins of genome complexity, Science, vol.302, pp.1401-1404, 2003. ,
Eukaryotic transposable elements and genome evolution, Trends in Genetics, vol.5, pp.103-107, 1989. ,
A unified classification system for eukaryotic transposable elements, Nature Reviews Genetics, vol.8, pp.973-982, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00169819
LTR-retrotransposons and MITEs: important players in the evolution of plant genomes, Current Opinion in Genetics and Development, vol.5, pp.814-821, 1995. ,
Tuned for Transposition: Molecular Determinants Underlying the Hyperactivity of a Stowaway MITE, Science, vol.325, pp.1391-1394, 2009. ,
It takes two transposons to tango: transposable-element-mediated chromosomal rearrangements, Trends in Genetics, vol.16, pp.461-468, 2000. ,
Structural dynamics of eukaryotic chromosome evolution, Science, vol.301, pp.793-797, 2003. ,
Chromosome evolution in eukaryotes: a multi-kingdom perspective, Trends in Genetics, vol.21, pp.673-682, 2005. ,
A Physical Map of the 1-Gigabase Bread Wheat Chromosome 3B, Science, vol.322, pp.101-104, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-00964135
Controlling elements and the gene, Cold Spring Harbor Symposia on Quantitative Biology, vol.21, pp.197-216, 1956. ,
Controlling elements and the gene, Cold Spring Harbor Symposia on Quantitative Biology, vol.21, pp.197-216, 1956. ,
Transposable elements and the epigenetic regulation of the genome, Nature Reviews Genetics, vol.8, pp.272-285, 2007. ,
A transposon-induced epigenetic change leads to sex determination in melon, Nature, vol.461, pp.1135-1138, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-01203855
Transposable elements and the evolution of regulatory networks, Nature Reviews Genetics, vol.9, pp.397-405, 2008. ,
Transcriptional Rewiring of the Sex Determining dmrt1 Gene Duplicate by Transposable Elements, PLoS Genetics, vol.6, p.1000844, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-02658600
, , 2006.
Ancient Exaptation of a CORE-SINE Retroposon into a Highly Conserved Mammalian Neuronal Enhancer of the, 2007. ,
, Proopiomelanocortin Gene. PLoS Genetics, vol.3
Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system, Nature, vol.394, pp.744-751, 1998. ,
Transposition of hAT elements links transposable elements and V(D)J recombination, Nature, vol.432, pp.995-1001, 2004. ,
Next-generation sequencing transforms today's biology, Nature Methods, vol.5, pp.16-18, 2008. ,
The B73 maize genome: complexity, diversity, and dynamics, Science, vol.326, pp.1112-1115, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00751527
Transposable elements in gene regulation and in the evolution of vertebrate genomes, Current Opinion in Genetics and Development, vol.19, pp.607-612, 2009. ,
Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome, Genome Biol, vol.1, issue.11, p.112, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-00134981
Initial sequencing and analysis of the human genome, Nature, vol.409, issue.6822, pp.860-921, 2001. ,
The B73 maize genome: complexity, diversity, and dynamics, Science, vol.326, issue.5956, pp.1112-1117, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00751527
Eukaryotic transposable elements and genome evolution, Trends Genet, vol.5, issue.4, pp.103-110, 1989. ,
A unified classification system for eukaryotic transposable elements, Nat Rev Genet, vol.8, issue.12, pp.973-82, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00169819
Evolution of genome size: new approaches to an old problem, Trends Genet, vol.17, issue.1, pp.23-31, 2001. ,
Doubling genome size without polyploidization ,
URL : https://hal.archives-ouvertes.fr/hal-00164404
Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita, Nature Biotechnology, vol.26, issue.8, pp.909-915, 2008. ,
,
,
,
The genome sequence of Drosophila melanogaster, Science, vol.287, issue.5461, pp.2185-2195, 2000. ,
Pesticide resistance via transposition-mediated adaptive gene truncation in Drosophila, Science, vol.309, issue.5735, pp.764-767, 2005. ,
Molecular characteristics of diverse populations are consistent with the hypothesis of a recent invasion of Drosophila melanogaster by mobile P elements, Molecular Biology and Evolution, vol.5, issue.3, pp.252-269, 1988. ,
The piwi-piRNA pathway provides an adaptive defense in the transposon arms race, Science, vol.318, issue.5851, pp.761-764, 2007. ,
Studies on the chemical nature of the substance inducing transformation of pneumococcal types : induction of transformation by a desoxyribonucleic acid fraction isolated from Pneumococcus type III, Journal of Experimental Medecine, vol.79, issue.2, pp.137-158, 1944. ,
Automated de novo identification of repeat sequence families in sequenced genomes, Genome Research, vol.12, issue.8, pp.1269-1276, 2002. ,
Meiotic recombination, noncoding DNA and genomic organization in Caenorhabditis elegans, Genetics, vol.141, issue.1, pp.159-179, 1995. ,
Genome evolution and adaptation in a long-term experiment with Escherichia coli, Nature, vol.461, issue.7268, pp.1243-1247, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00435992
Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome, PLoS Genetics, vol.5, issue.11, p.1000732, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00736178
Extreme Programming explained : embrace change, 1999. ,
Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome, Genome Biology, vol.7, issue.11, p.112, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-00134981
Discovering and detecting transposable elements in genome sequences, Briefings in Bioinformatics, vol.8, issue.6, pp.382-392, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-02665779
Sex brings transposons and genomes into conflict, Genetica, vol.107, issue.1, pp.289-295, 1999. ,
Ty elements transpose through an RNA intermediate, Cell, vol.40, issue.3, pp.491-500, 1985. ,
Evolution of the mammalian transcription factor binding repertoire via transposable elements, Genome Research, vol.18, issue.11, pp.1752-1762, 2008. ,
Gene regulation for higher cells : a theory, Science, vol.165, issue.891, pp.349-357, 1969. ,
Repetitive and non-repetitive DNA sequences and a speculation on the origins of evolutionary novelty, The Quarterly Review of Biology, vol.46, issue.2, pp.111-138, 1971. ,
Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets, Genomics, vol.91, issue.5, pp.467-475, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-00280496
DNA assembly with gaps (Dawg) : simulating sequence evolution, Bioinformatics, vol.21, issue.Suppl_3, pp.31-38, 2005. ,
The population dynamics of transposable elements, Genetical Research, vol.42, issue.1, pp.1-27, 1983. ,
Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces, The Plant Cell, vol.22, issue.6, pp.1686-1701, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00964451
, The Ectocarpus genome and the independent evolution of multicellularity in brown algae, vol.465, pp.617-621, 2010.
URL : https://hal.archives-ouvertes.fr/cea-00906990
Marker-assisted selection : an approach for precision plant breeding in the twenty-first century, Philosophical transactions of the Royal Society of London. Series B, Biological sciences, vol.363, pp.557-572, 1491. ,
An evolutionary view of human recombination, Nature Reviews Genetics, vol.8, issue.1, pp.23-34, 2006. ,
Extensive synteny conservation of holocentric chromosomes in Lepidoptera despite high rates of local genome rearrangements, Proceedings of the National Academy of Sciences, vol.107, issue.17, pp.7680-7685, 2010. ,
L'Origine des espèces. Flammarion, Paris. tel-00560242, pp.1-27, 1992. ,
The extended phenotype : the long reach of the gene, 1982. ,
Here, there, and everywhere : kinetochore function on holocentric chromosomes, Journal of Cell Biology, vol.153, pp.33-38, 2001. ,
Evolution, consequences and future of plant and animal domestication, Nature, vol.418, issue.6898, pp.700-707, 2002. ,
Inversions in the chromosomes of Drosophila pseudoobscura, Genetics, vol.23, issue.1, pp.28-64, 1938. ,
Isolation of an active human transposable element, Science, vol.254, issue.5039, pp.1805-1808, 1991. ,
Blastclust (NCBI software development toolkit), 6.1 edition, 2002. ,
Variation in crossing-over rates across chromosome 4 of Arabidopsis thaliana reveals the presence of meiotic recombination "hot spots, Genome Research, vol.16, issue.1, pp.106-114, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-00017439
PILER : identification and classification of genomic repeats, Bioinformatics, vol.21, issue.suppl_1, pp.152-158, 2005. ,
Structural dynamics of eukaryotic chromosome evolution, Science, vol.301, issue.5634, pp.793-797, 2003. ,
LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons, BMC Bioinformatics, vol.9, issue.1, p.18, 2008. ,
A synthetic oscillatory network of transcriptional regulators, Nature, vol.403, issue.6767, pp.335-338, 2000. ,
Non-mammalian c-integrases are encoded by giant transposable elements, Trends in Genetics, vol.21, issue.10, pp.551-552, 2005. ,
Eukaryotic transposable elements and genome evolution, Trends in Genetics, vol.5, issue.4, pp.103-107, 1989. ,
A model of segmental duplication formation in Drosophila melanogaster, Genome Research, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-02657996
The evolution of plant genomes : scaling up from a population perspective, Current Opinion in Genetics & Development, vol.18, issue.6, pp.565-570, 2008. ,
Genome annotation in plants and fungi : EuGene as a model platform, Current Bioinformatics, vol.3, issue.2, pp.87-97, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-02658120
Life with 6000 genes, Science, vol.274, issue.5287, pp.546-567, 1996. ,
The spandrels of San Marco and the Panglossian paradigm : a critique of the adaptationist programme, Proceedings of the Royal Society of London B, vol.205, pp.581-598, 1979. ,
Exaptation -a missing term in the science of form, Paleobiology, vol.8, issue.1, pp.4-15, 1982. ,
It takes two transposons to tango : transposable-elementmediated chromosomal rearrangements, Trends in Genetics, vol.16, issue.10, pp.461-468, 2000. ,
The evolution of altruistic behavior, The American Naturalist, vol.97, issue.896, pp.354-356, 1963. ,
The functional role of Pack-MULEs in rice inferred from purifying selection and expression profile, Plant Cell, vol.21, issue.1, pp.25-38, 2009. ,
The effect of linkage on limits to artificial selection, Genetical Research, vol.8, issue.3, pp.269-294, 1966. ,
Mission de réflexion sur l'organisation et le pilotage de l'INRA : internationalisation, efficacité, attractivité, 2009. ,
, Nature Genetics, vol.41, issue.12, pp.1275-1281, 2009.
A gene wiki for community annotation of gene function, PLoS Biology, vol.6, issue.7, p.175, 2008. ,
Molecular reconstruction of Sleeping Beauty, a Tc1-like transposon from fish, and its transposition in human cells, Cell, vol.91, issue.4, pp.501-510, 1997. ,
Translating Sleeping Beauty transposition into cellular therapies : victories and challenges, 2010. ,
Evolution and tinkering, Science, vol.196, issue.4295, pp.1161-1166, 1977. ,
Genetic regulatory mechanisms in the synthesis of proteins, Journal of Molecular Biology, vol.3, issue.3, pp.318-356, 1961. ,
Pack-MULE transposable elements mediate gene evolution in plants, Nature, vol.431, issue.7008, pp.569-573, 2004. ,
Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution, Nature Genetics, vol.39, issue.11, pp.1361-1368, 2007. ,
McClintock's controlling elements : the full story, Cytogenetics and Genome Research, vol.109, pp.90-103, 2005. ,
Large retrotransposon derivatives : abundant, conserved but nonautonomous retroelements of barley and related genomes, Genetics, vol.166, issue.3, pp.1437-1450, 2004. ,
Cassandra retrotransposons carry independently transcribed 5S RNA, Proceedings of the National Academy of Sciences, vol.105, issue.15, pp.5833-5838, 2008. ,
Efficient algorithms and software for detection of full-length LTR retrotransposons, J Bioinform Comput Biol, vol.4, issue.2, pp.197-216, 2006. ,
The transposable elements of the Drosophila melanogaster euchromatin : a genomics perspective, Genome Biology, issue.12, p.3, 2002. ,
Gain of virulence caused by insertion of a Pot3 transposon in a Magnaporthe grisea avirulence gene, Molecular Plant-Microbe Interactions, vol.14, issue.5, pp.671-674, 2001. ,
Rolling-circle transposons in eukaryotes, Proceedings of the National Academy of Sciences, vol.98, pp.8714-8719, 2001. ,
Self-synthesizing DNA transposons in eukaryotes, Proceedings of the National Academy of Sciences, vol.103, issue.12, pp.4540-4545, 2006. ,
Varying environments can speed up evolution, Proceedings of the National Academy of Sciences, vol.104, issue.34, pp.13711-13716, 2007. ,
BLAT -the BLAST-like alignment tool, Genome Research, vol.12, issue.4, pp.656-664, 2002. ,
Genome organization and evolution of the AVR-Pita avirulence gene family in the Magnaporthe grisea species complex, Molecular Plant-Microbe Interactions, vol.21, issue.5, pp.658-670, 2008. ,
Mapping and sequencing of structural variation from eight human genomes, Nature, vol.453, issue.7191, pp.56-64, 2008. ,
Hybrid dysgenesis in Drosophila melanogaster : a syndrome of aberrant traits including mutation, sterility and male recombination, Genetics, vol.86, issue.4, pp.813-833, 1977. ,
Evolutionary coupling between the deleteriousness of gene mutations and the amount of non-coding sequences, Journal of Theoretical Biology, vol.244, issue.4, pp.621-630, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00391449
The first steps of transposable elements invasion : parasitic strategy versus genetic drift, Genetics, vol.169, issue.2, pp.1033-1043, 2005. ,
Long-term evolution of transposable elements, Proceedings of the National Academy of Sciences, vol.104, issue.49, pp.19375-19380, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00265448
Identifying repeats and transposable elements in sequenced genomes : how to find your way through the dense forest of programs, Heredity, vol.104, issue.6, pp.520-533, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00539329
Performance and scalability of discriminative metrics for comparative gene identification in 12 Drosophila genomes, PLoS Computational Biology, vol.4, issue.4, p.1000067, 2008. ,
The endogenous retroviral locus ERVWE1 is a bona fide gene involved in hominoid placental physiology, Proceedings of the National Academy of Sciences, vol.101, issue.6, pp.1731-1736, 2004. ,
URL : https://hal.archives-ouvertes.fr/hal-00427686
Cause and effect in biology, Science, vol.134, pp.1501-1506, 1961. ,
LTR_STRUC : a novel search and identification program for LTR retrotransposons, Bioinformatics, vol.19, issue.3, pp.362-367, 2003. ,
The origin and behavior of mutable loci in maize, Proceedings of the National Academy of Sciences, vol.36, pp.344-355, 1950. ,
Controlling elements and the gene, Cold Spring Harbor Symposia on Quantitative Biology, vol.21, pp.197-216, 1956. ,
Some parallels between gene control systems in maize and in bacteria, The American Naturalist, vol.95, issue.884, pp.265-277, 1961. ,
Bac-derived markers for assaying the stem rust resistance gene, Sr2, in wheat breeding programs, Molecular Breeding, vol.22, issue.1, pp.15-24, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-00964225
Sequencing technologies -the next generation, Nature Reviews Genetics, vol.11, issue.1, pp.31-46, 2009. ,
,
,
The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus), Nature, vol.452, issue.7190, pp.991-996, 2008. ,
Exon shuffling by L1 retrotransposition, Science, vol.283, issue.5407, pp.1530-1534, 1999. ,
A history of molecular biology, 2000. ,
Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize, Nature Genetics, 2005. ,
Suffix-tree analyser (STAN) : looking for nucleotidic and peptidic patterns in chromosomes, Bioinformatics, vol.21, issue.24, pp.4408-4410, 2005. ,
Improved hit criteria for DNA local alignment, BMC Bioinformatics, vol.5, issue.1, pp.149-158, 2004. ,
YASS : enhancing the sensitivity of DNA similarity search, Nucleic Acids Research, vol.33, issue.suppl_2, pp.540-543, 2005. ,
Structures of P transposable elements and their sites of insertion and excision in the Drosophila melanogaster genome, Cell, vol.34, issue.1, pp.25-35, 1983. ,
So much "junk" DNA in our genome, Brookhaven symposia in biology, vol.23, pp.366-370, 1972. ,
Selfish DNA : the ultimate parasite, Nature, vol.284, issue.5757, pp.604-607, 1980. ,
ChIP-seq : advantages and challenges of a maturing technology, Nature Reviews Genetics, vol.10, issue.10, pp.669-680, 2009. ,
The Sorghum bicolor genome and the diversification of grasses, Nature, vol.457, issue.7229, pp.551-556, 2009. ,
Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through BAC-end sequencing on chromosome 3B, The Plant Journal, vol.48, issue.3, pp.463-474, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-00964354
A physical map of the 1-gigabase bread wheat chromosome 3B, Science, vol.322, issue.5898, pp.101-104, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-00964135
Insertion site-based polymorphism markers open new perspectives for genome saturation and marker-assisted selection in wheat, Plant Biotechnology Journal, vol.8, issue.2, pp.196-210, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00964403
Mutational equilibrium model of genome size evolution, Theoretical Population Biology, vol.61, issue.4, pp.531-544, 2002. ,
Genome rearrangements in mammalian evolution : lessons from human and mouse genomes, Genome Research, vol.13, issue.1, pp.37-45, 2003. ,
Dynamics of transposable elements in metapopulations : a model of P element invasion in Drosophila, Theoretical Population Biology, vol.54, issue.2, pp.175-193, 1998. ,
URL : https://hal.archives-ouvertes.fr/hal-02696142
Genetic algorithm-based model of evolutionary dynamics of class II transposable elements, Journal of Theoretical Biology, vol.213, issue.1, pp.21-30, 2001. ,
URL : https://hal.archives-ouvertes.fr/hal-02680860
Detection of new transposable element families in Drosophila melanogaster and Anopheles gambiae genomes, Journal of Molecular Evolution, vol.57, 2003. ,
URL : https://hal.archives-ouvertes.fr/hal-02677603
Combined evidence annotation of transposable elements in genome sequences, PLoS Computational Biology, vol.1, issue.2, pp.166-175, 2005. ,
URL : https://hal.archives-ouvertes.fr/inserm-00000104
P elements and MITE relatives in the whole genome sequence of Anopheles gambiae, BMC genomics, vol.7, issue.1, p.214, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-00096293
De novo identification of LTR retrotransposons in eukaryotic genomes, BMC Genomics, vol.8, p.90, 2007. ,
Recombination rate and the distribution of transposable elements in the Drosophila melanogaster genome, Genome Research, vol.12, issue.3, pp.400-407, 2002. ,
URL : https://hal.archives-ouvertes.fr/hal-00427298
The Hill-Robertson effect and the evolution of recombination, Genetics, vol.173, issue.3, pp.1793-1811, 2006. ,
Genetic transformation of Drosophila with transposable element vectors, Science, vol.218, issue.4570, pp.348-353, 1982. ,
Parasitism and the retrotransposon life cycle in plants : a hitchhiker's guide to the genome, Heredity, vol.97, issue.6, pp.381-388, 2006. ,
Empirical comparison of ab initio repeat finding programs, Nucleic Acids Research, vol.36, issue.7, pp.2284-2294, 2008. ,
The paleontology of intergene retrotransposons of maize, Nature Genetics, vol.20, issue.1, pp.43-45, 1998. ,
Feature point tracking and trajectory analysis for video imaging in cell biology, Journal of Structural Biology, vol.151, issue.2, pp.182-195, 2005. ,
Copy number variation and transposable elements feature in recent, ongoing adaptation at the Cyp6g1 locus, PLoS Genetics, vol.6, issue.6, p.1000998, 2010. ,
, The B73 maize genome : complexity, diversity, and dynamics, vol.326, pp.1112-1115, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00751527
Premeiotic instability of repeated sequences in Neurospora crassa, Annual Review of Genetics, vol.24, issue.1, pp.579-613, 1990. ,
Identification of a new, abundant superfamily of mammalian LTR-transposons, Nucleic Acids Research, vol.21, issue.8, pp.1863-1872, 1993. ,
Germline transformation of the silkworm Bombyx mori L. using a piggyBac transposon-derived vector, Nature Biotechnology, vol.18, issue.1, pp.81-84, 2000. ,
Model-based identification of Helitrons results in a new classification of their families in Arabidopsis thaliana, Gene, vol.403, issue.1-2, pp.18-28, 2007. ,
URL : https://hal.archives-ouvertes.fr/inria-00180376
, Analysis of the genome sequence of the flowering plant Arabidopsis thaliana, Nature, vol.408, issue.6814, pp.796-815, 2000.
, The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla, Nature, vol.449, issue.7161, pp.463-467, 2007.
, Genome sequence of the pea aphid Acyrthosiphon pisum, the International Aphid Genomics Consortium, vol.8, p.1000313, 2010.
, Initial sequencing and analysis of the human genome, the International Human Genome Sequencing Consortium, vol.409, pp.860-921, 2001.
Sharing data from large-scale biological research projects :a system of tripartite responsibility, Wellcome Trust, 2003. ,
A complementary transposon tool kit for Drosophila melanogaster using P and piggyBac, Nature Genetics, vol.36, issue.3, pp.283-287, 2004. ,
The geographic mosaic of coevolution, 2005. ,
Bursts of retrotransposition reproduced in Arabidopsis, Nature, vol.461, issue.7262, pp.423-426, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-01917186
RNA-Seq : a revolutionary tool for transcriptomics, Nature Reviews Genetics, vol.10, issue.1, pp.57-63, 2009. ,
Molecular structure of nucleic acids : a structure for deoxyribose nucleic acid, Nature, vol.171, issue.4356, pp.737-738, 1953. ,
A unified classification system for eukaryotic transposable elements, Nature Reviews Genetics, vol.8, issue.12, pp.973-982, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00169819
Adaptation and natural selection, 1966. ,
Terminal-repeat retrotransposons in miniature (TRIM) are involved in restructuring plant genomes, Proceedings of the National Academy of Sciences, vol.98, issue.24, pp.13778-13783, 2001. ,
Effects of recombination rate and gene density on transposable element distributions in Arabidopsis thaliana, Genome Research, vol.13, issue.8, pp.1897-1903, 2003. ,
Emergence of primate genes by retrotransposon-mediated sequence transduction, Proceedings of the National Academy of Sciences, vol.103, issue.47, pp.17608-17613, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-00119035
LTR_FINDER : an efficient tool for the prediction of full-length LTR retrotransposons, Nucleic Acids Research, vol.35, issue.suppl_2, pp.265-268, 2007. ,
Tuned for transposition : molecular determinants underlying the hyperactivity of a Stowaway MITE, Science, vol.325, issue.5946, pp.1391-1394, 2009. ,
Structure-based discovery and description of plant and animal Helitrons, Proceedings of the National Academy of Sciences, vol.106, issue.31, pp.12832-12837, 2009. ,
RJPrimers : unique transposable element insertion junction discovery and PCR primer design for marker development, Nucleic Acids Research, vol.38, issue.suppl_2, pp.313-320, 2010. ,
Transposition of hAT elements links transposable elements and V(D)J recombination, Nature, vol.432, issue.7020, pp.995-1001, 2004. ,
Quantifying the mechanisms for segmental duplications in mammalian genomes by statistical analysis and modeling, Proceedings of the National Academy of Sciences, vol.102, pp.4051-4056, 2005. ,
, , 2008.
UNSA, UMR 1301, 400 route des Chappes, F-06903 Sophia-Antipolis, France. 4 Laboratoire Interactions Plantes Micro-organismes, UMR 6243, 400 route des Chappes, F-06903 ,
, 10 Istituto per la Protezione delle Piante, Consiglio Nazionale delle Ricerche, 12 INRA, UR1164 Unité de Recherche en Génomique et Informatique (URGI)
Belfast BT9 7BL, UK. 19 Dipartimento di Biochimica e Biologia Molecolare ''E. Quagliariello'', University of Bari, Via Orabona 4, 70126 Bari, Italy. 20 Istituto Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Via G. Amendola, 122/D, 70126 Bari, Italy. 21 Department of Ecology and Evolution, Evolution des Régulations Endocriniennes, Muséum National d'Histoire Naturelle, 7 rue Cuvier, F-75005, vol.46 ,
for protection against plant defenses and immune system ,
Apomictic, polyphagous root-knot nematodes: exceptionally successful and damaging biotrophic root pathogens, Annu. Rev. Phytopathol, vol.39, pp.53-77, 2001. ,
Nematoda: genes, genomes and the evolution of parasitism, Adv. Parasitol, vol.54, pp.101-195, 2003. ,
MAP65-3 Microtubule-associated protein is essential for nematode-induced giant cell ontogenesis in Arabidopsis, Plant Cell, vol.20, pp.423-437, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-02111994
Root-knot nematodes manipulate plant cell functions during a compatible interaction, J. Plant Physiol, vol.165, pp.104-113, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-02140534
Genome sequence of the nematode C. elegans: a platform for investigating biology, Science, vol.282, pp.2012-2018, 1998. ,
The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics, PLoS Biol, vol.1, p.45, 2003. ,
Draft genome of the filarial nematode parasite Brugia malayi, Science, vol.317, pp.1756-1760, 2007. ,
Whole-genome sequence assembly for mammalian genomes: Arachne ,
, Genome Res, vol.13, pp.91-96, 2003.
Flow cytometry for parasite nematode genome size measurement, Mol. Biochem. Parasitol, vol.128, pp.91-93, 2003. ,
, An Advance Treatise on Meloidogyne, vol.1, pp.113-126, 1985.
Genetic variability and adaptive evolution in parthenogenetic root-knot nematodes, Heredity, vol.96, pp.282-289, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-02655706
Divergent gene copies in the asexual class Bdelloidea (Rotifera) separated before the bdelloid radiation or within bdelloid families, Proc. Natl. Acad. Sci. USA, vol.101, pp.1622-1625, 2004. ,
Cloning and characterization of two satellite DNAs in the low-C-value genome of the nematode Meloidogyne spp, Gene, vol.138, pp.175-180, 1994. ,
URL : https://hal.archives-ouvertes.fr/hal-02699889
Integrating alternative splicing detection into gene prediction, BMC Bioinformatics, vol.6, p.25, 2005. ,
URL : https://hal.archives-ouvertes.fr/hal-01417735
OrthoMCL: identification of ortholog groups for eukaryotic genomes, Genome Res, vol.13, pp.2178-2189, 2003. ,
Getting to the roots of parasitism by nematodes, Trends Parasitol, vol.20, pp.134-141, 2004. ,
Molecular cloning, expression, and enzymatic activity of a novel endogenous cellulase from the mulberry longicorn beetle, Apriona germari, Comp. Biochem. Physiol. B Biochem. Mol. Biol, vol.145, pp.220-229, 2006. ,
Plant degradation: a nematode expansin acting on plants, Nature, vol.427, p.30, 2004. ,
Cloning and characterization of an esophageal-gland-specific chorismate mutase from the phytoparasitic nematode Meloidogyne javanica, Mol. Plant Microbe Interact, vol.12, pp.328-336, 1999. ,
Cysteine proteases in phytopathogenic bacteria: identification of plant targets and activation of innate immunity, Curr. Opin. Plant Biol, vol.7, pp.384-390, 2004. ,
Regulation of the type III secretion system in phytopathogenic bacteria, Mol. Plant Microbe Interact, vol.19, pp.1159-1166, 2006. ,
A profile of putative parasitism genes expressed in the esophageal gland cells of the root-knot nematode Meloidogyne incognita, Mol. Plant Microbe Interact, vol.16, pp.376-381, 2003. ,
Xenobiotic detoxification in the nematode Caenorhabditis elegans, J. Exp. Zoolog. A Comp. Exp. Biol, vol.305, pp.720-730, 2006. ,
A systematic gene expression screen of Caenorhabditis elegans cytochrome P450 genes reveals CYP35 as strongly xenobiotic inducible, Arch. Biochem. Biophys, vol.395, pp.158-168, 2001. ,
Signaling in the immune response, 2006. ,
URL : https://hal.archives-ouvertes.fr/inserm-00193898
Resistance to antimicrobial peptides contributes to persistence of Salmonella typhimurium in the C. elegans intestine, Cell Microbiol, vol.10, pp.1259-1273, 2008. ,
The N-glycosylation pattern of Caenorhabditis elegans, Carbohydr. Res, vol.343, pp.2041-2049, 2007. ,
Evolutionary genomics of nuclear receptors: from 25 ancestral genes to derived endocrine systems, Mol. Biol. Evol, vol.21, pp.1923-1937, 2004. ,
Explosive lineage-specific expansion of the orphan nuclear receptor HNF4 in nematodes, J. Mol. Evol, vol.60, pp.577-586, 2005. ,
URL : https://hal.archives-ouvertes.fr/hal-02679767
The protein kinases of Caenorhabditis elegans: a model for signal transduction in multicellular organisms, Proc. Natl. Acad. Sci. USA, vol.96, pp.13603-13610, 1999. ,
The putative chemoreceptor families of C. elegans, 2006. ,
in Neuropeptide Systems as Targets for Parasite and Pest Control, 2008. ,
Somatic sex determination, 2006. ,
Sex-determinantion in Meloidogyne incognita and anatomical evidence of sexual reversal, J. Nematol, vol.14, pp.549-566, 1982. ,
Application of RNA interference to root-knot nematode genes encoding esophageal gland proteins ,
URL : https://hal.archives-ouvertes.fr/hal-02682478
, Mol. Plant Microbe Interact, vol.18, pp.615-620, 2005.
Engineering broad rootknot resistance in transgenic plants by RNAi silencing of a conserved and essential root-knot nematode parasitism gene, Proc. Natl. Acad. Sci. USA, vol.103, pp.14302-14306, 2006. ,
RNAi in Haemonchus contortus: a potential method for target validation, Trends Parasitol, vol.22, pp.495-499, 2006. ,
Bdelloid rotifers revisited, Proc. Natl. Acad. Sci. USA, vol.101, pp.2651-2652, 2004. ,
Evidence for the evolution of bdelloid rotifers without sexual reproduction or genetic exchange, Science, vol.288, pp.1211-1215, 2000. ,
Evidence for degenerate tetraploidy in bdelloid rotifers, Proc. Natl. Acad. Sci. USA 105, pp.5145-5149, 2008. ,
SpliceMachine: predicting splice sites from high-dimensional local context representations, Bioinformatics, vol.21, pp.1332-1338, 2005. ,
Engineering a software tool for gene structure prediction in higher organisms, Inf. Softw. Technol, vol.47, pp.965-978, 2005. ,
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res, vol.25, pp.3389-3402, 1997. ,
InterProScan: protein domains identifier, Nucleic Acids Res, vol.33, pp.116-120, 2005. ,
Genomics in C. elegans: so many genes, such a little worm, Genome Res, vol.15, pp.1651-1660, 2005. ,
, Supplementary Data and Methods for: Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita
, Philippe Castagnone-Sereno, vol.6, p.3
, Noureddine Hamamouch, vol.9
, Marc Robinson-Rechavi, vol.5, issue.5, 1920.
, Mark Blaxter 26 , Teresa Bleve-Zacheo 10 , Eric L. Davis 14, Baum, vol.15
, Hadi Quesneville, vol.18, issue.5, p.7
UMR 6243, 400 route des Chappes, F-06903 Sophia-Antipolis, France. 3 UNSA, UMR 1301, 400 route des Chappes, F-06903 Sophia-Antipolis, France. 4 Laboratoire Interactions Plantes Micro-organismes, UMR441/2594, 400 route des Chappes, F-06903, vol.52627 ,
,
, Case 932, 163 Av. de Luminy, F-13288
Amendola 165/a, vol.70126 ,
, France. 12 INRA, UR1164 Unité de Recherche en Génomique et Informatique (URGI), 523 place des terrasses de l'Agora, F-91034 Evry, France. 13 Biology Department, Woods Hole Oceanographic Institution,Co-op Building, vol.4, pp.1-27, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01518061
, CNRS, INRA, Institut Fédératif 128 Biosciences Gerland, Lyon Sud, 46 allée d'Italie, F-69364 Lyon Cedex 07, France. 17 USM 501 -Evolution des Régulations Endocriniennes, Muséum National d'Histoire Naturelle, 7 rue Cuvier, F-75005
Via Orabona 4, 70126 Bari, Italy. 20 Istituto Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Via G. Amendola, 122/D -70126 ,
22 Swiss Institute of Bioinformatics, quartier sorge, Bâtiment Genopode, CH -1015 Lausanne, Switzerland. 23 Plateforme Bioinformatique du Genopole Toulouse Midi-Pyrénées, GIS Toulouse Genopole, 24 Chemin de Borde Rouge, BP 52627, F-31320 Castanet Tolosan, France. 24 Unité de Biométrie et d'Intelligence Artificielle UR875, INRA, Chemin de Borde Rouge, BP, vol.52627, p.6709 ,
,
,
F-3288, Marseille cedex 09, France. Correspondence should be addressed to P.A. (pierre.abad@sophia.inra.fr). tel-00560242, vol.906, pp.1-27, 2011. ,
, 6 1.1 Why have we sequenced the Meloidogyne incognita genome?
,
,
,
,
,
10 2.2 Detection of scaffold pairs and triplets ,
, Repetitive and non protein-coding sequences
,
,
,
,
,
,
,
, Protein coding gene set
, Automatic functional annotation
, Expert functional annotation
, Carbohydrate Active enZymes (CAZymes)
, The genome of a lepidopteran model insect, the silkworm Bombyx mori, The International Silkworm Genome Consortium, vol.38, pp.1036-1045, 2008.
Ninety-seven million years of angiosperm-insect association: Paleobiological insights into the meaning of coevolution, Proc Natl Acad Sci, vol.91, pp.12278-12282, 1994. ,
An insect molecular clock dates the origin of the insects and accords with palaeontological and biogeographic landmarks, Mol Biol Evol, vol.19, pp.748-761, 2002. ,
A Fossil Noctuid Moth Egg from the Late Cretaceous of Eastern North America, Science, vol.219, pp.507-509, 1983. ,
, Evolution of the Insects, p.755, 2005.
Construction of a single nucleotide polymorphism linkage map for the silkworm, Bombyx mori, based on bacterial artificial chromosome end sequences, Genetics, vol.173, pp.151-161, 2006. ,
A BAC-based integrated linkage map of the silkworm Bombyx mori, Genome Biol, vol.9, p.21, 2008. ,
The ecology of Heliothis species in relation to agroecosystems, Annu Rev Entomol, vol.34, pp.17-52, 1989. ,
Heliothis/Helicoverpa Management: Emerging Trends and Strategies for Future Research, 2005. ,
Mitochondrial DNA analysis of field populations of Helicoverpa armigera (Lepidoptera: Noctuidae) and of its relationship to H. zea, BMC Evol Biol, vol.7, p.117, 2007. ,
Counting on comparative maps, Trends Genet, vol.14, pp.495-501, 1998. ,
Fourfold faster rate of genome rearrangement in nematodes than in Drosophila, Genome Res, vol.12, pp.857-867, 2002. ,
Quantification of insect genome divergence, Trends Genet, vol.23, pp.16-20, 2007. ,
Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster, Science, vol.298, pp.149-159, 2002. ,
Reconstructing the genomic architecture of ancestral mammals: Lessons from human, mouse, and rat genomes, Genome Res, vol.14, pp.507-516, 2004. ,
Conserved synteny of genes between chromosome 15 of Bombyx mori and a chromosome of Manduca sexta shown by five-color BAC-FISH, 2007. ,
, Genome, vol.50, pp.1061-1065
Synteny and chromosome evolution in the lepidoptera: Evidence from mapping in Heliconius melpomene, Genetics, vol.177, pp.417-426, 2007. ,
Highly conserved gene order and numerous novel repetitive elements in genomic regions linked to wing pattern variation in Heliconius butterflies, BMC Genomics, vol.9, p.345, 2008. ,
A gene-based linkage map for Bicyclus anynana butterflies allows for a comprehensive analysis of synteny with the lepidopteran reference genome, PLoS Genet, vol.5, p.1000366, 2009. ,
Extensive conserved synteny of genes between the karyotypes of Manduca sexta and Bombyx mori revealed by BAC-FISH mapping, PLoS One, vol.4, p.7465, 2009. ,
, Insights into social insects from the genome of the honeybee Apis mellifera, Honeybee Genome Sequencing Consortium, vol.443, pp.931-949, 2006.
Combined evidence annotation of transposable elements in genome sequences, PLOS Comput Biol, vol.1, pp.166-175, 2005. ,
URL : https://hal.archives-ouvertes.fr/inserm-00000104
Genome-wide screening and characterization of transposable elements and their distribution analysis in the silkworm, Bombyx mori. Insect Biochem Mol Biol, vol.38, pp.1046-1057, 2008. ,
Comparative mapping and genome rearrangement, pp.124-134, 1999. ,
Signaling versus punching hole: How do Bacillus thuringiensis toxins kill insect midgut cells?, Cell Mol Life Sci, vol.66, pp.1337-1349, 2009. ,
Diversity of aminopeptidases, derived from four lepidopteran gene duplications, and polycalins expressed in the midgut of Helicoverpa armigera: Identification of proteins binding the delta-endotoxin, Cry1Ac of Bacillus thuringiensis, Insect Biochem Mol Biol, vol.38, pp.685-696, 2008. ,
Characterization of Bacillus thuringiensis Cry toxin binding novel GPI anchored aminopeptidase from fat body of the moth Spodoptera litura, Biotechnol Lett, vol.29, pp.1651-1657, 2007. ,
Evolution of insect P450, Biochem Soc Trans, vol.34, pp.1252-1255, 2006. ,
Genome size and endopolyploidy in pyrethroid-resistant and susceptible strains of Heliothis virescens (Lepidoptera: Noctuidae), J Econ Entomol, vol.86, pp.1030-1034, 1993. ,
Synergy between sequence and size in large-scale genomics, Nat Rev Genet, vol.6, pp.699-708, 2005. ,
Evolution of genes and genomes on the Drosophila phylogeny, Nature, vol.450, pp.203-218, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-02667683
Mammalian non-LTR retrotransposons: For better or worse, in sickness and in health, Genome Res, vol.18, pp.343-358, 2008. ,
The human genome in the LINE of fire, Proc Natl Acad Sci, vol.105, pp.19033-19034, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-00345406
The genome sequence of Caenorhabditis briggsae: A platform for comparative genomics, PLoS Biol, vol.1, p.45, 2003. ,
How malleable is the eukaryotic genome? Extreme rate of chromosomal rearrangement in the genus Drosophila, Genome Res, vol.11, pp.230-239, 2001. ,
Chromosome evolution in eukaryotes: A multi-kingdom perspective, Trends Genet, vol.21, pp.673-682, 2005. ,
Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution, Genome Res, vol.15, pp.1-18, 2005. ,
Genome sequence of Aedes aegypti, a major arbovirus vector, Science, vol.316, pp.1718-1723, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00156214
Chromosomal rearrangement inferred from comparisons of 12 Drosophila genomes, Genetics, vol.179, pp.1657-1680, 2008. ,
Recovering genome rearrangements in the mammalian phylogeny, Genome Res, vol.19, pp.934-942, 2009. ,