Author Report for: Labadie KNo contact information in database for Labadie K
Raymond O, Gouzy J, Just J, Badouin H, Verdenaud M, Lemainque A, Vergne P, Moja S, Choisne N and Bendahmane M <36 more author(s)> Raymond O, Gouzy J, Just J, Badouin H, Verdenaud M, Lemainque A, Vergne P, Moja S, Choisne N, Pont C, Carrere S, Caissard JC, Couloux A, Cottret L, Aury JM, Szecsi J, Latrasse D, Madoui MA, Francois L, Fu X, Yang SH, Dubois A, Piola F, Larrieu A, Perez M, Labadie K, Perrier L, Govetto B, Labrousse Y, Villand P, Bardoux C, Boltz V, Lopez-Roques C, Heitzler P, Vernoux T, Vandenbussche M, Quesneville H, Boualem A, Bendahmane A, Liu C, Le Bris M, Salse J, Baudino S, Benhamed M, Wincker P, Bendahmane M (- 36) Ref: Nat Genet, 50:772, 2018 : PubMed ESTHER: Raymond_2018_Nat.Genet_50_772 PubMedSearch: Raymond 2018 Nat.Genet 50 772 PubMedID: 29713014 Gene_locus related to this paper: rosch-a0a2p6p237, rosch-a0a2p6r1h5, rosch-a0a2p6saq0, rosch-a0a2p6sap4, rosch-a0a2p6san0, rosch-a0a2p6san7, rosch-a0a2p6rkg2, rosch-a0a2p6pxu1, rosch-a0a2p6s382, rosch-a0a2p6s367, rosch-a0a2p6q0b7, rosch-a0a2p6pi87, rosch-a0a2p6p278, rosch-a0a2p6s545 Abstract Roses have high cultural and economic importance as ornamental plants and in the perfume industry. We report the rose whole-genome sequencing and assembly and resequencing of major genotypes that contributed to rose domestication. We generated a homozygous genotype from a heterozygous diploid modern rose progenitor, Rosa chinensis 'Old Blush'. Using single-molecule real-time sequencing and a meta-assembly approach, we obtained one of the most comprehensive plant genomes to date. Diversity analyses highlighted the mosaic origin of 'La France', one of the first hybrids combining the growth vigor of European species and the recurrent blooming of Chinese species. Genomic segments of Chinese ancestry identified new candidate genes for recurrent blooming. Reconstructing regulatory and secondary metabolism pathways allowed us to propose a model of interconnected regulation of scent and flower color. This genome provides a foundation for understanding the mechanisms governing rose traits and should accelerate improvement in roses, Rosaceae and ornamentals. Title: Two genomes of highly polyphagous lepidopteran pests (Spodoptera frugiperda, Noctuidae) with different host-plant ranges Gouin A, Bretaudeau A, Nam K, Gimenez S, Aury JM, Duvic B, Hilliou F, Durand N, Montagne N and Fournier P <55 more author(s)> Gouin A, Bretaudeau A, Nam K, Gimenez S, Aury JM, Duvic B, Hilliou F, Durand N, Montagne N, Darboux I, Kuwar S, Chertemps T, Siaussat D, Bretschneider A, Mone Y, Ahn SJ, Hanniger S, Grenet AG, Neunemann D, Maumus F, Luyten I, Labadie K, Xu W, Koutroumpa F, Escoubas JM, Llopis A, Mabeche-Coisne M, Salasc F, Tomar A, Anderson AR, Khan SA, Dumas P, Orsucci M, Guy J, Belser C, Alberti A, Noel B, Couloux A, Mercier J, Nidelet S, Dubois E, Liu NY, Boulogne I, Mirabeau O, Le Goff G, Gordon K, Oakeshott J, Consoli FL, Volkoff AN, Fescemyer HW, Marden JH, Luthe DS, Herrero S, Heckel DG, Wincker P, Kergoat GJ, Amselem J, Quesneville H, Groot AT, Jacquin-Joly E, Negre N, Lemaitre C, Legeai F, d'Alencon E, Fournier P (- 55) Ref: Sci Rep, 7:11816, 2017 : PubMed ESTHER: Gouin_2017_Sci.Rep_7_11816 PubMedSearch: Gouin 2017 Sci.Rep 7 11816 PubMedID: 28947760 Abstract Emergence of polyphagous herbivorous insects entails significant adaptation to recognize, detoxify and digest a variety of host-plants. Despite of its biological and practical importance - since insects eat 20% of crops - no exhaustive analysis of gene repertoires required for adaptations in generalist insect herbivores has previously been performed. The noctuid moth Spodoptera frugiperda ranks as one of the world's worst agricultural pests. This insect is polyphagous while the majority of other lepidopteran herbivores are specialist. It consists of two morphologically indistinguishable strains ("C" and "R") that have different host plant ranges. To describe the evolutionary mechanisms that both enable the emergence of polyphagous herbivory and lead to the shift in the host preference, we analyzed whole genome sequences from laboratory and natural populations of both strains. We observed huge expansions of genes associated with chemosensation and detoxification compared with specialist Lepidoptera. These expansions are largely due to tandem duplication, a possible adaptation mechanism enabling polyphagy. Individuals from natural C and R populations show significant genomic differentiation. We found signatures of positive selection in genes involved in chemoreception, detoxification and digestion, and copy number variation in the two latter gene families, suggesting an adaptive role for structural variation. Title: The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates Berthelot C, Brunet F, Chalopin D, Juanchich A, Bernard M, Noel B, Bento P, Da Silva C, Labadie K and Guiguen Y <20 more 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 (- 20) Ref: Nat Commun, 5:3657, 2014 : PubMed 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 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. Title: Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome 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: 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. | |||||||
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