Author Report for: Poulain JNo contact information in database for Poulain J
Leclere L, Horin C, Chevalier S, Lapebie P, Dru P, Peron S, Jager M, Condamine T, Pottin K and Copley RR <16 more author(s)> Leclere L, Horin C, Chevalier S, Lapebie P, Dru P, Peron S, Jager M, Condamine T, Pottin K, Romano S, Steger J, Sinigaglia C, Barreau C, Quiroga Artigas G, Ruggiero A, Fourrage C, Kraus JEM, Poulain J, Aury JM, Wincker P, Queinnec E, Technau U, Manuel M, Momose T, Houliston E, Copley RR (- 16) Ref: Nat Ecol Evol, 3:801, 2019 : PubMed ESTHER: Leclere_2019_Nat.Ecol.Evol_3_801 PubMedSearch: Leclere 2019 Nat.Ecol.Evol 3 801 PubMedID: 30858591 Gene_locus related to this paper: 9cnid-b7zf10, 9cnid-a0a069dlv7, 9cnid-a0a069duu8 Abstract Jellyfish (medusae) are a distinctive life-cycle stage of medusozoan cnidarians. They are major marine predators, with integrated neurosensory, muscular and organ systems. The genetic foundations of this complex form are largely unknown. We report the draft genome of the hydrozoan jellyfish Clytia hemisphaerica and use multiple transcriptomes to determine gene use across life-cycle stages. Medusa, planula larva and polyp are each characterized by distinct transcriptome signatures reflecting abrupt life-cycle transitions and all deploy a mixture of phylogenetically old and new genes. Medusa-specific transcription factors, including many with bilaterian orthologues, associate with diverse neurosensory structures. Compared to Clytia, the polyp-only hydrozoan Hydra has lost many of the medusa-expressed transcription factors, despite similar overall rates of gene content evolution and sequence evolution. Absence of expression and gene loss among Clytia orthologues of genes patterning the anthozoan aboral pole, secondary axis and endomesoderm support simplification of planulae and polyps in Hydrozoa, including loss of bilateral symmetry. Consequently, although the polyp and planula are generally considered the ancestral cnidarian forms, in Clytia the medusa maximally deploys the ancestral cnidarian-bilaterian transcription factor gene complement. Title: Pezizomycetes genomes reveal the molecular basis of ectomycorrhizal truffle lifestyle Murat C, Payen T, Noel B, Kuo A, Morin E, Chen J, Kohler A, Krizsan K, Balestrini R and Martin FM <40 more author(s)> Murat C, Payen T, Noel B, Kuo A, Morin E, Chen J, Kohler A, Krizsan K, Balestrini R, Da Silva C, Montanini B, Hainaut M, Levati E, Barry KW, Belfiori B, Cichocki N, Clum A, Dockter RB, Fauchery L, Guy J, Iotti M, Le Tacon F, Lindquist EA, Lipzen A, Malagnac F, Mello A, Molinier V, Miyauchi S, Poulain J, Riccioni C, Rubini A, Sitrit Y, Splivallo R, Traeger S, Wang M, Zifcakova L, Wipf D, Zambonelli A, Paolocci F, Nowrousian M, Ottonello S, Baldrian P, Spatafora JW, Henrissat B, Nagy LG, Aury JM, Wincker P, Grigoriev IV, Bonfante P, Martin FM (- 40) Ref: Nat Ecol Evol, 2:1956, 2018 : PubMed ESTHER: Murat_2018_Nat.Ecol.Evol_2_1956 PubMedSearch: Murat 2018 Nat.Ecol.Evol 2 1956 PubMedID: 30420746 Gene_locus related to this paper: 9pezi-a0a3n4l4q5, 9pezi-a0a3n4lpg7 Abstract Tuberaceae is one of the most diverse lineages of symbiotic truffle-forming fungi. To understand the molecular underpinning of the ectomycorrhizal truffle lifestyle, we compared the genomes of Piedmont white truffle (Tuber magnatum), Perigord black truffle (Tuber melanosporum), Burgundy truffle (Tuber aestivum), pig truffle (Choiromyces venosus) and desert truffle (Terfezia boudieri) to saprotrophic Pezizomycetes. Reconstructed gene duplication/loss histories along a time-calibrated phylogeny of Ascomycetes revealed that Tuberaceae-specific traits may be related to a higher gene diversification rate. Genomic features in Tuber species appear to be very similar, with high transposon content, few genes coding lignocellulose-degrading enzymes, a substantial set of lineage-specific fruiting-body-upregulated genes and high expression of genes involved in volatile organic compound metabolism. Developmental and metabolic pathways expressed in ectomycorrhizae and fruiting bodies of T. magnatum and T. melanosporum are unexpectedly very similar, owing to the fact that they diverged ~100 Ma. Volatile organic compounds from pungent truffle odours are not the products of Tuber-specific gene innovations, but rely on the differential expression of an existing gene repertoire. These genomic resources will help to address fundamental questions in the evolution of the truffle lifestyle and the ecology of fungi that have been praised as food delicacies for centuries. Title: Structural and functional partitioning of bread wheat chromosome 3B Choulet F, Alberti A, Theil S, Glover N, Barbe V, Daron J, Pingault L, Sourdille P, Couloux A and Feuillet C <21 more author(s)> Choulet F, Alberti A, Theil S, Glover N, Barbe V, Daron J, Pingault L, Sourdille P, Couloux A, Paux E, Leroy P, Mangenot S, Guilhot N, Le Gouis J, Balfourier F, Alaux M, Jamilloux V, Poulain J, Durand C, Bellec A, Gaspin C, Safar J, Dolezel J, Rogers J, Vandepoele K, Aury JM, Mayer K, Berges H, Quesneville H, Wincker P, Feuillet C (- 21) Ref: Science, 345:1249721, 2014 : PubMed ESTHER: Choulet_2014_Science_345_1249721 PubMedSearch: Choulet 2014 Science 345 1249721 PubMedID: 25035497 Gene_locus related to this paper: wheat-a0a080yuw6, wheat-w5d1z6, wheat-a0a077rex4, wheat-a0a077s1q2 Abstract 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. Title: Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida Collen J, Porcel B, Carre W, Ball SG, Chaparro C, Tonon T, Barbeyron T, Michel G, Noel B and Boyen C <48 more author(s)> Collen J, Porcel B, Carre W, Ball SG, Chaparro C, Tonon T, Barbeyron T, Michel G, Noel B, Valentin K, Elias M, Artiguenave F, Arun A, Aury JM, Barbosa-Neto JF, Bothwell JH, Bouget FY, Brillet L, Cabello-Hurtado F, Capella-Gutierrez S, Charrier B, Cladiere L, Cock JM, Coelho SM, Colleoni C, Czjzek M, Da Silva C, Delage L, Denoeud F, Deschamps P, Dittami SM, Gabaldon T, Gachon CM, Groisillier A, Herve C, Jabbari K, Katinka M, Kloareg B, Kowalczyk N, Labadie K, LeBlanc C, Lopez PJ, McLachlan DH, Meslet-Cladiere L, Moustafa A, Nehr Z, Nyvall Collen P, Panaud O, Partensky F, Poulain J, Rensing SA, Rousvoal S, Samson G, Symeonidi A, Weissenbach J, Zambounis A, Wincker P, Boyen C (- 48) Ref: Proc Natl Acad Sci U S A, 110:5247, 2013 : PubMed ESTHER: Collen_2013_Proc.Natl.Acad.Sci.U.S.A_110_5247 PubMedSearch: Collen 2013 Proc.Natl.Acad.Sci.U.S.A 110 5247 PubMedID: 23503846 Gene_locus related to this paper: chocr-r7qut2, chocr-r7qfm4, chocr-r7qf11 Abstract Red seaweeds are key components of coastal ecosystems and are economically important as food and as a source of gelling agents, but their genes and genomes have received little attention. Here we report the sequencing of the 105-Mbp genome of the florideophyte Chondrus crispus (Irish moss) and the annotation of the 9,606 genes. The genome features an unusual structure characterized by gene-dense regions surrounded by repeat-rich regions dominated by transposable elements. Despite its fairly large size, this genome shows features typical of compact genomes, e.g., on average only 0.3 introns per gene, short introns, low median distance between genes, small gene families, and no indication of large-scale genome duplication. The genome also gives insights into the metabolism of marine red algae and adaptations to the marine environment, including genes related to halogen metabolism, oxylipins, and multicellularity (microRNA processing and transcription factors). Particularly interesting are features related to carbohydrate metabolism, which include a minimalistic gene set for starch biosynthesis, the presence of cellulose synthases acquired before the primary endosymbiosis showing the polyphyly of cellulose synthesis in Archaeplastida, and cellulases absent in terrestrial plants as well as the occurrence of a mannosylglycerate synthase potentially originating from a marine bacterium. To explain the observations on genome structure and gene content, we propose an evolutionary scenario involving an ancestral red alga that was driven by early ecological forces to lose genes, introns, and intergenetic DNA; this loss was followed by an expansion of genome size as a consequence of activity of transposable elements. Title: The banana (Musa acuminata) genome and the evolution of monocotyledonous plants D'Hont A, Denoeud F, Aury JM, Baurens FC, Carreel F, Garsmeur O, Noel B, Bocs S, Droc G and Wincker P <54 more author(s)> D'Hont A, Denoeud F, Aury JM, Baurens FC, Carreel F, Garsmeur O, Noel B, Bocs S, Droc G, Rouard M, Da Silva C, Jabbari K, Cardi C, Poulain J, Souquet M, Labadie K, Jourda C, Lengelle J, Rodier-Goud M, Alberti A, Bernard M, Correa M, Ayyampalayam S, McKain MR, Leebens-Mack J, Burgess D, Freeling M, Mbeguie AMD, Chabannes M, Wicker T, Panaud O, Barbosa J, Hribova E, Heslop-Harrison P, Habas R, Rivallan R, Francois P, Poiron C, Kilian A, Burthia D, Jenny C, Bakry F, Brown S, Guignon V, Kema G, Dita M, Waalwijk C, Joseph S, Dievart A, Jaillon O, Leclercq J, Argout X, Lyons E, Almeida A, Jeridi M, Dolezel J, Roux N, Risterucci AM, Weissenbach J, Ruiz M, Glaszmann JC, Quetier F, Yahiaoui N, Wincker P (- 54) Ref: Nature, 488:213, 2012 : PubMed ESTHER: D'Hont_2012_Nature_488_213 PubMedSearch: D'Hont 2012 Nature 488 213 PubMedID: 22801500 Gene_locus related to this paper: musam-m0trz2, musam-m0swe0, musam-m0t8q2, musam-m0szm0, musam-m0s936, musam-m0tfg3, musam-m0tfg5, musam-m0tfg2, musam-m0sqy8, musam-m0tqf6, musam-m0sq07, musam-m0ubs4, musam-m0t8q3, musam-m0shq9, musam-m0u2a8, musam-m0tv21, musam-m0tuu7 Abstract Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to the well-studied Poales, which include cereals. Bananas are vital for food security in many tropical and subtropical countries and the most popular fruit in industrialized countries. The Musa domestication process started some 7,000 years ago in Southeast Asia. It involved hybridizations between diverse species and subspecies, fostered by human migrations, and selection of diploid and triploid seedless, parthenocarpic hybrids thereafter widely dispersed by vegetative propagation. Half of the current production relies on somaclones derived from a single triploid genotype (Cavendish). Pests and diseases have gradually become adapted, representing an imminent danger for global banana production. Here we describe the draft sequence of the 523-megabase genome of a Musa acuminata doubled-haploid genotype, providing a crucial stepping-stone for genetic improvement of banana. We detected three rounds of whole-genome duplications in the Musa lineage, independently of those previously described in the Poales lineage and the one we detected in the Arecales lineage. This first monocotyledon high-continuity whole-genome sequence reported outside Poales represents an essential bridge for comparative genome analysis in plants. As such, it clarifies commelinid-monocotyledon phylogenetic relationships, reveals Poaceae-specific features and has led to the discovery of conserved non-coding sequences predating monocotyledon-eudicotyledon divergence. Title: Pichia sorbitophila, an Interspecies Yeast Hybrid, Reveals Early Steps of Genome Resolution After Polyploidization Louis VL, Despons L, Friedrich A, Martin T, Durrens P, Casaregola S, Neuveglise C, Fairhead C, Marck C and Souciet JL <33 more author(s)> Louis VL, Despons L, Friedrich A, Martin T, Durrens P, Casaregola S, Neuveglise C, Fairhead C, Marck C, Cruz JA, Straub ML, Kugler V, Sacerdot C, Uzunov Z, Thierry A, Weiss S, Bleykasten C, De Montigny J, Jacques N, Jung P, Lemaire M, Mallet S, Morel G, Richard GF, Sarkar A, Savel G, Schacherer J, Seret ML, Talla E, Samson G, Jubin C, Poulain J, Vacherie B, Barbe V, Pelletier E, Sherman DJ, Westhof E, Weissenbach J, Baret PV, Wincker P, Gaillardin C, Dujon B, Souciet JL (- 33) Ref: G3 (Bethesda), 2:299, 2012 : PubMed ESTHER: Louis_2012_G3.(Bethesda)_2_299 PubMedSearch: Louis 2012 G3.(Bethesda) 2 299 PubMedID: 22384408 Gene_locus related to this paper: picso-g8ycc9, picso-g8yet0, picso-g8yb96, picso-g8ym39, erecy-g8jrp5, picso-g8y652 Abstract Polyploidization is an important process in the evolution of eukaryotic genomes, but ensuing molecular mechanisms remain to be clarified. Autopolyploidization or whole-genome duplication events frequently are resolved in resulting lineages by the loss of single genes from most duplicated pairs, causing transient gene dosage imbalance and accelerating speciation through meiotic infertility. Allopolyploidization or formation of interspecies hybrids raises the problem of genetic incompatibility (Bateson-Dobzhansky-Muller effect) and may be resolved by the accumulation of mutational changes in resulting lineages. In this article, we show that an osmotolerant yeast species, Pichia sorbitophila, recently isolated in a concentrated sorbitol solution in industry, illustrates this last situation. Its genome is a mosaic of homologous and homeologous chromosomes, or parts thereof, that corresponds to a recently formed hybrid in the process of evolution. The respective parental contributions to this genome were characterized using existing variations in GC content. The genomic changes that occurred during the short period since hybrid formation were identified (e.g., loss of heterozygosity, unilateral loss of rDNA, reciprocal exchange) and distinguished from those undergone by the two parental genomes after separation from their common ancestor (i.e., NUMT (NUclear sequences of MiTochondrial origin) insertions, gene acquisitions, gene location movements, reciprocal translocation). We found that the physiological characteristics of this new yeast species are determined by specific but unequal contributions of its two parents, one of which could be identified as very closely related to an extant Pichia farinosa strain. Title: Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea Amselem J, Cuomo CA, van Kan JA, Viaud M, Benito EP, Couloux A, Coutinho PM, de Vries RP, Dyer PS and Dickman M <62 more author(s)> Amselem J, Cuomo CA, van Kan JA, Viaud M, Benito EP, Couloux A, Coutinho PM, de Vries RP, Dyer PS, Fillinger S, Fournier E, Gout L, Hahn M, Kohn L, Lapalu N, Plummer KM, Pradier JM, Quevillon E, Sharon A, Simon A, ten Have A, Tudzynski B, Tudzynski P, Wincker P, Andrew M, Anthouard V, Beever RE, Beffa R, Benoit I, Bouzid O, Brault B, Chen Z, Choquer M, Collemare J, Cotton P, Danchin EG, Da Silva C, Gautier A, Giraud C, Giraud T, Gonzalez C, Grossetete S, Guldener U, Henrissat B, Howlett BJ, Kodira C, Kretschmer M, Lappartient A, Leroch M, Levis C, Mauceli E, Neuveglise C, Oeser B, Pearson M, Poulain J, Poussereau N, Quesneville H, Rascle C, Schumacher J, Segurens B, Sexton A, Silva E, Sirven C, Soanes DM, Talbot NJ, Templeton M, Yandava C, Yarden O, Zeng Q, Rollins JA, Lebrun MH, Dickman M (- 62) Ref: PLoS Genet, 7:e1002230, 2011 : PubMed ESTHER: Amselem_2011_PLoS.Genet_7_E1002230 PubMedSearch: Amselem 2011 PLoS.Genet 7 E1002230 PubMedID: 21876677 Gene_locus related to this paper: botci-cutas, botci-q6rki2, botf4-g2y7k8, botfb-dapb, botfu-g2xyd8, botfu-g2ynh8, scls1-a7e814, scls1-a7edc9, scls1-a7edh1, scls1-a7emm0, scls1-a7eti8, scls1-a7eu48, scls1-a7f208, scls1-dapb, botf4-g2xqp7, scls1-a7eqq8, botf4-g2xqc6, scls1-a7ebs4, botf4-g2xn51, scls1-a7f5m9, botf4-g2xti4, botf4-g2xtu7, botf4-g2yfp1, scls1-a7f534, botf4-g2yys3, scls1-a7erz9, botf4-g2y037, botf4-g2y0e1, scls1-a7f706, scls1-a7ewt6, botf4-g2yuj6, botf1-m7u3d1, botf1-m7u430, botf1-m7tei8, botf1-m7u0w9, botf1-m7tij6, botf1-m7u819, botf1-m7u6d8, botf1-m7tzd4, botf1-m7tqd7, botf1-m7tyz9, botf1-m7unl9, botf1-m7u429, botf1-m7u4s5, botf1-m7ul92, botf1-m7tx42, botf1-m7u9h4, botf1-m7u187, botf1-m7uz64, botf1-m7u4q4, botf1-m7u2f6, botf1-m7tt59, botf1-m7v3h2, botf1-m7u6c9, botf1-m7tud9, botf1-m7u309, scls1-a7et87, botf4-g2ylt4, scls1-a7f5a0, scls1-a7f900, botf4-g2yib9, scls1-a7f3m9, scls1-a7er46, botf4-g2y3y4, botf4-g2xyy5, botf1-m7uct5, scls1-a7ea78, scls1-kex1, scls1-cbpya, botfb-cbpya Abstract 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. Title: Complete genome sequence of Streptomyces cattleya NRRL 8057, a producer of antibiotics and fluorometabolites Barbe V, Bouzon M, Mangenot S, Badet B, Poulain J, Segurens B, Vallenet D, Marliere P, Weissenbach J Ref: Journal of Bacteriology, 193:5055, 2011 : PubMed ESTHER: Barbe_2011_J.Bacteriol_193_5055 PubMedSearch: Barbe 2011 J.Bacteriol 193 5055 PubMedID: 21868806 Gene_locus related to this paper: stren-f8jjf8, stren-f8jk65, stren-f8jly2, stren-f8jm04, stren-f8juv4, stren-f8k466, stren-f8jvj2, stren-f8k4s8 Abstract Streptomyces cattleya, a producer of the antibiotics thienamycin and cephamycin C, is one of the rare bacteria known to synthesize fluorinated metabolites. The genome consists of two linear replicons. The genes involved in fluorine metabolism and in the biosynthesis of the antibiotic thienamycin were mapped on both replicons. Title: Genome sequence of the stramenopile Blastocystis, a human anaerobic parasite Denoeud F, Roussel M, Noel B, Wawrzyniak I, Da Silva C, Diogon M, Viscogliosi E, Brochier-Armanet C, Couloux A and El Alaoui H <14 more author(s)> Denoeud F, Roussel M, Noel B, Wawrzyniak I, Da Silva C, Diogon M, Viscogliosi E, Brochier-Armanet C, Couloux A, Poulain J, Segurens B, Anthouard V, Texier C, Blot N, Poirier P, Ng GC, Tan KS, Artiguenave F, Jaillon O, Aury JM, Delbac F, Wincker P, Vivares CP, El Alaoui H (- 14) Ref: Genome Biol, 12:R29, 2011 : PubMed ESTHER: Denoeud_2011_Genome.Biol_12_R29 PubMedSearch: Denoeud 2011 Genome.Biol 12 R29 PubMedID: 21439036 Gene_locus related to this paper: blaho-d8m103, blaho-d8lw93 Abstract BACKGROUND: Blastocystis is a highly prevalent anaerobic eukaryotic parasite of humans and animals that is associated with various gastrointestinal and extraintestinal disorders. Epidemiological studies have identified different subtypes but no one subtype has been definitively correlated with disease. Title: Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations Rouxel T, Grandaubert J, Hane JK, Hoede C, van de Wouw AP, Couloux A, Dominguez V, Anthouard V, Bally P and Howlett BJ <31 more author(s)> Rouxel T, Grandaubert J, Hane JK, Hoede C, van de Wouw AP, Couloux A, Dominguez V, Anthouard V, Bally P, Bourras S, Cozijnsen AJ, Ciuffetti LM, Degrave A, Dilmaghani A, Duret L, Fudal I, Goodwin SB, Gout L, Glaser N, Linglin J, Kema GH, Lapalu N, Lawrence CB, May K, Meyer M, Ollivier B, Poulain J, Schoch CL, Simon A, Spatafora JW, Stachowiak A, Turgeon BG, Tyler BM, Vincent D, Weissenbach J, Amselem J, Quesneville H, Oliver RP, Wincker P, Balesdent MH, Howlett BJ (- 31) Ref: Nat Commun, 2:202, 2011 : PubMed ESTHER: Rouxel_2011_Nat.Commun_2_202 PubMedSearch: Rouxel 2011 Nat.Commun 2 202 PubMedID: 21326234 Gene_locus related to this paper: lepmc-q6q891, lepmj-e4zh04, lepmj-e4ziv6, lepmj-e4zju4, lepmj-e4zqu4, lepmj-e4zvh3, lepmj-e4zvl4, lepmj-e4zx66, lepmj-e5a0i2, lepmj-e5a510, lepmj-e5aau5, lepmj-e5acd1, lepmj-e5a4g5, lepmj-e4zhg2, lepmj-e4zuw5, lepmj-e5a2e0, lepmj-e4zpv2, lepmj-e4zxp4, lepmj-e4zpy5, lepmj-e5ae17, lepmj-e4ziv2, lepmj-e5a374, lepmj-e5ab81, lepmj-e4zgy1, lepmj-e4zg43, lepmj-kex1, lepmj-cbpya Abstract 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. Title: The genome of the mesopolyploid crop species Brassica rapa Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun JH, Bancroft I and Zhang Z <88 more author(s)> Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun JH, Bancroft I, Cheng F, Huang S, Li X, Hua W, Freeling M, Pires JC, Paterson AH, Chalhoub B, Wang B, Hayward A, Sharpe AG, Park BS, Weisshaar B, Liu B, Li B, Tong C, Song C, Duran C, Peng C, Geng C, Koh C, Lin C, Edwards D, Mu D, Shen D, Soumpourou E, Li F, Fraser F, Conant G, Lassalle G, King GJ, Bonnema G, Tang H, Belcram H, Zhou H, Hirakawa H, Abe H, Guo H, Jin H, Parkin IA, Batley J, Kim JS, Just J, Li J, Xu J, Deng J, Kim JA, Yu J, Meng J, Min J, Poulain J, Hatakeyama K, Wu K, Wang L, Fang L, Trick M, Links MG, Zhao M, Jin M, Ramchiary N, Drou N, Berkman PJ, Cai Q, Huang Q, Li R, Tabata S, Cheng S, Zhang S, Sato S, Sun S, Kwon SJ, Choi SR, Lee TH, Fan W, Zhao X, Tan X, Xu X, Wang Y, Qiu Y, Yin Y, Li Y, Du Y, Liao Y, Lim Y, Narusaka Y, Wang Z, Li Z, Xiong Z, Zhang Z (- 88) Ref: Nat Genet, 43:1035, 2011 : PubMed ESTHER: Wang_2011_Nat.Genet_43_1035 PubMedSearch: Wang 2011 Nat.Genet 43 1035 PubMedID: 21873998 Gene_locus related to this paper: braol-Q8GTM3, braol-Q8GTM4, brarp-m4ei94, brarp-m4c988, brana-a0a078j4a9, brana-a0a078e1m0, brana-a0a078cd75, brarp-m4dwa6, brana-a0a078j4f0, brana-a0a078cus4, brana-a0a078f8c2, brana-a0a078jql1, brana-a0a078dgj3, brana-a0a078hw50, brana-a0a078cuu0, brana-a0a078dfa9, brana-a0a078ic91, brarp-m4ctw3, brana-a0a078ca65, brana-a0a078ctc8, brana-a0a078h021, brana-a0a078jx23, brarp-m4da84, brarp-m4dwr7, brana-a0a078dh94, brana-a0a078h612, brana-a0a078j2t3, braol-a0a0d3dpb2, braol-a0a0d3dx76, brana-a0a078jxa8, brana-a0a078i2k3, brarp-m4cwq4, brarp-m4dcj8, brarp-m4eh17, brarp-m4eey4, brarp-m4dnj8, brarp-m4ey83, brarp-m4ey84 Abstract We report the annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage. We modeled 41,174 protein coding genes in the B. rapa genome, which has undergone genome triplication. We used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution. The extent of gene loss (fractionation) among triplicated genome segments varies, with one of the three copies consistently retaining a disproportionately large fraction of the genes expected to have been present in its ancestor. Variation in the number of members of gene families present in the genome may contribute to the remarkable morphological plasticity of Brassica species. The B. rapa genome sequence provides an important resource for studying the evolution of polyploid genomes and underpins the genetic improvement of Brassica oil and vegetable crops. Title: The Medicago genome provides insight into the evolution of rhizobial symbioses Young ND, Debelle F, Oldroyd GE, Geurts R, Cannon SB, Udvardi MK, Benedito VA, Mayer KF, Gouzy J and Roe BA <114 more author(s)> Young ND, Debelle F, Oldroyd GE, Geurts R, Cannon SB, Udvardi MK, Benedito VA, Mayer KF, Gouzy J, Schoof H, Van de Peer Y, Proost S, Cook DR, Meyers BC, Spannagl M, Cheung F, De Mita S, Krishnakumar V, Gundlach H, Zhou S, Mudge J, Bharti AK, Murray JD, Naoumkina MA, Rosen B, Silverstein KA, Tang H, Rombauts S, Zhao PX, Zhou P, Barbe V, Bardou P, Bechner M, Bellec A, Berger A, Berges H, Bidwell S, Bisseling T, Choisne N, Couloux A, Denny R, Deshpande S, Dai X, Doyle JJ, Dudez AM, Farmer AD, Fouteau S, Franken C, Gibelin C, Gish J, Goldstein S, Gonzalez AJ, Green PJ, Hallab A, Hartog M, Hua A, Humphray SJ, Jeong DH, Jing Y, Jocker A, Kenton SM, Kim DJ, Klee K, Lai H, Lang C, Lin S, Macmil SL, Magdelenat G, Matthews L, McCorrison J, Monaghan EL, Mun JH, Najar FZ, Nicholson C, Noirot C, O'Bleness M, Paule CR, Poulain J, Prion F, Qin B, Qu C, Retzel EF, Riddle C, Sallet E, Samain S, Samson N, Sanders I, Saurat O, Scarpelli C, Schiex T, Segurens B, Severin AJ, Sherrier DJ, Shi R, Sims S, Singer SR, Sinharoy S, Sterck L, Viollet A, Wang BB, Wang K, Wang M, Wang X, Warfsmann J, Weissenbach J, White DD, White JD, Wiley GB, Wincker P, Xing Y, Yang L, Yao Z, Ying F, Zhai J, Zhou L, Zuber A, Denarie J, Dixon RA, May GD, Schwartz DC, Rogers J, Quetier F, Town CD, Roe BA (- 114) Ref: Nature, 480:520, 2011 : PubMed ESTHER: Young_2011_Nature_480_520 PubMedSearch: Young 2011 Nature 480 520 PubMedID: 22089132 Gene_locus related to this paper: medtr-b7fki4, medtr-b7fmi1, medtr-g7itl1, medtr-g7iu67, medtr-g7izm0, medtr-g7j641, medtr-g7jtf8, medtr-g7jtg2, medtr-g7jtg4, medtr-g7kem3, medtr-g7kml3, medtr-g7ksx5, medtr-g7leb3, medtr-q1s5d8, medtr-q1s9m3, medtr-q1t171, medtr-g7k9e1, medtr-g7k9e3, medtr-g7k9e5, medtr-g7k9e8, medtr-g7k9e9, medtr-g7lbp2, medtr-g7lch3, medtr-g7ib94, medtr-g7ljk8, medtr-g7i6w5, medtr-g7kvg4, medtr-g7iam1, medtr-g7iam3, medtr-g7l754, medtr-g7jr41, medtr-g7l4f5, medtr-g7l755, medtr-a0a072vyl4, medtr-g7jwk8, medtr-a0a072vhg0, medtr-a0a072vrv9, medtr-g7kmk5, medtr-a0a072uuf6, medtr-a0a072urp3, medtr-g7zzc3, medtr-g7ie19, medtr-g7kst7, medtr-a0a072u5k5, medtr-a0a072v056, medtr-scp1 Abstract Legumes (Fabaceae or Leguminosae) are unique among cultivated plants for their ability to carry out endosymbiotic nitrogen fixation with rhizobial bacteria, a process that takes place in a specialized structure known as the nodule. Legumes belong to one of the two main groups of eurosids, the Fabidae, which includes most species capable of endosymbiotic nitrogen fixation. Legumes comprise several evolutionary lineages derived from a common ancestor 60 million years ago (Myr ago). Papilionoids are the largest clade, dating nearly to the origin of legumes and containing most cultivated species. Medicago truncatula is a long-established model for the study of legume biology. Here we describe the draft sequence of the M. truncatula euchromatin based on a recently completed BAC assembly supplemented with Illumina shotgun sequence, together capturing approximately 94% of all M. truncatula genes. A whole-genome duplication (WGD) approximately 58 Myr ago had a major role in shaping the M. truncatula genome and thereby contributed to the evolution of endosymbiotic nitrogen fixation. Subsequent to the WGD, the M. truncatula genome experienced higher levels of rearrangement than two other sequenced legumes, Glycine max and Lotus japonicus. M. truncatula is a close relative of alfalfa (Medicago sativa), a widely cultivated crop with limited genomics tools and complex autotetraploid genetics. As such, the M. truncatula genome sequence provides significant opportunities to expand alfalfa's genomic toolbox. Title: The Ectocarpus genome and the independent evolution of multicellularity in brown algae Cock JM, Sterck L, Rouze P, Scornet D, Allen AE, Amoutzias G, Anthouard V, Artiguenave F, Aury JM and Wincker P <67 more author(s)> Cock JM, Sterck L, Rouze P, Scornet D, Allen AE, Amoutzias G, Anthouard V, Artiguenave F, Aury JM, Badger JH, Beszteri B, Billiau K, Bonnet E, Bothwell JH, Bowler C, Boyen C, Brownlee C, Carrano CJ, Charrier B, Cho GY, Coelho SM, Collen J, Corre E, Da Silva C, Delage L, Delaroque N, Dittami SM, Doulbeau S, Elias M, Farnham G, Gachon CM, Gschloessl B, Heesch S, Jabbari K, Jubin C, Kawai H, Kimura K, Kloareg B, Kupper FC, Lang D, Le Bail A, LeBlanc C, Lerouge P, Lohr M, Lopez PJ, Martens C, Maumus F, Michel G, Miranda-Saavedra D, Morales J, Moreau H, Motomura T, Nagasato C, Napoli CA, Nelson DR, Nyvall-Collen P, Peters AF, Pommier C, Potin P, Poulain J, Quesneville H, Read B, Rensing SA, Ritter A, Rousvoal S, Samanta M, Samson G, Schroeder DC, Segurens B, Strittmatter M, Tonon T, Tregear JW, Valentin K, von Dassow P, Yamagishi T, Van de Peer Y, Wincker P (- 67) Ref: Nature, 465:617, 2010 : PubMed ESTHER: Cock_2010_Nature_465_617 PubMedSearch: Cock 2010 Nature 465 617 PubMedID: 20520714 Gene_locus related to this paper: ectsi-d7fm61, ectsi-d7fs16, ectsi-d7fsv3, ectsi-d7fte8, ectsi-d7fux6, ectsi-d7fvr0, ectsi-d7fvu4, ectsi-d7fwk0, ectsi-d7fyh7, ectsi-d7g0w7, ectsi-d7g6g5, ectsi-d7g484, ectsi-d7g686, ectsi-d8lca9, ectsi-d8lfv2, ectsi-d8lqg6, ectsi-d8ltj9, ectsi-d7fjz2, ectsi-d7g376 Abstract Brown algae (Phaeophyceae) are complex photosynthetic organisms with a very different evolutionary history to green plants, to which they are only distantly related. These seaweeds are the dominant species in rocky coastal ecosystems and they exhibit many interesting adaptations to these, often harsh, environments. Brown algae are also one of only a small number of eukaryotic lineages that have evolved complex multicellularity (Fig. 1). We report the 214 million base pair (Mbp) genome sequence of the filamentous seaweed Ectocarpus siliculosus (Dillwyn) Lyngbye, a model organism for brown algae, closely related to the kelps (Fig. 1). Genome features such as the presence of an extended set of light-harvesting and pigment biosynthesis genes and new metabolic processes such as halide metabolism help explain the ability of this organism to cope with the highly variable tidal environment. The evolution of multicellularity in this lineage is correlated with the presence of a rich array of signal transduction genes. Of particular interest is the presence of a family of receptor kinases, as the independent evolution of related molecules has been linked with the emergence of multicellularity in both the animal and green plant lineages. The Ectocarpus genome sequence represents an important step towards developing this organism as a model species, providing the possibility to combine genomic and genetic approaches to explore these and other aspects of brown algal biology further. Title: Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate Denoeud F, Henriet S, Mungpakdee S, Aury JM, Da Silva C, Brinkmann H, Mikhaleva J, Olsen LC, Jubin C and Chourrout D <46 more author(s)> Denoeud F, Henriet S, Mungpakdee S, Aury JM, Da Silva C, Brinkmann H, Mikhaleva J, Olsen LC, Jubin C, Canestro C, Bouquet JM, Danks G, Poulain J, Campsteijn C, Adamski M, Cross I, Yadetie F, Muffato M, Louis A, Butcher S, Tsagkogeorga G, Konrad A, Singh S, Jensen MF, Huynh Cong E, Eikeseth-Otteraa H, Noel B, Anthouard V, Porcel BM, Kachouri-Lafond R, Nishino A, Ugolini M, Chourrout P, Nishida H, Aasland R, Huzurbazar S, Westhof E, Delsuc F, Lehrach H, Reinhardt R, Weissenbach J, Roy SW, Artiguenave F, Postlethwait JH, Manak JR, Thompson EM, Jaillon O, Du Pasquier L, Boudinot P, Liberles DA, Volff JN, Philippe H, Lenhard B, Roest Crollius H, Wincker P, Chourrout D (- 46) Ref: Science, 330:1381, 2010 : PubMed ESTHER: Denoeud_2010_Science_330_1381 PubMedSearch: Denoeud 2010 Science 330 1381 PubMedID: 21097902 Gene_locus related to this paper: oikdi-ACHE, oikdi-cholike.1, oikdi-cholike.2, oikdi-e4wug8, oikdi-e4ww04, oikdi-e4wxm9, oikdi-e4x0y9, oikdi-e4x1t6, oikdi-e4x2c7.1, oikdi-e4x2c7.2, oikdi-e4x4v7, oikdi-e4x5i7, oikdi-e4x5s6, oikdi-e4x6c7, oikdi-e4x6i0, oikdi-e4x7y6, oikdi-e4xa91, oikdi-e4xe86, oikdi-e4xeg3, oikdi-e4xgg8, oikdi-e4xiw0, oikdi-e4xk51, oikdi-e4xl53, oikdi-e4xm24, oikdi-e4xm43, oikdi-e4xn79, oikdi-e4xp62, oikdi-e4xpy1, oikdi-e4xqm4, oikdi-e4xtm1, oikdi-e4xug7, oikdi-e4xv59, oikdi-e4xw55, oikdi-e4xwt6, oikdi-e4xxh8, oikdi-e4y5n1, oikdi-e4y7j8, oikdi-e4y8s7, oikdi-e4ya76, oikdi-e4ydw0, oikdi-e4yi65, oikdi-e4yp15, oikdi-e4yp69, oikdi-e4yst1, oikdi-e4yvr0, oikdi-e4yvu0, oikdi-e4x630, oikdi-e4ykb2, oikdi-e4wt97, oikdi-e4ws23 Abstract Genomes of animals as different as sponges and humans show conservation of global architecture. Here we show that multiple genomic features including transposon diversity, developmental gene repertoire, physical gene order, and intron-exon organization are shattered in the tunicate Oikopleura, belonging to the sister group of vertebrates and retaining chordate morphology. Ancestral architecture of animal genomes can be deeply modified and may therefore be largely nonadaptive. This rapidly evolving animal lineage thus offers unique perspectives on the level of genome plasticity. It also illuminates issues as fundamental as the mechanisms of intron gain. Title: Comparative genomics of protoploid Saccharomycetaceae Souciet JL, Dujon B, Gaillardin C, Johnston M, Baret PV, Cliften P, Sherman DJ, Weissenbach J, Westhof E and Talla E <44 more author(s)> Souciet JL, Dujon B, Gaillardin C, Johnston M, Baret PV, Cliften P, Sherman DJ, Weissenbach J, Westhof E, Wincker P, Jubin C, Poulain J, Barbe V, Segurens B, Artiguenave F, Anthouard V, Vacherie B, Val ME, Fulton RS, Minx P, Wilson R, Durrens P, Jean G, Marck C, Martin T, Nikolski M, Rolland T, Seret ML, Casaregola S, Despons L, Fairhead C, Fischer G, Lafontaine I, Leh V, Lemaire M, De Montigny J, Neuveglise C, Thierry A, Blanc-Lenfle I, Bleykasten C, Diffels J, Fritsch E, Frangeul L, Goeffon A, Jauniaux N, Kachouri-Lafond R, Payen C, Potier S, Pribylova L, Ozanne C, Richard GF, Sacerdot C, Straub ML, Talla E (- 44) Ref: Genome Res, 19:1696, 2009 : PubMed ESTHER: Souciet_2009_Genome.Res_19_1696 PubMedSearch: Souciet 2009 Genome.Res 19 1696 PubMedID: 19525356 Gene_locus related to this paper: lactc-c5dci9, lactc-c5ddi5, lactc-c5dew5, lactc-c5dez1, lactc-c5df11, lactc-c5dfh7, lactc-c5dgd1, lactc-c5dif7, lactc-c5din7, lactc-c5dja0, lactc-c5dm95, lactc-c5dn06, lactc-c5dnn9, lactc-c5e2g8, lactc-c5e3n5, lactc-c5e375, zygrc-c5drr0, zygrc-c5dvh0, zygrc-c5dvl2, zygrc-c5dvx0, zygrc-c5dvz8, zygrc-c5dx83, zygrc-c5dxn5, zygrc-c5dxq9, zygrc-c5e0w1, zygrc-c5e1e4, zygrc-c5e1h2, zygro-a0a1q2zt01, 9sach-a0a0p1kuu1, lactc-kex1, zygrc-kex1 Abstract Our knowledge of yeast genomes remains largely dominated by the extensive studies on Saccharomyces cerevisiae and the consequences of its ancestral duplication, leaving the evolution of the entire class of hemiascomycetes only partly explored. We concentrate here on five species of Saccharomycetaceae, a large subdivision of hemiascomycetes, that we call "protoploid" because they diverged from the S. cerevisiae lineage prior to its genome duplication. We determined the complete genome sequences of three of these species: Kluyveromyces (Lachancea) thermotolerans and Saccharomyces (Lachancea) kluyveri (two members of the newly described Lachancea clade), and Zygosaccharomyces rouxii. We included in our comparisons the previously available sequences of Kluyveromyces lactis and Ashbya (Eremothecium) gossypii. Despite their broad evolutionary range and significant individual variations in each lineage, the five protoploid Saccharomycetaceae share a core repertoire of approximately 3300 protein families and a high degree of conserved synteny. Synteny blocks were used to define gene orthology and to infer ancestors. Far from representing minimal genomes without redundancy, the five protoploid yeasts contain numerous copies of paralogous genes, either dispersed or in tandem arrays, that, altogether, constitute a third of each genome. Ancient, conserved paralogs as well as novel, lineage-specific paralogs were identified. Title: The genome sequence of the model ascomycete fungus Podospora anserina Espagne E, Lespinet O, Malagnac F, Da Silva C, Jaillon O, Porcel BM, Couloux A, Aury JM, Segurens B and Silar P <25 more author(s)> Espagne E, Lespinet O, Malagnac F, Da Silva C, Jaillon O, Porcel BM, Couloux A, Aury JM, Segurens B, Poulain J, Anthouard V, Grossetete S, Khalili H, Coppin E, Dequard-Chablat M, Picard M, Contamine V, Arnaise S, Bourdais A, Berteaux-Lecellier V, Gautheret D, de Vries RP, Battaglia E, Coutinho PM, Danchin EG, Henrissat B, Khoury RE, Sainsard-Chanet A, Boivin A, Pinan-Lucarre B, Sellem CH, Debuchy R, Wincker P, Weissenbach J, Silar P (- 25) Ref: Genome Biol, 9:R77, 2008 : PubMed ESTHER: Espagne_2008_Genome.Biol_9_R77 PubMedSearch: Espagne 2008 Genome.Biol 9 R77 PubMedID: 18460219 Gene_locus related to this paper: podan-b2a8u1, podan-b2a9c4, podan-b2a9k6, podan-b2aa90, podan-b2ab33, podan-b2abs0, podan-b2ac17, podan-b2ack2, podan-b2ad07, podan-b2adj6, podan-b2adk0, podan-b2ae59, podan-b2aee7, podan-b2af51, podan-b2afn5, podan-b2afu6, podan-b2akq7, podan-b2aly0, podan-b2am11, podan-b2an24, podan-b2ank1, podan-b2apa8, podan-b2api8, podan-b2apj6, podan-b2arl9, podan-b2arz7, podan-b2ase4, podan-b2atn0, podan-b2au46, podan-b2aun9, podan-b2av47, podan-b2ava6, podan-b2avm3, podan-b2avu5, podan-b2avx3, podan-b2awk8, podan-b2axk2, podan-b2axz2, podan-b2b1p7, podan-b2b5e4, podan-b2b6n7, podan-b2b069, podan-b2b073, podan-b2b395, podan-dapb, podan-b2afr0, podan-b2a9k8, podan-b2atb3, podan-b2aca3, podan-b2arv3, podan-b2ank5, podan-b2ax54, podan-b2ad56, podan-b2anm1, podan-b2aya1, podan-b2b164, podan-a0a090d4h4, podan-a0a090ccl8, podan-b2b5p4, podan-b2azp1, podan-b2af75, podan-b2alm5, podan-b2ass5, podan-b2aez8, podan-kex1, podan-cbpya Abstract BACKGROUND: The 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. RESULTS: We 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. CONCLUSION: The 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. Title: Comparative analysis of Acinetobacters: three genomes for three lifestyles Vallenet D, Nordmann P, Barbe V, Poirel L, Mangenot S, Bataille E, Dossat C, Gas S, Kreimeyer A and Cruveiller S <10 more author(s)> Vallenet D, Nordmann P, Barbe V, Poirel L, Mangenot S, Bataille E, Dossat C, Gas S, Kreimeyer A, Lenoble P, Oztas S, Poulain J, Segurens B, Robert C, Abergel C, Claverie JM, Raoult D, Medigue C, Weissenbach J, Cruveiller S (- 10) Ref: PLoS ONE, 3:e1805, 2008 : PubMed ESTHER: Vallenet_2008_PLoS.ONE_3_E1805 PubMedSearch: Vallenet 2008 PLoS.ONE 3 E1805 PubMedID: 18350144 Gene_locus related to this paper: acib1-e8pgf8, acib3-b7guy6, acib3-b7h156, acib3-metx, aciba-d0c992, aciba-k1epl1, aciba-k6lkl9, acibc-b2huf4, acibc-b2i0a2, acibc-b2i0w9, acibc-b2i2b0, acibs-b0vt32, acibt-a3m1g6, acibt-a3m5r6, acibt-a3m5t3, acibt-a3m5x2, acibt-a3m627, acibt-a3m707, aciby-b0v723, acica-d0s0a7, aciju-d0sj67, aciba-f5iht4, aciba-a0a009wzt4 Abstract Acinetobacter baumannii is the source of numerous nosocomial infections in humans and therefore deserves close attention as multidrug or even pandrug resistant strains are increasingly being identified worldwide. Here we report the comparison of two newly sequenced genomes of A. baumannii. The human isolate A. baumannii AYE is multidrug resistant whereas strain SDF, which was isolated from body lice, is antibiotic susceptible. As reference for comparison in this analysis, the genome of the soil-living bacterium A. baylyi strain ADP1 was used. The most interesting dissimilarities we observed were that i) whereas strain AYE and A. baylyi genomes harbored very few Insertion Sequence elements which could promote expression of downstream genes, strain SDF sequence contains several hundred of them that have played a crucial role in its genome reduction (gene disruptions and simple DNA loss); ii) strain SDF has low catabolic capacities compared to strain AYE. Interestingly, the latter has even higher catabolic capacities than A. baylyi which has already been reported as a very nutritionally versatile organism. This metabolic performance could explain the persistence of A. baumannii nosocomial strains in environments where nutrients are scarce; iii) several processes known to play a key role during host infection (biofilm formation, iron uptake, quorum sensing, virulence factors) were either different or absent, the best example of which is iron uptake. Indeed, strain AYE and A. baylyi use siderophore-based systems to scavenge iron from the environment whereas strain SDF uses an alternate system similar to the Haem Acquisition System (HAS). Taken together, all these observations suggest that the genome contents of the 3 Acinetobacters compared are partly shaped by life in distinct ecological niches: human (and more largely hospital environment), louse, soil. Title: The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N and Wincker P <46 more author(s)> Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, Vezzi A, Legeai F, Hugueney P, Dasilva C, Horner D, Mica E, Jublot D, Poulain J, Bruyere C, Billault A, Segurens B, Gouyvenoux M, Ugarte E, Cattonaro F, Anthouard V, Vico V, Del Fabbro C, Alaux M, Di Gaspero G, Dumas V, Felice N, Paillard S, Juman I, Moroldo M, Scalabrin S, Canaguier A, Le Clainche I, Malacrida G, Durand E, Pesole G, Laucou V, Chatelet P, Merdinoglu D, Delledonne M, Pezzotti M, Lecharny A, Scarpelli C, Artiguenave F, Pe ME, Valle G, Morgante M, Caboche M, Adam-Blondon AF, Weissenbach J, Quetier F, Wincker P (- 46) Ref: Nature, 449:463, 2007 : PubMed ESTHER: Jaillon_2007_Nature_449_463 PubMedSearch: Jaillon 2007 Nature 449 463 PubMedID: 17721507 Gene_locus related to this paper: vitvi-a5b6n6, vitvi-a5b7c0, vitvi-a5b8l9, vitvi-a5bji4, vitvi-a5bxd7, vitvi-a5c1g2, vitvi-a5c8p7, vitvi-a7ntu2, vitvi-a7pnb4, vitvi-a7pus9, vitvi-a7q3d1, vitvi-a7qpz3, vitvi-BIG8.1, vitvi-d7sqb8, vitvi-d7ssp2, vitvi-d7sx57, vitvi-d7t734, vitvi-d7t940, vitvi-d7tef1, vitvi-d7tg96, vitvi-d7tle9, vitvi-d7tmb8, vitvi-d7tpk8, vitvi-d7tve2, vitvi-d7tvr0, vitvi-d7ubd6, vitvi-f6hhx5, vitvi-f6hi76, vitvi-f6hqe0, vitvi-f6hzf1.1, vitvi-f6hzf1.2, vitvi-d7ssd7, vitvi-d7ssd8, vitvi-d7ssd9, vitvi-d7u935, vitvi-f6gyw1, vitvi-f6gyw2, vitvi-f6gyw4, vitvi-f6hqf1, vitvi-f6hqf4, vitvi-d7tum4, vitvi-d7tba3, vitvi-d7stm8, vitvi-d7t3j3, vitvi-d7uce5, vitvi-f6he55, vitvi-d7thp4, vitvi-d7tfe6, vitvi-e0cv10, vitvi-f6gtp7, vitvi-f6hva3, vitvi-d7tqu0, vitvi-f6hqq0, vitvi-d7tci5, vitvi-d7sut7, vitvi-d7sut6, vitvi-f6h317, vitvi-f6h318, vitvi-f6hsf1, vitvi-f6hqd1, vitvi-f6hqd0, vitvi-f6hfp6, vitvi-d7u2i4, vitvi-f6gsx7, vitvi-d7si01, vitvi-d7si06 Abstract 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. Title: Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia Aury JM, Jaillon O, Duret L, Noel B, Jubin C, Porcel BM, Segurens B, Daubin V, Anthouard V and Wincker P <33 more author(s)> Aury JM, Jaillon O, Duret L, Noel B, Jubin C, Porcel BM, Segurens B, Daubin V, Anthouard V, Aiach N, Arnaiz O, Billaut A, Beisson J, Blanc I, Bouhouche K, Camara F, Duharcourt S, Guigo R, Gogendeau D, Katinka M, Keller AM, Kissmehl R, Klotz C, Koll F, Le Mouel A, Lepere G, Malinsky S, Nowacki M, Nowak JK, Plattner H, Poulain J, Ruiz F, Serrano V, Zagulski M, Dessen P, Betermier M, Weissenbach J, Scarpelli C, Schachter V, Sperling L, Meyer E, Cohen J, Wincker P (- 33) Ref: Nature, 444:171, 2006 : PubMed ESTHER: Aury_2006_Nature_444_171 PubMedSearch: Aury 2006 Nature 444 171 PubMedID: 17086204 Gene_locus related to this paper: parte-a0bds8, parte-a0bga5, parte-a0bnp2, parte-a0bnt1, parte-a0bpr4, parte-a0btv5, parte-a0byt1, parte-a0bz94, parte-a0c0b8, parte-a0c0q4, parte-a0c1z8, parte-a0c3e0, parte-a0c9f4, parte-a0c962, parte-a0cb90, parte-a0cck1, parte-a0cj40, parte-a0cq13, parte-a0cqw8, parte-a0crq3, parte-a0cu52, parte-a0cur9, parte-a0cxu4, parte-a0cyf3, parte-a0czs5, parte-a0d1l8, parte-a0d9i7, parte-a0d589, parte-a0de29, parte-a0dem3, parte-a0dg79, parte-a0diq2, parte-a0dk36, parte-a0dkh0, parte-a0dld4, parte-a0dnw2, parte-a0drp9, parte-a0drx0, parte-a0duj9, parte-a0dvl0, parte-a0dwm9, parte-a0dy72, parte-a0dz74, parte-a0e0g8, parte-a0e0z4, parte-a0e1p0, parte-a0e4m9, parte-a0e8v9, parte-a0e9r1, parte-a0e581, parte-a0ecy9, parte-a0ecz4, parte-a0ef67, parte-a0d7k3 Abstract The duplication of entire genomes has long been recognized as having great potential for evolutionary novelties, but the mechanisms underlying their resolution through gene loss are poorly understood. Here we show that in the unicellular eukaryote Paramecium tetraurelia, a ciliate, most of the nearly 40,000 genes arose through at least three successive whole-genome duplications. Phylogenetic analysis indicates that the most recent duplication coincides with an explosion of speciation events that gave rise to the P. aurelia complex of 15 sibling species. We observed that gene loss occurs over a long timescale, not as an initial massive event. Genes from the same metabolic pathway or protein complex have common patterns of gene loss, and highly expressed genes are over-retained after all duplications. The conclusion of this analysis is that many genes are maintained after whole-genome duplication not because of functional innovation but because of gene dosage constraints. Title: Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype Jaillon O, Aury JM, Brunet F, Petit JL, Stange-Thomann N, Mauceli E, Bouneau L, Fischer C, Ozouf-Costaz C and Roest Crollius H <51 more author(s)> Jaillon O, Aury JM, Brunet F, Petit JL, Stange-Thomann N, Mauceli E, Bouneau L, Fischer C, Ozouf-Costaz C, Bernot A, Nicaud S, Jaffe D, Fisher S, Lutfalla G, Dossat C, Segurens B, Dasilva C, Salanoubat M, Levy M, Boudet N, Castellano S, Anthouard V, Jubin C, Castelli V, Katinka M, Vacherie B, Biemont C, Skalli Z, Cattolico L, Poulain J, de Berardinis V, Cruaud C, Duprat S, Brottier P, Coutanceau JP, Gouzy J, Parra G, Lardier G, Chapple C, McKernan KJ, McEwan P, Bosak S, Kellis M, Volff JN, Guigo R, Zody MC, Mesirov J, Lindblad-Toh K, Birren B, Nusbaum C, Kahn D, Robinson-Rechavi M, Laudet V, Schachter V, Quetier F, Saurin W, Scarpelli C, Wincker P, Lander ES, Weissenbach J, Roest Crollius H (- 51) Ref: Nature, 431:946, 2004 : PubMed ESTHER: Jaillon_2004_Nature_431_946 PubMedSearch: Jaillon 2004 Nature 431 946 PubMedID: 15496914 Gene_locus related to this paper: tetng-3neur, tetng-4neur, tetng-ACHE, tetng-BCHE, tetng-h3cfz4, tetng-h3ci57, tetng-h3cl30, tetng-h3cnh2, tetng-nlgn2b, tetng-h3czr1, tetng-h3dbr5, tetng-nlgn2a, tetng-nlgn3b, tetng-q4ref8, tetng-q4rjp3, tetng-q4rjy3, tetng-q4rk53, tetng-q4rk63, tetng-q4rk66, tetng-q4rkk3, tetng-q4rli3, tetng-q4rn09, tetng-q4rqj4, tetng-q4rqz6, tetng-q4rr22, tetng-q4rru9, tetng-q4rtq6, tetng-q4rvf8, tetng-q4rwa0, tetng-q4rx90, tetng-q4ryv8, tetng-q4ryz3, tetng-q4s0h8, tetng-q4s5x0, tetng-q4s6r1, tetng-q4s6t6, tetng-q4s7e3, tetng-q4s7x6, tetng-q4s8t5, tetng-q4s9w9, tetng-q4s050, tetng-q4s091, tetng-q4s144, tetng-q4s309, tetng-q4s578, tetng-q4sal4, tetng-q4sbm6, tetng-q4sbp0, tetng-q4sbu0, tetng-q4sd49, tetng-q4ser6, tetng-q4sfm7, tetng-q4sgm5, tetng-q4sgv2, tetng-q4sh74, tetng-q4shl7, tetng-q4si60, tetng-q4sie5, tetng-q4sku6, tetng-q4smu0, tetng-q4smy3, tetng-q4snp0, tetng-q4snq3, tetng-q4spa7, tetng-q4spq0, tetng-q4sqr3, tetng-q4sty0, tetng-q4suu2, tetng-q4suz1, tetng-q4sxh3, tetng-q4syn6, tetng-q4szk0, tetng-q4szy0, tetng-q4t3m9, tetng-q4t4a1, tetng-q4t6m1, tetng-q4t7r6, tetng-q4t173, tetng-q4t826, tetng-q4t920, tetng-q4ta33, tetng-q4tab8, tetng-q4tb62, tetng-q4tbe2, tetng-h3dbw2, tetng-h3cpc8, tetng-h3cjy0, tetng-h3d966, tetng-h3d3e3, tetng-h3d961, tetng-h3ctg6, tetng-h3dde8, tetng-h3dde9, tetng-h3det9, tetng-h3cre8, tetng-h3dfb4, tetng-h3clj8 Abstract Tetraodon nigroviridis is a freshwater puffer fish with the smallest known vertebrate genome. Here, we report a draft genome sequence with long-range linkage and substantial anchoring to the 21 Tetraodon chromosomes. Genome analysis provides a greatly improved fish gene catalogue, including identifying key genes previously thought to be absent in fish. Comparison with other vertebrates and a urochordate indicates that fish proteins have diverged markedly faster than their mammalian homologues. Comparison with the human genome suggests approximately 900 previously unannotated human genes. Analysis of the Tetraodon and human genomes shows that whole-genome duplication occurred in the teleost fish lineage, subsequent to its divergence from mammals. The analysis also makes it possible to infer the basic structure of the ancestral bony vertebrate genome, which was composed of 12 chromosomes, and to reconstruct much of the evolutionary history of ancient and recent chromosome rearrangements leading to the modern human karyotype. | |||||||
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