Publications HAL du labo/EPI 104665;1002240

2009

Journal articles

titre
Resistance to Plasmopara viticola in grapevine ‘Bianca’ is controlled by a major dominant gene causing localised necrosis at the infection site
auteur
Diana Bellin, Elisa Peressotti, Didier Merdinoglu, Sabine Wiedemann-Merdinoglu, Anne-Francoise Adam-Blondon, Guido Cipriani, Michele Morgante, Raffaele Testolin, Gabriele Di Gaspero
article
TAG Theoretical and Applied Genetics, 2009, 120 (1), pp.163-176. ⟨10.1007/s00122-009-1167-2⟩
DOI
DOI : 10.1007/s00122-009-1167-2
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titre
Hunting down fungal secretomes using liquid-phase IEF prior to high resolution 2-DE
auteur
Delphine D. Vincent, Marie-Helene Balesdent, Julien Gibon, Stéphane Claverol, Delphine Lapaillerie, Anne-Marie Lomenech, Francoise F. Blaise, Thierry T. Rouxel, Francis Martin, Marc Bonneu, Joelle J. Amselem, Victoria Dominguez, Barbara J. Howlett, Patrick Wincker, Johann J. Joets, Marc-Henri Lebrun, Christophe Plomion
article
Electrophoresis, 2009, 30 (23), pp.4118-4136. ⟨10.1002/elps.200900415⟩
resume
The secreted proteins (secretome) of fungi play a key role in interactions of pathogenic and symbiotic fungi with plants. Using the plant pathogenic fungus Leptosphaeria maculans and symbiont Laccaria bicolor grown in culture, we have established a proteomic protocol for extraction, concentration and resolution of the fungal secretome. As no proteomic data were available on mycelium tissues from both L. maculans and L. bicolor, mycelial proteins were studied; they also helped verifying the purity of secretome samples. The quality of protein extracts was initially assessed by both 1-DE and 2-DE using first a broad pH range for IEF, and then narrower acidic and basic pH ranges, prior to 2-DE. Compared with the previously published protocols for which only dozens of 2-D spots were recovered from fungal secretome samples, up to approximately 2000 2-D spots were resolved by our method. MS identification of proteins along several pH gradients confirmed this high resolution, as well as the presence of major secretome markers such as endopolygalacturonases, -glucanosyltransferases, pectate lyases and endoglucanases. Shotgun proteomic experiments evidenced the enrichment of secreted protein within the liquid medium. This is the first description of the proteome of L. maculans and L. bicolor, and the first application of liquid-phase IEF to any fungal extracts.
DOI
DOI : 10.1002/elps.200900415
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titre
Bounds arc consistency for weighted CSPs
auteur
Matthias Zytnicki, Christine Gaspin, Simon de Givry, Thomas Schiex
article
Journal of Artificial Intelligence Research, 2009, 35, pp.593-621. ⟨10.1613/jair.2797⟩
resume
The Weighted Constraint Satisfaction Problem (WCSP) framework allows representing and solving problems involving both hard constraints and cost functions. It has been ap- plied to various problems, including resource allocation, bioinformatics, scheduling, etc. To solve such problems, solvers usually rely on branch-and-bound algorithms equipped with local consistency filtering, mostly soft arc consistency. However, these techniques are not well suited to solve problems with very large domains. Motivated by the resolution of an RNA gene localization problem inside large genomic sequences, and in the spirit of bounds consistency for large domains in crisp CSPs, we introduce soft bounds arc consistency, a new weighted local consistency specifically designed for WCSP with very large domains. Compared to soft arc consistency, BAC provides significantly improved time and space asymptotic complexity. In this paper, we show how the semantics of cost functions can be exploited to further improve the time complexity of BAC. We also compare both in theory and in practice the efficiency of BAC on a WCSP with bounds consistency enforced on a crisp CSP using cost variables. On two different real problems modeled as WCSP, including our RNA gene localization problem, we observe that maintaining bounds arc con- sistency outperforms arc consistency and also improves over bounds consistency enforced on a constraint model with cost variables.
DOI
DOI : 10.1613/jair.2797
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https://hal.inrae.fr/hal-02668467/file/Bounds%20arc%20consistency%20for%20weighted%20CSPs_MZ%20CG%20SDG%20TS_1.pdf BibTex

2008

Journal articles

titre
Genome-wide studies highlight indirect links between human replication origins and gene regulation.
auteur
Jean-Charles Cadoret, Françoise Meisch, Vahideh Hassan-Zadeh, Isabelle Luyten, Claire Guillet, L. Duret, Hadi Quesneville, Marie-Noëlle Prioleau
article
Proceedings of the National Academy of Sciences of the United States of America, 2008, 105 (41), pp.15837-42. ⟨10.1073/pnas.0805208105⟩
resume
To get insights into the regulation of replication initiation, we systematically mapped replication origins along 1% of the human genome in HeLa cells. We identified 283 origins, 10 times more than previously known. Origin density is strongly correlated with genomic landscapes, with clusters of closely spaced origins in GC-rich regions and no origins in large GC-poor regions. Origin sequences are evolutionarily conserved, and half of them map within or near CpG islands. Most of the origins overlap transcriptional regulatory elements, providing further evidence of a connection with gene regulation. Moreover, we identify c-JUN and c-FOS as important regulators of origin selection. Half of the identified replication initiation sites do not have an open chromatin configuration, showing the absence of a direct link with gene regulation. Replication timing analyses coupled with our origin mapping suggest that a relatively strict origin-timing program regulates the replication of the human genome.
DOI
DOI : 10.1073/pnas.0805208105
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https://hal.science/hal-00332341/file/2008_Cadoret_Proceedings%20of%20the%20National%20Academy%20of%20Sciences%20of%20the%20United%20States%20of%20America_1.pdf BibTex
titre
Promoter DNA hypermethylation and gene repression in undifferentiated Arabidopsis cells
auteur
Maria Berdasco, Rubén Alcázar, María Victoria García-Ortiz, Esteban Ballestar, Agustín F Fernández, Teresa Roldán-Arjona, Antonio F Tiburcio, Teresa Altabella, Nicolas Buisine, Hadi Quesneville, Antoine Baudry, Loic L. Lepiniec, Miguel Alaminos, Roberto Rodriguez, Alan Lloyd, Vincent Colot, Judith Bender, María Jesús Canal, Manel Esteller, Mario F Fraga
article
PLoS ONE, 2008, 3 (10), pp.e3306. ⟨10.1371/journal.pone.0003306⟩
resume
Maintaining and acquiring the pluripotent cell state in plants is critical to tissue regeneration and vegetative multiplication. Histone-based epigenetic mechanisms are important for regulating this undifferentiated state. Here we report the use of genetic and pharmacological experimental approaches to show that Arabidopsis cell suspensions and calluses specifically repress some genes as a result of promoter DNA hypermethylation. We found that promoters of the MAPK12, GSTU10 and BXL1 genes become hypermethylated in callus cells and that hypermethylation also affects the TTG1, GSTF5, SUVH8, fimbrin and CCD7 genes in cell suspensions. Promoter hypermethylation in undifferentiated cells was associated with histone hypoacetylation and primarily occurred at CpG sites. Accordingly, we found that the process specifically depends on MET1 and DRM2 methyltransferases, as demonstrated with DNA methyltransferase mutants. Our results suggest that promoter DNA methylation may be another important epigenetic mechanism for the establishment and/or maintenance of the undifferentiated state in plant cells.
DOI
DOI : 10.1371/journal.pone.0003306
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https://hal.inrae.fr/hal-02661856/file/2008_Berdasco_Plosone_1.pdf BibTex
titre
Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita
auteur
Pierre Abad, Jerome Gouzy, Jean-Marc Aury, Philippe Castagnone-Sereno, Etienne Danchin, Emeline Deleury, Laetitia Perfus-Barbeoch, Véronique Anthouard, François Artiguenave, Vivian C. Blok, Marie-Cécile Caillaud, Pedro M Coutinho, Corinne da Silva, Francesca de Luca, Florence Deau, Magali Esquibet, Timothée Flutre, Jared V. Goldstone, Noureddine Hamamouch, Tarek Hewezi, Olivier Jaillon, Claire Jubin, Paola Leonetti, Marc Magliano, Tom R. Maier, Gabriel V Markov, Paul Mcveigh, Graziano Pesole, Julie Poulain, Marc Robinson-Rechavi, Erika Sallet, Béatrice Ségurens, Delphine Steinbach, Tom Tytgat, Edgardo Ugarte, Cyril van Ghelder, Pasqua Veronico, Thomas J. Baum, Mark Blaxter, Teresa Bleve-Zacheo, Eric L. Davis, J.J. Ewbank, Bruno Favery, Eric Grenier, Bernard Henrissat, John T. Jones, Vincent Laudet, Aaron G. Maule, Hadi Quesneville, Marie-Noelle Rosso, Thomas Schiex, Geert Smant, Jean Weissenbach, Patrick Wincker
article
Nature Biotechnology, 2008, 26 (8), pp.909-915. ⟨10.1038/nbt.1482⟩
resume
Plant-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
DOI
DOI : 10.1038/nbt.1482
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titre
Physical mapping in large genomes: accelerating anchoring of BAC contigs to genetic maps through in silico analysis
auteur
Etienne Paux, Fabrice F. Legeai, Nicolas N. Guilhot, Anne-Francoise A.F. Adam-Blondon, Michael M. Alaux, Jerome J. Salse, Pierre Sourdille, Philippe Leroy, Catherine C. Feuillet
article
Functional and Integrative Genomics, 2008, 8 (1), pp.29-32. ⟨10.1007/s10142-007-0068-1⟩
resume
Anchored physical maps represent essential frameworks for map-based cloning, comparative genomics studies, and genome sequencing projects. High throughput anchoring can be achieved by polymerase chain reaction (PCR) screening of bacterial artificial chromosome (BAC) library pools with molecular markers. However, for large genomes such as wheat, the development of high dimension pools and the number of reactions that need to be performed can be extremely large making the screening laborious and costly. To improve the cost efficiency of anchoring in such large genomes, we have developed a new software named Elephant (electronic physical map anchoring tool) that combines BAC contig information generated by FingerPrinted Contig with results of BAC library pools screening to identify BAC addresses with a minimal amount of PCR reactions. Elephant was evaluated during the construction of a physical map of chromosome 3B of hexaploid wheat. Results show that a one dimensional pool screening can be sufficient to anchor a BAC contig while reducing the number of PCR by 384-fold thereby demonstrating that Elephant is an efficient and cost-effective toot to support physical mapping in large genomes.
DOI
DOI : 10.1007/s10142-007-0068-1
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titre
The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis
auteur
F. Martin, A. Aerts, D. Ahrén, A. Brun, E. G. J. Danchin, F. Duchaussoy, J. Gibon, Annegret Kohler, E. Lindquist, V. Pereda, A. Salamov, H. J. Shapiro, J. Wuyts, D. Blaudez, Marc Buée, P. Brokstein, B. Canbäck, D. Cohen, P. E. Courty, P. M. Coutinho, C. Delaruelle, J. C. Detter, Aurélie Deveau, S. Difazio, Sébastien Duplessis, L. Fraissinet-Tachet, E. Lucic, P. Frey-Klett, Claire Veneault-Fourrey, I. Feussner, G. Gay, J. Grimwood, P. J. Hoegger10, P. Jain, S. Kilaru, J. Labbé, Y. C. Lin, V. Legué, F. Le Tacon, R. Marmeisse, D. Melayah, B. Montanini, M. Muratet, U. Nehls, H. Niculita-Hirzel, M. P. Oudot-Le Secq, M. Peter, H. Quesneville, B. Rajashekar, M. Reich, N. Rouhier, J. Schmutz, T. Yin, M. Chalot, Bernard Henrissat, U. Kües, S. Lucas, Y. van de Peer, G. K. Podila, A. Polle, P. J. Pukkila, P. M. Richardson, P. Rouzé, I. R. Sanders, J. E. Stajich, A. Tunlid, G. Tuskan, I. V. Grigoriev
article
Nature, 2008, 452 (7183), pp.88-93. ⟨10.1038/nature06556⟩
resume
Mycorrhizal symbioses—the union of roots and soil fungi—are universal in terrestrial ecosystems and may have been fundamental to land colonization by plants1,2. Boreal, temperate and montane forests all depend on ectomycorrhizae1. Identification of the primary factors that regulate symbiotic development and metabolic activity will therefore open the door to understanding the role of ectomycorrhizae in plant development and physiology, allowing the full ecological significance of this symbiosis to be explored. Here we report the genome sequence of the ectomycorrhizal basidiomycete Laccaria bicolor (Fig. 1) and highlight gene sets involved in rhizosphere colonization and symbiosis. This 65-megabase genome assembly contains 20,000 predicted protein-encoding genes and a very large number of transposons and repeated sequences. We detected unexpected genomic features, most notably a battery of effector-type small secreted proteins (SSPs) with unknown function, several of which are only expressed in symbiotic tissues. The most highly expressed SSP accumulates in the proliferating hyphae colonizing the host root. The ectomycorrhizae-specific SSPs probably have a decisive role in the establishment of the symbiosis. The unexpected observation that the genome of L. bicolor lacks carbohydrate-active enzymes involved in degradation of plant cell walls, but maintains the ability to degrade non-plant cell wall polysaccharides, reveals the dual saprotrophic and biotrophic lifestyle of the mycorrhizal fungus that enables it to grow within both soil and living plant roots. The predicted gene inventory of the L. bicolor genome, therefore, points to previously unknown mechanisms of symbiosis operating in biotrophic mycorrhizal fungi. The availability of this genome provides an unparalleled opportunity to develop a deeper understanding of the processes by which symbionts interact with plants within their ecosystem to perform vital functions in the carbon and nitrogen cycles that are fundamental to sustainable plant productivity.
DOI
DOI : 10.1038/nature06556
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https://hal.science/halsde-00261893/file/martin_2008_1.pdf BibTex
titre
A Physical Map of the 1-Gigabase Bread Wheat Chromosome 3B
auteur
Etienne Paux, Pierre Sourdille, Jerome J. Salse, Cyrille C. Saintenac, Frédéric Choulet, Philippe Leroy, Abraham A. Korol, Monika M. Michalak, Shahryar S. Kianian, Wolfgang W. Spielmeyer, Evans E. Lagudah, Daryl D. Somers, Andrzej A. Kilian, Michael M. Alaux, Sonia S. Vautrin, Helene H. Berges, Kellye K. Eversole, Rudi R. Appels, Jan J. Safar, Hana H. Simkova, Jaroslav J. Dolezel, Michel M. Bernard, Catherine C. Feuillet
article
Science, 2008, 322 (5898), pp.101-104. ⟨10.1126/science.1161847⟩
resume
As the staple food for 35% of the world's population, wheat is one of the most important crop species. To date, sequence- based tools to accelerate wheat improvement are lacking. As part of the international effort to sequence the 17- billion- base- pair hexaploid bread wheat genome ( 2n = 6x = 42 chromosomes), we constructed a bacterial artificial chromosome ( BAC)based integrated physical map of the largest chromosome, 3B, that alone is 995 megabases. A chromosome- specific BAC library was used to assemble 82% of the chromosome into 1036 contigs that were anchored with 1443 molecular markers, providing a major resource for genetic and genomic studies. This physical map establishes a template for the remaining wheat chromosomes and demonstrates the feasibility of constructing physical maps in large, complex, polyploid genomes with a chromosome- based approach.
DOI
DOI : 10.1126/science.1161847
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titre
Interactions entre éléments transposables et gènes du tabac
auteur
Q.T. Bui, J Tran, N Maunoury, F Dorlhac de Borne, H Quesneville, M-A Grandbastien
article
Bulletin de l’Association pour la Recherche sur les Nicotianées, 2008, pp.26-34
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2007

Journal articles

titre
LTR retrotransposons in rice (Oryza sativa, L.): recent burst amplifications followed by rapid DNA loss
auteur
Clémentine Vitte, Olivier Panaud, Hadi H. Quesneville
article
BMC Genomics, 2007, 8 (1), pp.218. ⟨10.1186/1471-2164-8-218⟩
resume
Background: LTR retrotransposons are one of the main causes for plant genome size and structure evolution, along with polyploidy. The characterization of their amplification and subsequent elimination of the genomes is therefore a major goal in plant evolutionary genomics. To address the extent and timing of these forces, we performed a detailed analysis of 41 LTR retrotransposon families in rice. Results: Using a new method to estimate the insertion date of both truncated and complete copies, we estimated these two forces more accurately than previous studies based on other methods. We show that LTR retrotransposons have undergone bursts of amplification within the past 5 My. These bursts vary both in date and copy number among families, revealing that each family has a particular amplification history. The number of solo LTR varies among families and seems to correlate with LTR size, suggesting that solo LTR formation is a family-dependent process. The deletion rate estimate leads to the prediction that the half-life of LTR retrotransposon sequences evolving neutrally is about 19 My in rice, suggesting that other processes than the formation of small deletions are prevalent in rice DNA removal. Conclusion: Our work provides insights into the dynamics of LTR retrotransposons in the rice genome. We show that transposable element families have distinct amplification patterns, and that the turn-over of LTR retrotransposons sequences is rapid in the rice genome.
DOI
DOI : 10.1186/1471-2164-8-218
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https://hal.science/hal-02114382/file/1471-2164-8-218_1.pdf BibTex
titre
Spip and Squiq, two novel rice non-autonomous LTR retro-element families related to RIRE3 and RIRE8
auteur
Clémentine Vitte, Cristian Chaparro, Hadi H. Quesneville, Olivier Panaud
article
Plant Science, 2007, 172 (1), pp.8-19. ⟨10.1016/j.plantsci.2006.07.008⟩
DOI
DOI : 10.1016/j.plantsci.2006.07.008
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titre
Discovering and detecting transposable elements in genome sequences
auteur
Casey M Bergman, Hadi Quesneville
article
Briefings in Bioinformatics, 2007, 8 (6), pp.382-392. ⟨10.1093/bib/bbm048⟩
resume
The contribution of transposable elements (TEs) to genome structure and evolution as well as their impact on genome sequencing, assembly, annotation and alignment has generated increasing interest in developing new methods for their computational analysis. Here we review the diversity of innovative approaches to identify and annotate TEs in the post-genomic era, covering both the discovery of new TE families and the detection of individual TE copies in genome sequences. These approaches span a broad spectrum in computational biology including de novo, homology-based, structure-based and comparative genomic methods. We conclude that the integration and visualization of multiple approaches and the development of new conceptual representations for TE annotation will further advance the computational analysis of this dynamic component of the genome.
DOI
DOI : 10.1093/bib/bbm048
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titre
The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.
auteur
Olivier Jaillon, Jean-Marc Aury, Benjamin Noel, Alberto Policriti, Christian Clepet, Alberto Cassagrande, Nathalie Choisne, Sébastien Aubourg, Nicola Vitulo, Claire Jubin, Alessandro Vezzi, Fabrice Legeai, Philippe Hugueney, Corinne da Silva, David Horner, Erica Mica, Delphine Jublot, Julie Poulain, Clémence Bruyère, Alain Billaut, Béatrice Ségurens, Michel Gouyvenoux, Edgardo Ugarte, Federica Cattorano, Véronique Anthouard, Virginie Vico, Christian del Fabbro, Michaël Alaux, Gabriele Di Gaspero, Vincent Dumas, Nicoletta Felice, Sophie Paillard, Irena Juman, Marco Moroldo, Simone Scalabrin, Aurélie Canaguier, Isabelle Le Clainche, Giorgio Malacrida, Eléonore Durand, Graziano Pesole, Valérie Laucou, Philippe Chatelet, Didier Merdinoglu, Massimo Delledonne, Mario Pezzotti, Alain Lecharny, Claude Scarpelli, François Artiguenave, M. Enrico Pé, Giorgio Valle, Michele Morgante, Michel Caboche, Anne-Françoise Adam-Blondon, Jean Weissenbach, Francis Quétier, Patrick Wincker
article
Nature, 2007, 449 (7161), pp.463-7. ⟨10.1038/nature06148⟩
resume
The analysis of the first plant genomes provided unexpected evidence for genome duplication events in species that had previously been considered as true diploids on the basis of their genetics. These polyploidization events may have had important consequences in plant evolution, in particular for species radiation and adaptation and for the modulation of functional capacities. Here we report a high-quality draft of the genome sequence of grapevine (Vitis vinifera) obtained from a highly homozygous genotype. The draft sequence of the grapevine genome is the fourth one produced so far for flowering plants, the second for a woody species and the first for a fruit crop (cultivated for both fruit and beverage). Grapevine was selected because of its important place in the cultural heritage of humanity beginning during the Neolithic period. Several large expansions of gene families with roles in aromatic features are observed. The grapevine genome has not undergone recent genome duplication, thus enabling the discovery of ancestral traits and features of the genetic organization of flowering plants. This analysis reveals the contribution of three ancestral genomes to the grapevine haploid content. This ancestral arrangement is common to many dicotyledonous plants but is absent from the genome of rice, which is a monocotyledon. Furthermore, we explain the chronology of previously described whole-genome duplication events in the evolution of flowering plants.
DOI
DOI : 10.1038/nature06148
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https://inria.hal.science/inria-00180136/file/nature06148_1.pdf BibTex
titre
AphidBase: a database for aphid genomic resources
auteur
Jean-Pierre Gauthier, Fabrice Legeai, Alain Zasadzinski, Claude Rispe, Denis Tagu
article
Bioinformatics, 2007, 23 (6), pp.783-784. ⟨10.1093/bioinformatics/btl682⟩
resume
AphidBase aims to (i) store recently acquired genomic resources on aphids and (ii) compare them to other insect resources as functional annotation tools. For that, the Drosophila melanogaster genome has been loaded in the database using the GMOD open source software for a comparison with the 17 069 pea aphid unique transcripts (contigs) and the 13 639 gene transcripts of the Anopheles gambiae. Links to FlyBase and A.gambiae Entrez databases allow a rapid characterization of the putative functions of the aphid sequences. Text mining of the D.melanogaster literature was performed to construct a network of co-cited gene or protein names, which should facilitate functional annotation of aphid homolog sequences. AphidBase represents one of the first genomic databases for a hemipteran insect. AVAILABILITY: http://w3.rennes.inra.fr/AphidBase.
DOI
DOI : 10.1093/bioinformatics/btl682
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titre
A model of segmental duplication formation in Drosophila melanogaster
auteur
Anna-Sophie Fiston-Lavier, Dominique Anxolabéhère, Hadi Quesneville
article
Genome Research, 2007, 17 (10), pp.1458-1470. ⟨10.1101/gr.6208307⟩
resume
Segmental duplications (SDs) are low-copy repeats of DNA segments that have long been recognized to be involved in genome organization and evolution. But, to date, the mechanism of their formation remains obscure. We propose a model for SD formation that we name "duplication-dependent strand annealing" (DDSA). This model is a variant of the synthesis-dependent strand annealing (SDSA) model--a double-strand break (DSB) homologous repair model. DSB repair in Drosophila melanogaster genome usually occurs primarily through homologous repair, more preferentially through the SDSA model. The DDSA model predicts that after a DSB, the search for an ectopic homologous region--here a repeat--initiates the repair. As expected by the model, the analysis of SDs detected by a computational analysis of the D. melanogaster genome indicates a high enrichment in transposable elements at SD ends. It shows moreover a preferential location of SDs in heterochromatic regions. The model has the advantage of also predicting specific traces left during synthesis. The observed traces support the DDSA model as one model of formation of SDs in D. melanogaster genome. The analysis of these DDSA signatures suggests moreover a sequestration of the dissociated strand in the repair complex.
DOI
DOI : 10.1101/gr.6208307
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https://hal.inrae.fr/hal-02657996/file/Genome%20Res.-2007-Fiston-Lavier-1458-70_1.pdf BibTex
titre
Evolution of genes and genomes on the Drosophila phylogeny
auteur
. Drosophila 12 Genomes Consortium, Andrew G Clark, Michael B Eisen, Douglas R Smith, Casey M Bergman, Brian Oliver, Therese A Markow, Thomas C Kaufman, Manolis Kellis, William Gelbart, Venky N Iyer, Daniel A Pollard, Timothy B Sackton, Amanda M. Larracuente, Nadia D Singh, Jose P Abad, Dawn N Abt, Boris Adryan, Montserrat Aguade, Hiroshi Akashi, Wyatt W Anderson, Charles F Aquadro, David H Ardell, Roman Arguello, Carlo G Artieri, Daniel A Barbash, Daniel Barker, Paolo Barsanti, Phil Batterham, Serafim Batzoglou, Dave Begun, Arjun Bhutkar, Enrico Blanco, Stephanie A Bosak, Robert K Bradley, Adrianne D Brand, Michael R Brent, Angela N Brooks, Randall H Brown, Roger K Butlin, Corrado Caggese, Brian R Calvi, A Bernardo de Carvalho, Anat Caspi, Sergio Castrezana, Susan E Celniker, Jean L Chang, Charles Chapple, Sourav Chatterji, Asif Chinwalla, Alberto Civetta, Sandra W Clifton, Josep M Comeron, James C Costello, Jerry A Coyne, Jennifer Daub, Robert G David, Arthur L Delcher, Kim Delehaunty, Chuong B Do, Heather Ebling, Kevin Edwards, Thomas Eickbush, Jay D Evans, Alan Filipski, Sven Findeiss, Eva Freyhult, Lucinda Fulton, Robert Fulton, Ana C L Garcia, Anastasia Gardiner, David A Garfield, Barry E Garvin, Greg Gibson, Don Gilbert, Sante Gnerre, Jennifer Godfrey, Robert Good, Valer Gotea, Brenton Gravely, Anthony J Greenberg, Sam Griffiths-Jones, Samuel Gross, Roderic Guigo, Erik A Gustafson, Wilfried Haerty, Matthew W Hahn, Daniel L Halligan, Aaron L Halpern, Gillian M Halter, Mira V Han, Andreas Heger, Ladeana Hillier, Angie S Hinrichs, Ian Holmes, Roger A Hoskins, Melissa J Hubisz, Dan Hultmark, Melanie A Huntley, David B Jaffe, Santosh Jagadeeshan, William R Jeck, Justin Johnson, Corbin D Jones, William C Jordan, Gary H Karpen, Eiko Kataoka, Peter D Keightley, Pouya Kheradpour, Ewen F Kirkness, Leonardo B Koerich, Karsten Kristiansen, Dave Kudrna, Rob J Kulathinal, Sudhir Kumar, Roberta Kwok, Eric Lander, Charles H Langley, Richard Lapoint, Brian P Lazzaro, So-Jeong Lee, Lisa Levesque, Ruiqiang Li, Chiao-Feng Lin, Michael F Lin, Kerstin Lindblad-Toh, Ana Llopart, Manyuan Long, Lloyd Low, Elena Lozovsky, Jian Lu, Meizhong Luo, Carlos A Machado, Wojciech Makalowski, Mar Marzo, Muneo Matsuda, Luciano Matzkin, Bryant Mcallister, Carolyn S Mcbride, Brendan Mckernan, Kevin Mckernan, Maria Mendez-Lago, Patrick Minx, Michael U Mollenhauer, Kristi Montooth, Stephen M Mount, Xu Mu, Eugene Myers, Barbara Negre, Stuart Newfeld, Rasmus Nielsen, Mohamed a F Noor, Patrick O'Grady, Lior Pachter, Montserrat Papaceit, Matthew J Parisi, Michael Parisi, Leopold Parts, Jakob S Pedersen, Graziano Pesole, Adam M Phillippy, Chris P Ponting, Mihai Pop, Damiano Porcelli, Jeffrey R Powell, Sonja Prohaska, Kim Pruitt, Marta Puig, Hadi Quesneville, Kristipati Ravi Ram, David Rand, Matthew D Rasmussen, Laura K Reed, Robert Reenan, Amy Reily, Karin A Remington, Tania T Rieger, Michael G Ritchie, Charles Robin, Yu-Hui Rogers, Claudia Rohde, Julio Rozas, Marc J Rubenfield, Alfredo Ruiz, Susan Russo, Steven L Salzberg, Alejandro Sanchez-Gracia, David J Saranga, Hajime Sato, Stephen W Schaeffer, Michael C Schatz, Todd Schlenke, Russell Schwartz, Carmen Segarra, Rama S Singh, Laura Sirot, Marina Sirota, Nicholas B Sisneros, Chris D Smith, Temple F Smith, John Spieth, Deborah E Stage, Alexander Stark, Wolfgang Stephan, Robert L Strausberg, Sebastian Strempel, David Sturgill, Granger Sutton, Granger G Sutton, Wei Tao, Sarah Teichmann, Yoshiko N Tobari, Yoshihiko Tomimura, Jason M Tsolas, Vera L S Valente, Eli Venter, J Craig Venter, Saverio Vicario, Filipe G Vieira, Albert J Vilella, Alfredo Villasante, Brian Walenz, Jun Wang, Marvin Wasserman, Thomas Watts, Derek Wilson, Richard K Wilson, Rod A Wing, Mariana F Wolfner, Alex Wong, Gane Ka-Shu Wong, Chung-I Wu, Gabriel Wu, Daisuke Yamamoto, Hsiao-Pei Yang, Shiaw-Pyng Yang, James A Yorke, Kiyohito Yoshida, Evgeny Zdobnov, Peili Zhang, Yu Zhang, Aleksey V Zimin, Jennifer Baldwin, Amr Abdouelleil, Jamal Abdulkadir, Adal Abebe, Brikti Abera, Justin Abreu, St Christophe Acer, Lynne Aftuck, Allen Alexander, Peter An, Erica Anderson, Scott Anderson, Harindra Arachi, Marc Azer, Pasang Bachantsang, Andrew Barry, Tashi Bayul, Aaron Berlin, Daniel Bessette, Toby Bloom, Jason Blye, Leonid Boguslavskiy, Claude Bonnet, Boris Boukhgalter, Imane Bourzgui, Adam Brown, Patrick Cahill, Sheridon Channer, Yama Cheshatsang, Lisa Chuda, Mieke Citroen, Alville Collymore, Patrick Cooke, Maura Costello, Katie d'Aco, Riza Daza, Georgius de Haan, Stuart Degray, Christina Demaso, Norbu Dhargay, Kimberly Dooley, Erin Dooley, Missole Doricent, Passang Dorje, Kunsang Dorjee, Alan Dupes, Richard Elong, Jill Falk, Abderrahim Farina, Susan Faro, Diallo Ferguson, Sheila Fisher, Chelsea D Foley, Alicia Franke, Dennis Friedrich, Loryn Gadbois, Gary Gearin, Christina R Gearin, Georgia Giannoukos, Tina Goode, Joseph Graham, Edward Grandbois, Sharleen Grewal, Kunsang Gyaltsen, Nabil Hafez, Birhane Hagos, Jennifer Hall, Charlotte Henson, Andrew Hollinger, Tracey Honan, Monika D Huard, Leanne Hughes, Brian Hurhula, M Erii Husby, Asha Kamat, Ben Kanga, Seva Kashin, Dmitry Khazanovich, Peter Kisner, Krista Lance, Marcia Lara, William Lee, Niall Lennon, Frances Letendre, Rosie Levine, Alex Lipovsky, Xiaohong Liu, Jinlei Liu, Shangtao Liu, Tashi Lokyitsang, Yeshi Lokyitsang, Rakela Lubonja, Annie Lui, Pen Macdonald, Vasilia Magnisalis, Kebede Maru, Charles Matthews, William Mccusker, Susan Mcdonough, Teena Mehta, James Meldrim, Louis Meneus, Oana Mihai, Atanas Mihalev, Tanya Mihova, Rachel Mittelman, Valentine Mlenga, Anna Montmayeur, Leonidas Mulrain, Adam Navidi, Jerome Naylor, Tamrat Negash, Thu Nguyen, Nga Nguyen, Robert Nicol, Choe Norbu, Nyima Norbu, Nathaniel Novod, Barry O'Neill, Sahal Osman, Eva Markiewicz, Otero L Oyono, Christopher Patti, Pema Phunkhang, Fritz Pierre, Margaret Priest, Sujaa Raghuraman, Filip Rege, Rebecca Reyes, Cecil Rise, Peter Rogov, Keenan Ross, Elizabeth Ryan, Sampath Settipalli, Terry Shea, Ngawang Sherpa, Lu Shi, Diana Shih, Todd Sparrow, Jessica Spaulding, John Stalker, Nicole Stange-Thomann, Sharon Stavropoulos, Catherine Stone, Christopher Strader, Senait Tesfaye, Talene Thomson, Yama Thoulutsang, Dawa Thoulutsang, Kerri Topham, Ira Topping, Tsamla Tsamla, Helen Vassiliev, Andy Vo, Tsering Wangchuk, Tsering Wangdi, Michael Weiand, Jane Wilkinson, Shailendra Yadav, Geneva Young, Qing Yu, Lisa Zembek, Danni Zhong, Andrew Zimmer, Zac Zwirko, David B Jaffe, Pablo Alvarez, Will Brockman, Jonathan Butler, Cheewhye Chin, Sante Gnerre, Manfred Grabherr, Michael Kleber, Evan Mauceli, Iain Maccallum
article
Nature, 2007, 450 (7167), pp.203-18. ⟨10.1038/nature06341⟩
resume
Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
DOI
DOI : 10.1038/nature06341
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2006

Journal articles

titre
Single-nucleotide polymorphism frequency in a set of selected lines of bread wheat (Triticum aestivum L.)
auteur
Catherine Ravel, Sébastien Praud, Alain Murigneux, Aurelie Canaguier, Frederic Sapet, Delphine Steinbach, François Balfourier, Philippe Dufour, Paul Chalhoub, Dominique Brunel, Michel Beckert, Gilles Charmet
article
Genome, 2006, 49 (9), pp.1131-1139. ⟨10.1139/G06-067⟩
resume
Information on single-nucleotide polymorphisms (SNPs) in hexaploid bread wheat is still scarce. The goal of this study was to detect SNPs in wheat and examine their frequency. Twenty-six bread wheat lines from different origins worldwide were used. Specific PCR-products were obtained from 21 genes and directly sequenced. SNPs were discovered from the alignment of these sequences. The overall sequence polymorphism observed in this sample appears to be low; 64 single-base polymorphisms were detected in ~21.5 kb (i.e., 1 SNP every 335 bp). The level of polymorphism is highly variable among the different genes studied. Fifty percent of the genes studied contained no sequence polymorphism, whereas most SNPs detected were located in only 2 genes. As expected, taking into account a synthetic line created with a wild Triticum tauschii parent increases the level of polymorphism (101 SNPs; 1 SNP every 212 bp). The detected SNPs are available at http://urgi.versailles.inra.fr/GnpSNP. Data on linkage disequilibrium (LD) are still preliminary. They showed a significant level of LD in the 2 most polymorphic genes. To conclude, the genome size of hexaploid wheat and its low level of polymorphism complicate SNP discovery in this species.
DOI
DOI : 10.1139/G06-067
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titre
Anchoring of a large set of markers onto a BAC library for the development of a draft physical map of the grapevine genome
auteur
Didier Lamoureux, Anne Bernole, Isabelle Le Clainche, Sarah Tual, Vincent Thareau, Sophie Paillard, Fabrice Legeai, Carole Dossat, Patrick Wincker, Marylin Oswald, Didier Merdinoglu, Cécile Vignault, Serge Delrot, Michel Caboche, Boulos Chalhoub, Anne-Françoise Adam-Blondon
article
TAG Theoretical and Applied Genetics, 2006, 113 (2), pp.344-356. ⟨10.1007/s00122-006-0301-7⟩
resume
Five hundred and six EST-derived markers, 313 SSR markers and 26 BAC end-derived or SCAR markers were anchored by PCR on a subset of a Cabernet Sauvignon BAC library representing six genome equivalents pooled in three dimensions. In parallel, the 12,351 EST clusters of the grapevine UniGene set (build #11) from NCBI were used to design 12,125 primers pairs and perform electronic PCR on 67,543 nonredundant BAC-end sequences. This in silico experiment yielded 1,140 positive results concerning 638 different markers, among which 602 had not been already anchored by PCR. The data obtained will provide an easier access to the regulatory sequences surrounding important genes (represented by ESTs). In total, 1,731 islands of BAC clones (set of overlapping BAC clones containing at least one common marker) were obtained and 226 of them contained at least one genetically mapped anchor. These assigned islands are very useful because they will link the genetic map and the future fingerprint-based physical map and because they allowed us to indirectly place 93 ESTs on the genetic map. The islands containing two or more mapped SSR markers were also used to assess the quality of the integrated genetic map of the grapevine genome.
DOI
DOI : 10.1007/s00122-006-0301-7
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titre
Large-scale gene discovery in the pea aphid Acyrthosiphon pisum (Hemiptera)
auteur
Beatriz Sabater-Munoz, Fabrice Legeai, Claude Rispe, Joël Bonhomme, Peter Dearden, Carole Dossat, Aymeric Duclert, Jean-Pierre Gauthier, Danièle Giblot Ducray, Wayne Hunter, Phat Dang, Srini Kambhampati, David Martinez-Torres, Teresa Cortes, Andrès Moya, Atsushi Nakabachi, Cathy Philippe, Nathalie Prunier-Leterme, Yvan Rahbé, Jean-Christophe Simon, David L. Stern, Patrick Wincker, Denis Tagu
article
Genome Biology, 2006, 7-3 (r21), pp.1-11. ⟨10.1186/gb-2006-7-3-r21⟩
resume
Aphids are the leading pests in agricultural crops. A large-scale sequencing of 40,904 ESTs from the pea aphid Acyrthosiphon pisum was carried out to define a catalog of 12,082 unique transcripts. A strong AT bias was found, indicating a compositional shift between Drosophila melanogaster and A. pisum. An in silico profiling analysis characterized 135 transcripts specific to pea-aphid tissues (relating to bacteriocytes and parthenogenetic embryos). This project is the first to address the genetics of the Hemiptera and of a hemimetabolous insect.
DOI
DOI : 10.1186/gb-2006-7-3-r21
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2005

Journal articles

titre
GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts
auteur
Sebastien Aubourg, Veronique Brunaud, Clémence Bruyère, J. Mark Cock, Richard Cooke, Annick Cottet, Arnaud Couloux, Patrice Dehais, Gilbert Deléage, Aymeric Duclert, Manuel Echeverria, Aimée Eschbach, Denis Falconet, Ghislain Filippi, Christine Gaspin, Christophe Geourjon, Jean-Michel Grienenberger, Guy Houlné, Elisabeth Jamet, Frédéric Lechauve, Olivier Leleu, Philippe Leroy, Régis Mache, Christian Meyer, Hafed Nedjari, Ion Negrutiu, Valérie Orsini, Eric Peyretaillade, Cyril Pommier, Jeroen Raes, Jean-Loup Risler, Stéphane Rivière, Stéphane Rombauts, Pierre Rouzé, Michel Schneider, Philippe Schwob, Ian Small, Ghislain Soumayet-Kampetenga, Darko Stankovski, Claire Toffano, Michael Tognolli, Michel Caboche, Alain Lecharny
article
Nucleic Acids Research, 2005, 33, pp.D641-D646. ⟨10.1093/nar/gki115⟩
resume
Genomic projects heavily depend on genome annotations and are limited by the current deficiencies in the published predictions of gene structure and function. It follows that, improved annotation will allow better data mining of genomes, and more secure planning and design of experiments. The purpose of the GeneFarm project is to obtain homogeneous, reliable, documented and traceable annotations for Arabidopsis nuclear genes and gene products, and to enter them into an added-value database. This re-annotation project is being performed exhaustively on every member of each gene family. Performing a family-wide annotation makes the task easier and more efficient than a gene-by-gene approach since many features obtained for one gene can be extrapolated to some or all the other genes of a family. A complete annotation procedure based on the most efficient prediction tools available is being used by 16 partner laboratories, each contributing annotated families from its field of expertise. A database, named GeneFarm, and an associated user-friendly interface to query the annotations have been developed. More than 3000 genes distributed over 300 families have been annotated and are available at http://genoplante-info.infobiogen.fr/Genefarm/ . Furthermore, collaboration with the Swiss Institute of Bioinformatics is underway to integrate the GeneFarm data into the protein knowledgebase Swiss-Prot.
DOI
DOI : 10.1093/nar/gki115
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https://hal.science/hal-01189162/file/Pub05-mia-001_1.pdf BibTex
titre
Gene identification in the oomycete pathogen Phytophthora parasitica during in vitro vegetative growth through expressed sequence tags
auteur
Franck Panabières, Eric Galiana, Joelle Le Berre, Joelle J. Amselem
article
Fungal Genetics and Biology, 2005, 42 (7), pp.611-623. ⟨10.1016/j.fgb.2005.03.002⟩
DOI
DOI : 10.1016/j.fgb.2005.03.002
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titre
Recurrent recruitment of the THAP DNA-binding domain and molecular domestication of the P-transposable element
auteur
Hadi Quesneville, D Nouaud, D Anxolabéhère
article
Molecular Biology and Evolution, 2005, 22 (3), pp.741-746. ⟨10.1093/molbev/msi064⟩
resume
The recently described THAP domain motif characterizes a DNA-binding domain (DBD) that is widely conserved in human and in animals. It presents a similarity with the DBD of the P element transposase of D. melanogaster. We show here that the P Drosophila neogenes derived from P-transposable elements conserve the THAP domain. Moreover, secondary rearrangements by exon shuffling indicate the recurrent recruitment of this domain by the host genome. As P sequences and THAP genes are found together in many animal genomes, we discuss the possibility that the THAP proteins have acquired their domain as a result of recurrent molecular domestication of P-transposable elements.
DOI
DOI : 10.1093/molbev/msi064
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titre
Comparative analysis of BAC and whole genome shotgun sequences from an Anopheles gambiae region related to Plasmodium encapsulation
auteur
Karin Eiglmeier, Patrick Wincker, Laurence Cattolico, Véronique Anthouard, Inge Holm, Ralph Eckenberg, Hadi Quesneville, Olivier Jaillon, Frank H Collins, Jean Weissenbach, Paul T Brey, Charles W Roth
article
Insect Biochemistry and Molecular Biology, 2005, 35 (8), pp.799-814. ⟨10.1016/j.ibmb.2005.02.020⟩
resume
The only natural mechanism of malaria transmission in sub-Saharan Africa is the mosquito, generally Anopheles gambiae. Blocking malaria parasite transmission by stopping the development of Plasmodium in the insect vector would provide a useful alternative to the current methods of malaria control. Toward this end, it is important to understand the molecular basis of the malaria parasite refractory phenotype in An. gambiae mosquito strains. We have selected and sequenced six bacterial artificial chromosome (BAC) clones from the Pen-1 region that is the major quantitative trait locus involved in Plasmodium encapsulation. The sequence and the annotation of five overlapping BAC clones plus one adjacent, but not contiguous clone, totaling 585kb of genomic sequence from the centromeric end of the Pen-1 region of the PEST strain were compared to that of the genome sequence of the same strain produced by the whole genome shotgun technique. This project identified 23 putative mosquito genes plus putative copies of the retrotransposable elements BEL12 and TRANSIBN1_AG in the six BAC clones. Nineteen of the predicted genes are most similar to their Drosophila melanogaster homologs while one is more closely related to vertebrate genes. Comparison of these new BAC sequences plus previously published BAC sequences to the cognate region of the assembled genome sequence identified three retrotransposons present in one sequence version but not the other. One of these elements, Indy, has not been previously described. These observations provide evidence for the recent active transposition of these elements and demonstrate the plasticity of the Anopheles genome. The BAC sequences strongly support the public whole genome shotgun assembly and automatic annotation while also demonstrating the benefit of complementary genome sequences and of human curation. Importantly, the data demonstrate the differences in the genome sequence of an individual mosquito compared to that of a hypothetical, average genome sequence generated by whole genome shotgun assembly.
DOI
DOI : 10.1016/j.ibmb.2005.02.020
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2004

Journal articles

titre
Predotar: a tool for rapidly screening proteomes for N-terminal targeting sequences
auteur
Ian Small, Nemo Peeters, F. Legeai, Claire Lurin
article
Proteomics, 2004, 4 (6), pp.1581-1590. ⟨10.1002/pmic.200300776⟩
DOI
DOI : 10.1002/pmic.200300776
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titre
Detection of transposable elements by their compositional bias
auteur
Olivier Andrieu, Anna-Sophie Fiston, Dominique Anxolabéhère, Hadi Quesneville
article
BMC Bioinformatics, 2004, 5 (94), pp.1-13. ⟨10.1186/1471-2105-5-94⟩
resume
Background: Transposable elements (TE) are mobile genetic entities present in nearly all genomes. Previous work has shown that TEs tend to have a different nucleotide composition than the host genes, either considering codon usage bias or dinucleotide frequencies. We show here how these compositional differences can be used as a tool for detection and analysis of TE sequences. Results: We compared the composition of TE sequences and host gene sequences using probabilistic models of nucleotide sequences. We used hidden Markov models (HMM), which take into account the base composition of the sequences (occurrences of words n nucleotides long, with n ranging here from 1 to 4) and the heterogeneity between coding and non-coding parts of sequences. We analyzed three sets of sequences containing class I TEs, class II TEs and genes respectively in three species: Drosophila melanogaster, Cænorhabditis elegans and Arabidopsis thaliana. Each of these sets had a distinct, homogeneous composition, enabling us to distinguish between the two classes of TE and the genes. However the particular base composition of the TEs differed in the three species studied. Conclusions: This approach can be used to detect and annotate TEs in genomic sequences and complements the current homology-based TE detection methods. Furthermore, the HMM method is able to identify the parts of a sequence in which the nucleotide composition resembles that of a coding region of a TE. This is useful for the detailed annotation of TE sequences, which may contain an ancient, highly diverged coding region that is no longer fully functional.
DOI
DOI : 10.1186/1471-2105-5-94
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titre
Annotated expressed sequence tags for studies of the regulation of reproductive modes in aphids
auteur
Denis Tagu, N. Prunier-Leterme, F. Legeai, J.-P Gauthier, A Duclert, B. Sabater-Munoz, J Bonhomme, Jean-Christophe Simon
article
Insect Biochemistry and Molecular Biology, 2004, 34, pp.809 - 822. ⟨10.1016/j.ibmb.2004.05.001⟩
resume
The damaging effect of aphids to crops is largely determined by the spectacular rate of increase of populational expansion due to their parthenogenetic generations. Despite this, the molecular processes triggering the transition between the parthenogenetic and sexual phases between their annual life cycle have received little attention. Here, we describe a collection of genes from the cereal aphid Rhopalosiphum padi expressed during the switch from parthenogenetic to sexual reproduction. After cDNA cloning and sequencing, 726 expressed sequence tags (EST) were annotated. The R. padi EST collection contained a substantial number (139) of bacterial endosymbiont sequences. The majority of R. padi cDNAs encoded either unknown proteins (56%) or housekeeping polypeptides (38%). The large proportion of sequences without similarities in the databases is related to both their small size and their high GC content, corresponding probably to the presence of 5 0-unstranslated regions. Fifteen genes involved in developmental and differentiation events were identified by similarity to known genes. Some of these may be useful candidates for markers of the early steps of sexual differentiation. #
DOI
DOI : 10.1016/j.ibmb.2004.05.001
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2003

Journal articles

titre
Hoppel, a P-like element without introns: a P-element ancestral structure or a retrotranscription derivative?
auteur
Daphné Reiss, Hadi Quesneville, Danielle Nouaud, Olivier Andrieu, Dominique Anxolabéhère
article
Molecular Biology and Evolution, 2003, 20 (6), pp.869-879. ⟨10.1093/molbev/msg090⟩
resume
An in silico search for P-transposable-element-related sequences in the Drosophila melanogaster genome allowed us to detect sequences that are similar to P-element transposases. These sequences are located in the central region of 3.4-kb Hoppel elements, a class II transposon. Polymerase chain reaction (PCR) analysis of the insertional polymorphism revealed that these elements are mobile. The 3.4-kb elements are the longest copies of this family ever found. They contain an open reading frame that is long enough to encode a transposase, suggesting that the 3.4-kb elements are the full-length copies of the Hoppel family. Multiple alignments of several P-element transposases from different species and the Hoppel-element-encoded peptide showed that all of the P-element introns and the 5' region of the transposase are absent from the Hoppel sequence. Sequence analysis combined with reverse transcriptase PCR analysis showed that the 3.4-kb Hoppel elements are intronless. P and Hoppel not only share similar amino acid sequences but also have terminal inverted repeats of the same length (31 bp), and their excision footprints present a similar structure, which suggests that their transposases are functionally very similar. Thus, we propose that the Hoppel element family be included in the P-element superfamily. Two evolutionary scenarios are discussed considering the presence /absence of introns within the P-element superfamily.
DOI
DOI : 10.1093/molbev/msg090
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https://hal.inrae.fr/hal-02676873/file/Mol%20Biol%20Evol-2003-Reiss-869-79_1.pdf BibTex
titre
Detection of new transposable element families in Drosophila melanogaster and Anopheles gambiae genomes
auteur
Hadi Quesneville, Danielle Nouaud, Dominique Anxolabéhère
article
Journal of Molecular Evolution, 2003, 57 Suppl 1, pp.S50-S59. ⟨10.1007/s00239-003-0007-2⟩
resume
The techniques that are usually used to detect transposable elements (TEs) in nucleic acid sequences rely on sequence similarity with previously characterized elements. However, these methods are likely to miss many elements in various organisms. We tested two strategies for the detection of unknown elements. The first, which we call "TBLASTX strategy," searches for TE sequences by comparing the six-frame translations of the nucleic acid sequences of known TEs with the genomic sequence of interest. The second, "repeat-based strategy," searches genomic sequences for long repeats and clusters them in groups of similar sequences. TE copies from a given family are expected to cluster together. We tested the Drosophila melanogaster genomic sequence and the recently sequenced Anopheles gambiae genome in which most TEs remain unknown. We showed that the "TBLASTX strategy" is very efficient as it detected at least 332 new TE families in D. melanogaster and 400 in A. gambiae. This was unexpected in Drosophila as TEs of this organism have been extensively studied. The "repeat-based strategy" appeared to be very inefficient because of two problems: (i) TE copies are heavily deleted and few copies share homologous regions, and (ii) segmental duplications are frequent and it is not easy to distinguish them from TE copies.
DOI
DOI : 10.1007/s00239-003-0007-2
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titre
GénoPlante-Info (GPI): a collection of databases and bioinformatics resources for plant genomics
auteur
Dylan Samson, F. Legeai, Emmanuelle Karsenty, Sébastien Reboux, J.B. Veyrieras, J. Just, Emmanuel Barillot
article
Nucleic Acids Research, 2003, 31 (1), pp.179-182. ⟨10.1093/nar/gkg060⟩
resume
Genoplante is a partnership program between public French institutes (INRA, CIRAD, IRD and CNRS) and private companies (Biogemma, Bayer CropScience and Bioplante) that aims at developing genome analysis programs for crop species (corn, wheat, rapeseed, sunflower and pea) and model plants (Arabidopsis and rice). The outputs of these programs form a wealth of information (genomic sequence, transcriptome, proteome, allelic variability, mapping and synteny, and mutation data) and tools (databases, interfaces, analysis software), that are being integrated and made public at the public bioinformatics resource centre of Genoplante: GenoPlante-Info (GPI). This continuous flood of data and tools is regularly updated and will grow continuously during the coming two years. Access to the GPI databases and tools is available at http://genoplante-info.infobiogen.fr/.
DOI
DOI : 10.1093/nar/gkg060
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https://hal.inrae.fr/hal-02682546/file/2003_Samson_Nucleic%20Acids%20Research_1.pdf BibTex
titre
Recurrent exon shuffling between distant P-element families
auteur
Danielle Nouaud, Hadi Quesneville, Dominique Anxolabéhère
article
Molecular Biology and Evolution, 2003, 20 (2), pp.190-199. ⟨10.1093/molbev/msg036⟩
resume
Two independent stationary P-related neogenes had been previously described in the Drosophila obscura species group and in the Drosophila montium species subgroup. In Drosophila melanogaster, P-transposable elements can encode an 87 kDa transposase and a 66 kDa repressor, but the P-neogenes have only conserved the capacity to encode a 66 kDa repressor-like protein specified by the first three exons. We have previously analyzed the genomic modifications associated with the transition of a P-element into the montium P-neogene, the coding capacity of which has been conserved for around 20 Myr ( Nouaud, D., and D. Anxolabéhère. 1997. Mol. Biol. Evol. 14:1132-1144). Here we show that the P-neogene of some species of the montium subgroup presents a new structure involving the capture of an additional exon from a very distant P-element subfamily. This additional exon is inserted either upstream or downstream of the first exon of the P-neogene. As a result of alternative splicing, these modified neogenes can produce, in addition to the repressor-like protein, a new protein which differs only by the NH2-terminal region. We hypothesize that this protein diversity within an organism results in a functional diversification due to the selective advantage associated with the domestication of the P-neogene in these species. Moreover, the autonomous P-element which provides the additional exons is still present in the genome. Its nucleotide sequence is more than 45% distant from the previously defined P-type element (M-type, O-type, T-type) and defines a new P-type element subfamily referred to as the K-type.
DOI
DOI : 10.1093/molbev/msg036
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https://hal.inrae.fr/hal-02678803/file/Mol%20Biol%20Evol-2003-Nouaud-190-9_1.pdf BibTex

2001

Journal articles

titre
Genetic algorithm-based model of evolutionary dynamics of class II transposable elements
auteur
Hadi Quesneville, Dominique Anxolabéhère
article
Journal of Theoretical Biology, 2001, 213 (1), pp.21-30. ⟨10.1006/jtbi.2001.2401⟩
resume
We propose a new conceptual framework to study the dynamics of transposable elements. Based on a genetic algorithm, our model is designed as a self-organizing system. Our results show that transposable elements could emerge from a single endonuclease gene. The DNA repair mechanisms appear to condition the emergence success of class II TEs. Antagonist selective forces acting on transposable elements and their hosts induce by their opposition differences in the sequence evolution of the functional domains and of the copies.
DOI
DOI : 10.1006/jtbi.2001.2401
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2000

Journal articles

titre
The triangle test statistic (TTS): a test of genetic homogeneity using departure from the triangle constraints in IBD distribution among affected sib-pairs
auteur
M.H. Dizier, Hadi Quesneville, B. Prum, H. Selinger-Leneman, F. Clerget-Darpoux
article
Annals of Human Genetics, 2000, 64 (Part 5), pp.433-442. ⟨10.1046/j.1469-1809.2000.6450433.x⟩
resume
The proportions of affected sibs sharing 2, 1 or 0 identical by descent parental marker alleles have been shown to conform to the 'triangle constraints' (Suarez, 1978; Holmans, 1993). It has also been shown (Dudoit & Speed, 1999) that the constraints are verified provided certain assumptions hold. In this study we explore a realistic situation in which the constraints fail due to the presence of a factor in which the sibs differ, a factor on which penetrance depends. This factor may be a characteristic of the trait (severe vs. mild form), or the presence/absence of an associated trait or an environmental factor. We show that under such situations, using the triangle constraints may lead to important loss of power to detect linkage by the MLS test. We propose here an alternative approach in order to detect both linkage and heterogeneity.
DOI
DOI : 10.1046/j.1469-1809.2000.6450433.x
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02696378/file/j.1469-1809.2000.6450433.x_1.pdf BibTex
titre
Search for multifactorial disease susceptibility genes in founder populations
auteur
C. Bourgain, E. Genin, Hadi Quesneville, F. Clerget-Darpoux
article
Annals of Human Genetics, 2000, 64 (3), pp.255-265. ⟨10.1046/j.1469-1809.2000.6430255.x⟩
resume
The current challenge in biomedical research is to detect genetic risk factors involved in common complex diseases. The power to detect their role is generally poor in populations that have been large for a long time. It has been suggested that the power may be increased by taking advantage of the specificity of founder populations: linkage disequilibrium spanning larger regions and kinship coefficients being stronger than in large populations. A new method is proposed here, the Maximum Identity Length Contrast (MILC) which, in contrast with other existing methods, does not make the assumption of unique ancestry for the genetic risk factors. It is thus appropriate for a search for common genetic risk factors for complex diseases. Statistical properties of the method are discussed in realistic contexts.
DOI
DOI : 10.1046/j.1469-1809.2000.6430255.x
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02696948/file/j.1469-1809.2000.6430255.x_1.pdf BibTex