Arnaud Couloux
Centre national de la recherche scientifique
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Featured researches published by Arnaud Couloux.
PLOS Genetics | 2011
Joelle Amselem; Christina A. Cuomo; Jan A. L. van Kan; Muriel Viaud; Ernesto P. Benito; Arnaud Couloux; Pedro M. Coutinho; Ronald P. de Vries; Paul S. Dyer; Sabine Fillinger; Elisabeth Fournier; Lilian Gout; Matthias Hahn; Linda T. Kohn; Nicolas Lapalu; Kim M. Plummer; Jean-Marc Pradier; Emmanuel Quévillon; Amir Sharon; Adeline Simon; Arjen ten Have; Bettina Tudzynski; Paul Tudzynski; Patrick Wincker; Marion Andrew; Véronique Anthouard; Ross E. Beever; Rolland Beffa; Isabelle Benoit; Ourdia Bouzid
Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38–39 Mb genomes include 11,860–14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared to <1% of B. cinerea. The arsenal of genes associated with necrotrophic processes is similar between the species, including genes involved in plant cell wall degradation and oxalic acid production. Analysis of secondary metabolism gene clusters revealed an expansion in number and diversity of B. cinerea–specific secondary metabolites relative to S. sclerotiorum. The potential diversity in secondary metabolism might be involved in adaptation to specific ecological niches. Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between S. sclerotiorum and B. cinerea. The organization of the mating-type loci differs, and their structures provide evidence for the evolution of heterothallism from homothallism. These data shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating. This resource should facilitate the functional studies designed to better understand what makes these fungi such successful and persistent pathogens of agronomic crops.
Nature | 2010
Francis L. Martin; Annegret Kohler; Claude Murat; Raffaella Balestrini; Pedro M. Coutinho; Olivier Jaillon; Barbara Montanini; Emmanuelle Morin; Benjamin Noel; Riccardo Percudani; Bettina Porcel; Andrea Rubini; Antonella Amicucci; Joelle Amselem; Véronique Anthouard; Sergio Arcioni; François Artiguenave; Jean-Marc Aury; Paola Ballario; Angelo Bolchi; Andrea Brenna; Annick Brun; Marc Buee; Brandi Cantarel; Gérard Chevalier; Arnaud Couloux; Corinne Da Silva; Sébastien Duplessis; Stefano Ghignone; Benoı̂t Hilselberger
The Périgord black truffle (Tuber melanosporum Vittad.) and the Piedmont white truffle dominate today’s truffle market. The hypogeous fruiting body of T. melanosporum is a gastronomic delicacy produced by an ectomycorrhizal symbiont endemic to calcareous soils in southern Europe. The worldwide demand for this truffle has fuelled intense efforts at cultivation. Identification of processes that condition and trigger fruit body and symbiosis formation, ultimately leading to efficient crop production, will be facilitated by a thorough analysis of truffle genomic traits. In the ectomycorrhizal Laccaria bicolor, the expansion of gene families may have acted as a ‘symbiosis toolbox’. This feature may however reflect evolution of this particular taxon and not a general trait shared by all ectomycorrhizal species. To get a better understanding of the biology and evolution of the ectomycorrhizal symbiosis, we report here the sequence of the haploid genome of T. melanosporum, which at ∼125 megabases is the largest and most complex fungal genome sequenced so far. This expansion results from a proliferation of transposable elements accounting for ∼58% of the genome. In contrast, this genome only contains ∼7,500 protein-coding genes with very rare multigene families. It lacks large sets of carbohydrate cleaving enzymes, but a few of them involved in degradation of plant cell walls are induced in symbiotic tissues. The latter feature and the upregulation of genes encoding for lipases and multicopper oxidases suggest that T. melanosporum degrades its host cell walls during colonization. Symbiosis induces an increased expression of carbohydrate and amino acid transporters in both L. bicolor and T. melanosporum, but the comparison of genomic traits in the two ectomycorrhizal fungi showed that genetic predispositions for symbiosis—‘the symbiosis toolbox’—evolved along different ways in ascomycetes and basidiomycetes.
Nature Communications | 2011
Thierry Rouxel; Grandaubert J; James K. Hane; Hoede C; van de Wouw Ap; Arnaud Couloux; Dominguez; Anthouard; Bally P; Bourras S; Anton J. Cozijnsen; Ciuffetti Lm; Degrave A; Dilmaghani A; Duret L; Fudal I; Goodwin Sb; Lilian Gout; Nicolas Glaser; Linglin J; Kema Gh; Lapalu N; Lawrence Cb; May K; Michel Meyer; Benedicte Ollivier; Julie Poulain; Schoch Cl; Simon A; Spatafora Jw
Fungi are of primary ecological, biotechnological and economic importance. Many fundamental biological processes that are shared by animals and fungi are studied in fungi due to their experimental tractability. Many fungi are pathogens or mutualists and are model systems to analyse effector genes and their mechanisms of diversification. In this study, we report the genome sequence of the phytopathogenic ascomycete Leptosphaeria maculans and characterize its repertoire of protein effectors. The L. maculans genome has an unusual bipartite structure with alternating distinct guanine and cytosine-equilibrated and adenine and thymine (AT)-rich blocks of homogenous nucleotide composition. The AT-rich blocks comprise one-third of the genome and contain effector genes and families of transposable elements, both of which are affected by repeat-induced point mutation, a fungal-specific genome defence mechanism. This genomic environment for effectors promotes rapid sequence diversification and underpins the evolutionary potential of the fungus to adapt rapidly to novel host-derived constraints.
Science | 2014
Frédéric Choulet; Adriana Alberti; Sébastien Theil; Natasha Glover; Valérie Barbe; Josquin Daron; Lise Pingault; Pierre Sourdille; Arnaud Couloux; Etienne Paux; Philippe Leroy; Sophie Mangenot; Nicolas Guilhot; Jacques Le Gouis; François Balfourier; Michael Alaux; Véronique Jamilloux; Julie Poulain; Céline Durand; Arnaud Bellec; Christine Gaspin; Jan Safar; Jaroslav Dolezel; Jane Rogers; Klaas Vandepoele; Jean-Marc Aury; Klaus F. X. Mayer; Hélène Bergès; Hadi Quesneville; Patrick Wincker
We produced a reference sequence of the 1-gigabase chromosome 3B of hexaploid bread wheat. By sequencing 8452 bacterial artificial chromosomes in pools, we assembled a sequence of 774 megabases carrying 5326 protein-coding genes, 1938 pseudogenes, and 85% of transposable elements. The distribution of structural and functional features along the chromosome revealed partitioning correlated with meiotic recombination. Comparative analyses indicated high wheat-specific inter- and intrachromosomal gene duplication activities that are potential sources of variability for adaption. In addition to providing a better understanding of the organization, function, and evolution of a large and polyploid genome, the availability of a high-quality sequence anchored to genetic maps will accelerate the identification of genes underlying important agronomic traits.
Genome Biology | 2008
Eric Espagne; Olivier Lespinet; Fabienne Malagnac; Corinne Da Silva; Olivier Jaillon; Betina M. Porcel; Arnaud Couloux; Jean-Marc Aury; Béatrice Segurens; Julie Poulain; Véronique Anthouard; Sandrine Grossetete; Hamid Khalili; Evelyne Coppin; Michelle Déquard-Chablat; Marguerite Picard; Véronique Contamine; Sylvie Arnaise; Anne Bourdais; Véronique Berteaux-Lecellier; Daniel Gautheret; Ronald P. de Vries; Evy Battaglia; Pedro M. Coutinho; Etienne Danchin; Bernard Henrissat; Riyad El Khoury; Annie Sainsard-Chanet; Antoine Boivin; Bérangère Pinan-Lucarré
BackgroundThe dung-inhabiting ascomycete fungus Podospora anserina is a model used to study various aspects of eukaryotic and fungal biology, such as ageing, prions and sexual development.ResultsWe present a 10X draft sequence of P. anserina genome, linked to the sequences of a large expressed sequence tag collection. Similar to higher eukaryotes, the P. anserina transcription/splicing machinery generates numerous non-conventional transcripts. Comparison of the P. anserina genome and orthologous gene set with the one of its close relatives, Neurospora crassa, shows that synteny is poorly conserved, the main result of evolution being gene shuffling in the same chromosome. The P. anserina genome contains fewer repeated sequences and has evolved new genes by duplication since its separation from N. crassa, despite the presence of the repeat induced point mutation mechanism that mutates duplicated sequences. We also provide evidence that frequent gene loss took place in the lineages leading to P. anserina and N. crassa. P. anserina contains a large and highly specialized set of genes involved in utilization of natural carbon sources commonly found in its natural biotope. It includes genes potentially involved in lignin degradation and efficient cellulose breakdown.ConclusionThe features of the P. anserina genome indicate a highly dynamic evolution since the divergence of P. anserina and N. crassa, leading to the ability of the former to use specific complex carbon sources that match its needs in its natural biotope.
The Plant Cell | 2010
Frédéric Choulet; Thomas Wicker; Camille Rustenholz; Etienne Paux; Jérôme Salse; Philippe Leroy; Stéphane Schlub; Marie Christine Le Paslier; Ghislaine Magdelenat; Catherine Gonthier; Arnaud Couloux; Hikmet Budak; James Breen; Michael O. Pumphrey; Sixin Liu; Xiuying Kong; Jizeng Jia; Marta Gut; Dominique Brunel; James A. Anderson; Bikram S. Gill; R. Appels; Beat Keller; Catherine Feuillet
This article describes the molecular analysis of large contiguous sequences produced from the bread wheat genome. It provides novel insights into the number, distribution, and density of genes along chromosome 3B and reveals an unexpectedly high amount of noncollinear genes compared to model grass genomes. To improve our understanding of the organization and evolution of the wheat (Triticum aestivum) genome, we sequenced and annotated 13-Mb contigs (18.2 Mb) originating from different regions of its largest chromosome, 3B (1 Gb), and produced a 2x chromosome survey by shotgun Illumina/Solexa sequencing. All regions carried genes irrespective of their chromosomal location. However, gene distribution was not random, with 75% of them clustered into small islands containing three genes on average. A twofold increase of gene density was observed toward the telomeres likely due to high tandem and interchromosomal duplication events. A total of 3222 transposable elements were identified, including 800 new families. Most of them are complete but showed a highly nested structure spread over distances as large as 200 kb. A succession of amplification waves involving different transposable element families led to contrasted sequence compositions between the proximal and distal regions. Finally, with an estimate of 50,000 genes per diploid genome, our data suggest that wheat may have a higher gene number than other cereals. Indeed, comparisons with rice (Oryza sativa) and Brachypodium revealed that a high number of additional noncollinear genes are interspersed within a highly conserved ancestral grass gene backbone, supporting the idea of an accelerated evolution in the Triticeae lineages.
Scientific Reports | 2017
Anaïs Gouin; Anthony Bretaudeau; Kiwoong Nam; Sylvie Gimenez; Jean-Marc Aury; Bernard Duvic; Frédérique Hilliou; Nicolas Durand; Nicolas Montagné; Isabelle Darboux; Suyog S. Kuwar; Thomas Chertemps; David Siaussat; Anne Bretschneider; Yves Moné; Seung-Joon Ahn; Sabine Hänniger; Anne-Sophie Gosselin Grenet; David Neunemann; Florian Maumus; Isabelle Luyten; Karine Labadie; Wei Xu; Fotini Koutroumpa; Jean-Michel Escoubas; Angel Llopis; Martine Maïbèche-Coisne; Fanny Salasc; Archana Tomar; Alisha Anderson
Emergence of polyphagous herbivorous insects entails significant adaptation to recognize, detoxify and digest a variety of host-plants. Despite of its biological and practical importance - since insects eat 20% of crops - no exhaustive analysis of gene repertoires required for adaptations in generalist insect herbivores has previously been performed. The noctuid moth Spodoptera frugiperda ranks as one of the world’s worst agricultural pests. This insect is polyphagous while the majority of other lepidopteran herbivores are specialist. It consists of two morphologically indistinguishable strains (“C” and “R”) that have different host plant ranges. To describe the evolutionary mechanisms that both enable the emergence of polyphagous herbivory and lead to the shift in the host preference, we analyzed whole genome sequences from laboratory and natural populations of both strains. We observed huge expansions of genes associated with chemosensation and detoxification compared with specialist Lepidoptera. These expansions are largely due to tandem duplication, a possible adaptation mechanism enabling polyphagy. Individuals from natural C and R populations show significant genomic differentiation. We found signatures of positive selection in genes involved in chemoreception, detoxification and digestion, and copy number variation in the two latter gene families, suggesting an adaptive role for structural variation.
Journal of Molecular Biology | 2009
Haeyoung Jeong; Valérie Barbe; Choong Hoon Lee; David Vallenet; Dong Su Yu; Sang Haeng Choi; Arnaud Couloux; Seung Won Lee; Laurence Cattolico; Cheol Goo Hur; Hong Seog Park; Béatrice Segurens; Sun Chang Kim; Tae Kwang Oh; Richard E. Lenski; F.William Studier; Patrick Daegelen; Jihyun F. Kim
Escherichia coli K-12 and B have been the subjects of classical experiments from which much of our understanding of molecular genetics has emerged. We present here complete genome sequences of two E. coli B strains, REL606, used in a long-term evolution experiment, and BL21(DE3), widely used to express recombinant proteins. The two genomes differ in length by 72,304 bp and have 426 single base pair differences, a seemingly large difference for laboratory strains having a common ancestor within the last 67 years. Transpositions by IS1 and IS150 have occurred in both lineages. Integration of the DE3 prophage in BL21(DE3) apparently displaced a defective prophage in the lambda attachment site of B. As might have been anticipated from the many genetic and biochemical experiments comparing B and K-12 over the years, the B genomes are similar in size and organization to the genome of E. coli K-12 MG1655 and have >99% sequence identity over approximately 92% of their genomes. E. coli B and K-12 differ considerably in distribution of IS elements and in location and composition of larger mobile elements. An unexpected difference is the absence of a large cluster of flagella genes in B, due to a 41 kbp IS1-mediated deletion. Gene clusters that specify the LPS core, O antigen, and restriction enzymes differ substantially, presumably because of horizontal transfer. Comparative analysis of 32 independently isolated E. coli and Shigella genomes, both commensals and pathogenic strains, identifies a minimal set of genes in common plus many strain-specific genes that constitute a large E. coli pan-genome.
Nature | 2013
Jean-François Flot; Boris Hespeels; Xiang Li; Benjamin Noel; Irina R. Arkhipova; Etienne Danchin; Andreas Hejnol; Bernard Henrissat; Romain Koszul; Jean-Marc Aury; Valérie Barbe; Roxane Marie Barthélémy; Jens Bast; Georgii A. Bazykin; Olivier Chabrol; Arnaud Couloux; Martine Da Rocha; Corinne Da Silva; Eugene Gladyshev; Philippe Gouret; Oskar Hallatschek; Bette Hecox-Lea; Karine Labadie; Benjamin Lejeune; Oliver Piskurek; Julie Poulain; Fernando Rodriguez; Joseph F. Ryan; O. Vakhrusheva; Eric Wajnberg
Loss of sexual reproduction is considered an evolutionary dead end for metazoans, but bdelloid rotifers challenge this view as they appear to have persisted asexually for millions of years. Neither male sex organs nor meiosis have ever been observed in these microscopic animals: oocytes are formed through mitotic divisions, with no reduction of chromosome number and no indication of chromosome pairing. However, current evidence does not exclude that they may engage in sex on rare, cryptic occasions. Here we report the genome of a bdelloid rotifer, Adineta vaga (Davis, 1873), and show that its structure is incompatible with conventional meiosis. At gene scale, the genome of A. vaga is tetraploid and comprises both anciently duplicated segments and less divergent allelic regions. However, in contrast to sexual species, the allelic regions are rearranged and sometimes even found on the same chromosome. Such structure does not allow meiotic pairing; instead, we find abundant evidence of gene conversion, which may limit the accumulation of deleterious mutations in the absence of meiosis. Gene families involved in resistance to oxidation, carbohydrate metabolism and defence against transposons are significantly expanded, which may explain why transposable elements cover only 3% of the assembled sequence. Furthermore, 8% of the genes are likely to be of non-metazoan origin and were probably acquired horizontally. This apparent convergence between bdelloids and prokaryotes sheds new light on the evolutionary significance of sex.
Systematic Biology | 2012
Astrid Cruaud; Nina Rønsted; Bhanumas Chantarasuwan; Lien-Siang Chou; Wendy L. Clement; Arnaud Couloux; Benjamin R. Cousins; Gwenaëlle Genson; Rhett D. Harrison; Paul Hanson; Martine Hossaert-McKey; Roula Jabbour-Zahab; Emmanuelle Jousselin; Carole Kerdelhué; Finn Kjellberg; Carlos Lopez-Vaamonde; John Peebles; Yan-Qiong Peng; Rodrigo Augusto Santinelo Pereira; Tselil Schramm; Rosichon Ubaidillah; Simon van Noort; George D. Weiblen; Da Rong Yang; Anak Yodpinyanee; Ran Libeskind-Hadas; James M. Cook; Jean Yves Rasplus; Vincent Savolainen
It is thought that speciation in phytophagous insects is often due to colonization of novel host plants, because radiations of plant and insect lineages are typically asynchronous. Recent phylogenetic comparisons have supported this model of diversification for both insect herbivores and specialized pollinators. An exceptional case where contemporaneous plant-insect diversification might be expected is the obligate mutualism between fig trees (Ficus species, Moraceae) and their pollinating wasps (Agaonidae, Hymenoptera). The ubiquity and ecological significance of this mutualism in tropical and subtropical ecosystems has long intrigued biologists, but the systematic challenge posed by >750 interacting species pairs has hindered progress toward understanding its evolutionary history. In particular, taxon sampling and analytical tools have been insufficient for large-scale cophylogenetic analyses. Here, we sampled nearly 200 interacting pairs of fig and wasp species from across the globe. Two supermatrices were assembled: on an average, wasps had sequences from 77% of 6 genes (5.6 kb), figs had sequences from 60% of 5 genes (5.5 kb), and overall 850 new DNA sequences were generated for this study. We also developed a new analytical tool, Jane 2, for event-based phylogenetic reconciliation analysis of very large data sets. Separate Bayesian phylogenetic analyses for figs and fig wasps under relaxed molecular clock assumptions indicate Cretaceous diversification of crown groups and contemporaneous divergence for nearly half of all fig and pollinator lineages. Event-based cophylogenetic analyses further support the codiversification hypothesis. Biogeographic analyses indicate that the present-day distribution of fig and pollinator lineages is consistent with a Eurasian origin and subsequent dispersal, rather than with Gondwanan vicariance. Overall, our findings indicate that the fig-pollinator mutualism represents an extreme case among plant-insect interactions of coordinated dispersal and long-term codiversification. [Biogeography; coevolution; cospeciation; host switching; long-branch attraction; phylogeny.].