Author Report for: Denoeud FNo contact information in database for Denoeud F
Chalhoub B, Denoeud F, Liu S, Parkin IA, Tang H, Wang X, Chiquet J, Belcram H, Tong C and Wincker P <70 more 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 (- 70) Ref: Science, 345:950, 2014 : PubMed 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 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. Title: The coffee genome provides insight into the convergent evolution of caffeine biosynthesis Denoeud F, Carretero-Paulet L, Dereeper A, Droc G, Guyot R, Pietrella M, Zheng C, Alberti A, Anthony F and Lashermes P <54 more 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 (- 54) Ref: Science, 345:1181, 2014 : PubMed 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 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. Title: Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea Parkin IA, Koh C, Tang H, Robinson SJ, Kagale S, Clarke WE, Town CD, Nixon J, Krishnakumar V and Sharpe AG <22 more author(s)> Parkin IA, Koh C, Tang H, Robinson SJ, Kagale S, Clarke WE, Town CD, Nixon J, Krishnakumar V, Bidwell SL, Denoeud F, Belcram H, Links MG, Just J, Clarke C, Bender T, Huebert T, Mason AS, Pires JC, Barker G, Moore J, Walley PG, Manoli S, Batley J, Edwards D, Nelson MN, Wang X, Paterson AH, King G, Bancroft I, Chalhoub B, Sharpe AG (- 22) Ref: Genome Biol, 15:R77, 2014 : PubMed ESTHER: Parkin_2014_Genome.Biol_15_R77 PubMedSearch: Parkin 2014 Genome.Biol 15 R77 PubMedID: 24916971 Gene_locus related to this paper: braol-a0a0d3dpb2, braol-a0a0d3dx76, brana-a0a078jxa8, brana-a0a078i2k3, braol-a0a0d3ef55, braol-a0a0d3bur9, braol-a0a0d3ck99, braol-a0a0d3cns1, braol-a0a0d3e654, brana-a0a078i6d2, braol-a0a0d3a922 Abstract BACKGROUND: Brassica oleracea is a valuable vegetable species that has contributed to human health and nutrition for hundreds of years and comprises multiple distinct cultivar groups with diverse morphological and phytochemical attributes. In addition to this phenotypic wealth, B. oleracea offers unique insights into polyploid evolution, as it results from multiple ancestral polyploidy events and a final Brassiceae-specific triplication event. Further, B. oleracea represents one of the diploid genomes that formed the economically important allopolyploid oilseed, Brassica napus. A deeper understanding of B. oleracea genome architecture provides a foundation for crop improvement strategies throughout the Brassica genus. 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: 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: 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: Perigord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis Martin F, Kohler A, Murat C, Balestrini R, Coutinho PM, Jaillon O, Montanini B, Morin E, Noel B and Wincker P <41 more 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 (- 41) Ref: Nature, 464:1033, 2010 : PubMed 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 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. | |||||||
|
