Da Silva C

References (13)

Title : Pezizomycetes genomes reveal the molecular basis of ectomycorrhizal truffle lifestyle - Murat_2018_Nat.Ecol.Evol_2_1956
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
Ref : Nat Ecol Evol , 2 :1956 , 2018
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.
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

Title : The coffee genome provides insight into the convergent evolution of caffeine biosynthesis - Denoeud_2014_Science_345_1181
Author(s) : Denoeud F , Carretero-Paulet L , Dereeper A , Droc G , Guyot R , Pietrella M , Zheng C , Alberti A , Anthony F , Aprea G , Aury JM , Bento P , Bernard M , Bocs S , Campa C , Cenci A , Combes MC , Crouzillat D , Da Silva C , Daddiego L , De Bellis F , Dussert S , Garsmeur O , Gayraud T , Guignon V , Jahn K , Jamilloux V , Joet T , Labadie K , Lan T , Leclercq J , Lepelley M , Leroy T , Li LT , Librado P , Lopez L , Munoz A , Noel B , Pallavicini A , Perrotta G , Poncet V , Pot D , Priyono , Rigoreau M , Rouard M , Rozas J , Tranchant-Dubreuil C , VanBuren R , Zhang Q , Andrade AC , Argout X , Bertrand B , de Kochko A , Graziosi G , Henry RJ , Jayarama , Ming R , Nagai C , Rounsley S , Sankoff D , Giuliano G , Albert VA , Wincker P , Lashermes P
Ref : Science , 345 :1181 , 2014
Abstract : Coffee is a valuable beverage crop due to its characteristic flavor, aroma, and the stimulating effects of caffeine. We generated a high-quality draft genome of the species Coffea canephora, which displays a conserved chromosomal gene order among asterid angiosperms. Although it shows no sign of the whole-genome triplication identified in Solanaceae species such as tomato, the genome includes several species-specific gene family expansions, among them N-methyltransferases (NMTs) involved in caffeine production, defense-related genes, and alkaloid and flavonoid enzymes involved in secondary compound synthesis. Comparative analyses of caffeine NMTs demonstrate that these genes expanded through sequential tandem duplications independently of genes from cacao and tea, suggesting that caffeine in eudicots is of polyphyletic origin.
ESTHER : Denoeud_2014_Science_345_1181
PubMedSearch : Denoeud_2014_Science_345_1181
PubMedID: 25190796
Gene_locus related to this paper: cofca-a0a068vi93 , cofca-a0a068uy77 , cofca-a0a068tzh7 , cofca-a0a068tuj7 , cofca-a0a068v983 , cofca-a0a068tnj0 , cofca-a0a068tyf7 , cofca-a0a068u1v4.1 , cofca-a0a068vks5 , cofar-a0a6p6xcv5

Title : The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates - Berthelot_2014_Nat.Commun_5_3657
Author(s) : Berthelot C , Brunet F , Chalopin D , Juanchich A , Bernard M , Noel B , Bento P , Da Silva C , Labadie K , Alberti A , Aury JM , Louis A , Dehais P , Bardou P , Montfort J , Klopp C , Cabau C , Gaspin C , Thorgaard GH , Boussaha M , Quillet E , Guyomard R , Galiana D , Bobe J , Volff JN , Genet C , Wincker P , Jaillon O , Roest Crollius H , Guiguen Y
Ref : Nat Commun , 5 :3657 , 2014
Abstract : Vertebrate evolution has been shaped by several rounds of whole-genome duplications (WGDs) that are often suggested to be associated with adaptive radiations and evolutionary innovations. Due to an additional round of WGD, the rainbow trout genome offers a unique opportunity to investigate the early evolutionary fate of a duplicated vertebrate genome. Here we show that after 100 million years of evolution the two ancestral subgenomes have remained extremely collinear, despite the loss of half of the duplicated protein-coding genes, mostly through pseudogenization. In striking contrast is the fate of miRNA genes that have almost all been retained as duplicated copies. The slow and stepwise rediploidization process characterized here challenges the current hypothesis that WGD is followed by massive and rapid genomic reorganizations and gene deletions.
ESTHER : Berthelot_2014_Nat.Commun_5_3657
PubMedSearch : Berthelot_2014_Nat.Commun_5_3657
PubMedID: 24755649
Gene_locus related to this paper: oncmy-a0a060yri0 , oncmy-a0a060.1 , oncmy-a0a060.2 , oncmy-a0a060wwk7 , oncmy-a0a060wr62 , oncmy-a0a060wae0 , oncmy-a0a060wcy0 , oncmy-a0a060wwk2 , oncmy-a0a060wxj2 , oncmy-a0a060y4g9 , oncmy-a0a060w9c6 , oncmy-a0a060y4c5 , oncmy-a0a060yjg0 , oncmy-a0a060yqr9 , oncmy-a0a060w5s8 , oncmy-a0a060vy20 , oncmy-a0a060w006 , oncmy-a0a060y788 , oncmy-a0a060yt95 , oncmy-a0a060xce0 , oncmy-a0a060yqu0 , oncmy-a0a060xjp0 , oncmy-a0a060xym5 , oncmy-a0a060xqc7 , oncmy-a0a060xjn9 , oncmy-a0a060wwr6 , oncmy-a0a060xgb0 , oncmy-a0a060xey2 , oncmy-a0a060yle3 , oncmy-a0a060y6u5

Title : Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome - Chalhoub_2014_Science_345_950
Author(s) : Chalhoub B , Denoeud F , Liu S , Parkin IA , Tang H , Wang X , Chiquet J , Belcram H , Tong C , Samans B , Correa M , Da Silva C , Just J , Falentin C , Koh CS , Le Clainche I , Bernard M , Bento P , Noel B , Labadie K , Alberti A , Charles M , Arnaud D , Guo H , Daviaud C , Alamery S , Jabbari K , Zhao M , Edger PP , Chelaifa H , Tack D , Lassalle G , Mestiri I , Schnel N , Le Paslier MC , Fan G , Renault V , Bayer PE , Golicz AA , Manoli S , Lee TH , Thi VH , Chalabi S , Hu Q , Fan C , Tollenaere R , Lu Y , Battail C , Shen J , Sidebottom CH , Canaguier A , Chauveau A , Berard A , Deniot G , Guan M , Liu Z , Sun F , Lim YP , Lyons E , Town CD , Bancroft I , Meng J , Ma J , Pires JC , King GJ , Brunel D , Delourme R , Renard M , Aury JM , Adams KL , Batley J , Snowdon RJ , Tost J , Edwards D , Zhou Y , Hua W , Sharpe AG , Paterson AH , Guan C , Wincker P
Ref : Science , 345 :950 , 2014
Abstract : Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72x genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.
ESTHER : Chalhoub_2014_Science_345_950
PubMedSearch : Chalhoub_2014_Science_345_950
PubMedID: 25146293
Gene_locus related to this paper: braol-Q8GTM3 , braol-Q8GTM4 , brana-a0a078j4a9 , brana-a0a078e1m0 , brana-a0a078cd75 , brana-a0a078evd3 , brana-a0a078j4f0 , brana-a0a078cta5 , brana-a0a078cus4 , brana-a0a078f8c2 , brana-a0a078jql1 , brana-a0a078dgj3 , brana-a0a078hw50 , brana-a0a078cuu0 , brana-a0a078iyl8 , brana-a0a078dfa9 , brana-a0a078ic91 , brana-a0a078cnf7 , brana-a0a078fh41 , brana-a0a078ca65 , brana-a0a078ctc8 , brana-a0a078h021 , brana-a0a078h0h8 , brana-a0a078jx23 , brana-a0a078ci96 , brana-a0a078cqd7 , brana-a0a078dh94 , brana-a0a078h612 , brana-a0a078ild2 , brana-a0a078j2t3 , braol-a0a0d3dpb2 , braol-a0a0d3dx76 , brana-a0a078jxa8 , brana-a0a078i2k3 , braol-a0a0d3ef55 , brarp-m4dcj8 , brana-a0a078fw53 , brana-a0a078itf3 , brana-a0a078jsn1 , brana-a0a078jrt9 , brana-a0a078i6d2 , brana-a0a078jku0 , brana-a0a078fss7 , brana-a0a078i1l0 , brana-a0a078i402

Title : Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida - Collen_2013_Proc.Natl.Acad.Sci.U.S.A_110_5247
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
Ref : Proc Natl Acad Sci U S A , 110 :5247 , 2013
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.
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

Title : Enzymatic catalyzed palm oil hydrolysis under ultrasound irradiation: diacylglycerol synthesis - Awadallak_2013_Ultrason.Sonochem_20_1002
Author(s) : Awadallak JA , Voll F , Ribas MC , Da Silva C , Filho LC , da Silva EA
Ref : Ultrason Sonochem , 20 :1002 , 2013
Abstract : Diacylglycerol (DAG) rich oils have an organoleptic property like that of regular edible oils, but these oils do not tend to be accumulated as fat. Palm oil ranks first in the world in terms of edible oil production owing to its low cost. The aim of this study was to propose a new methodology to produce diacylglycerol by hydrolysis of palm oil using Lipozyme RM IM commercial lipase as a catalyst under ultrasound irradiation. The reactions were carried out at 55 degreeC with two different methods. First, the reaction system was exposed to ultrasonic waves for the whole reaction time, which led to enzymatic inactivation and water evaporation. Ultrasound was then used to promote emulsification of the water/oil system before the hydrolysis reaction, avoiding contact between the probe and the enzymes. An experimental design was used to optimize the ultrasound-related parameters and maximize the hydrolysis rate, and in these conditions, with a change in equilibrium, DAG production was evaluated. Better reaction conditions were achieved for the second method: 11.20 wt.% (water+oil mass) water content, 1.36 wt.% (water+oil mass) enzyme load, 12 h of reaction time, 1.2 min and 200 W of exposure to ultrasound. In these conditions diacylglycerol yield was 34.17 wt.%.
ESTHER : Awadallak_2013_Ultrason.Sonochem_20_1002
PubMedSearch : Awadallak_2013_Ultrason.Sonochem_20_1002
PubMedID: 23402907

Title : The banana (Musa acuminata) genome and the evolution of monocotyledonous plants - D'Hont_2012_Nature_488_213
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
Ref : Nature , 488 :213 , 2012
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.
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

Title : Genome sequence of the stramenopile Blastocystis, a human anaerobic parasite - Denoeud_2011_Genome.Biol_12_R29
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
Ref : Genome Biol , 12 :R29 , 2011
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.
RESULTS: Here we report the 18.8 Mb genome sequence of a Blastocystis subtype 7 isolate, which is the smallest stramenopile genome sequenced to date. The genome is highly compact and contains intriguing rearrangements. Comparisons with other available stramenopile genomes (plant pathogenic oomycete and diatom genomes) revealed effector proteins potentially involved in the adaptation to the intestinal environment, which were likely acquired via horizontal gene transfer. Moreover, Blastocystis living in anaerobic conditions harbors mitochondria-like organelles. An incomplete oxidative phosphorylation chain, a partial Krebs cycle, amino acid and fatty acid metabolisms and an iron-sulfur cluster assembly are all predicted to occur in these organelles. Predicted secretory proteins possess putative activities that may alter host physiology, such as proteases, protease-inhibitors, immunophilins and glycosyltransferases. This parasite also possesses the enzymatic machinery to tolerate oxidative bursts resulting from its own metabolism or induced by the host immune system.
CONCLUSIONS: This study provides insights into the genome architecture of this unusual stramenopile. It also proposes candidate genes with which to study the physiopathology of this parasite and thus may lead to further investigations into Blastocystis-host interactions.
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

Title : Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea - Amselem_2011_PLoS.Genet_7_e1002230
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
Ref : PLoS Genet , 7 :e1002230 , 2011
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.
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 , scls1-a7ecx1

Title : Perigord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis - Martin_2010_Nature_464_1033
Author(s) : Martin F , Kohler A , Murat C , Balestrini R , Coutinho PM , Jaillon O , Montanini B , Morin E , Noel B , Percudani R , Porcel B , Rubini A , Amicucci A , Amselem J , Anthouard V , Arcioni S , Artiguenave F , Aury JM , Ballario P , Bolchi A , Brenna A , Brun A , Buee M , Cantarel B , Chevalier G , Couloux A , Da Silva C , Denoeud F , Duplessis S , Ghignone S , Hilselberger B , Iotti M , Marcais B , Mello A , Miranda M , Pacioni G , Quesneville H , Riccioni C , Ruotolo R , Splivallo R , Stocchi V , Tisserant E , Viscomi AR , Zambonelli A , Zampieri E , Henrissat B , Lebrun MH , Paolocci F , Bonfante P , Ottonello S , Wincker P
Ref : Nature , 464 :1033 , 2010
Abstract : The Perigord 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 approximately 125 megabases is the largest and most complex fungal genome sequenced so far. This expansion results from a proliferation of transposable elements accounting for approximately 58% of the genome. In contrast, this genome only contains approximately 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.
ESTHER : Martin_2010_Nature_464_1033
PubMedSearch : Martin_2010_Nature_464_1033
PubMedID: 20348908
Gene_locus related to this paper: 9pezi-d5g8f4 , 9pezi-d5gi84 , 9pezi-d5gph4 , tubmm-d5g4w2 , tubmm-d5g4w3 , tubmm-d5g4w6 , tubmm-d5g5r5 , tubmm-d5g8z4 , tubmm-d5g938 , tubmm-d5ga65 , tubmm-d5gcz1 , tubmm-d5giz0 , tubmm-d5gkr8 , tubmm-d5glm4 , tubmm-d5gnw0 , tubmm-dapb , tubmm-d5gfj1 , tubmm-d5gpf4 , tubmm-TmEst2 , tubmm-TmEst1 , tubmm-TmEst3 , 9pezi-a0a292py12 , tubmm-kex1

Title : The Ectocarpus genome and the independent evolution of multicellularity in brown algae - Cock_2010_Nature_465_617
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
Ref : Nature , 465 :617 , 2010
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.
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

Title : Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate - Denoeud_2010_Science_330_1381
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
Ref : Science , 330 :1381 , 2010
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.
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

Title : The genome sequence of the model ascomycete fungus Podospora anserina - Espagne_2008_Genome.Biol_9_R77
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
Ref : Genome Biol , 9 :R77 , 2008
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.
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