Author Report for: Choisne NNo contact information in database for Choisne N
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: 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 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: Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography Normand P, Lapierre P, Tisa LS, Gogarten JP, Alloisio N, Bagnarol E, Bassi CA, Berry AM, Bickhart DM and Benson DR <30 more author(s)> Normand P, Lapierre P, Tisa LS, Gogarten JP, Alloisio N, Bagnarol E, Bassi CA, Berry AM, Bickhart DM, Choisne N, Couloux A, Cournoyer B, Cruveiller S, Daubin V, Demange N, Francino MP, Goltsman E, Huang Y, Kopp OR, Labarre L, Lapidus A, Lavire C, Marechal J, Martinez M, Mastronunzio JE, Mullin BC, Niemann J, Pujic P, Rawnsley T, Rouy Z, Schenowitz C, Sellstedt A, Tavares F, Tomkins JP, Vallenet D, Valverde C, Wall LG, Wang Y, Medigue C, Benson DR (- 30) Ref: Genome Res, 17:7, 2007 : PubMed ESTHER: Normand_2007_Genome.Res_17_7 PubMedSearch: Normand 2007 Genome.Res 17 7 PubMedID: 17151343 Gene_locus related to this paper: frasn-a8leg3, fraaa-q0rau9, fraaa-q0rbj9, fraaa-q0rc03, fraaa-q0rc89, fraaa-q0rci1, fraaa-q0rdx4, fraaa-q0ref4, fraaa-q0rel4, fraaa-q0req5, fraaa-q0rev2, fraaa-q0rfl4, fraaa-q0rfz5, fraaa-q0rhz6, fraaa-q0rjm3, fraaa-q0rjt2, fraaa-q0rkm8, fraaa-q0rkv5, fraaa-q0rl43, fraaa-q0rlp9, fraaa-q0rm04, fraaa-q0rmn2, fraaa-q0rmz5, fraaa-q0rqg7, fraaa-q0rr69, fraaa-q0rrm7, fraaa-q0rs07, fraaa-q0rt07, fraaa-q0rt55, fraaa-q0rt70, fraaa-q0rt91, fraaa-q0rtc4, fraaa-q0rte4, fraaa-q0rtv2, fraaa-q0rum6, frasc-q2j5v5, frasc-q2j8e6, frasc-q2jct6, frasn-a8kx42, frasn-a8kyp2, frasn-A8L0F8, frasn-a8l0g7, frasn-a8l1j7, frasn-a8l1t9, frasn-a8l4h8, frasn-a8l7f8, frasn-a8l8i4, frasn-a8l8k8, frasn-a8l9e9, frasn-a8l051, frasn-a8l115, frasn-a8l161, frasn-a8l265, frasn-a8l268, frasn-a8l720, frasn-a8l745, frasn-a8l755, frasn-a8l875, frasn-a8lab3, frasn-a8lag3, frasn-a8lb99, frasn-a8lbd8, frasn-a8lbj7, frasn-a8lbj8, frasn-a8lby7, frasn-a8ldb7, frasn-a8ldd0, frasn-a8le91, frasn-a8leg6, frasn-a8leq6, frasn-a8let0, frasn-a8lf43, frasn-a8lfg3, frasn-a8lfl1, frasn-a8lgw1, frasn-a8lgy1, frasc-q2j553, frasn-a8l2m3, fraaa-q0rd38, frasc-q2j6h2, frasn-a8lfl3, frasn-a8leg7, frasn-a8l5b8, fraaa-q0rgz4, fraaa-q0rtv3, frasn-a8le98, frasn-a8leb4 Abstract Soil bacteria that also form mutualistic symbioses in plants encounter two major levels of selection. One occurs during adaptation to and survival in soil, and the other occurs in concert with host plant speciation and adaptation. Actinobacteria from the genus Frankia are facultative symbionts that form N(2)-fixing root nodules on diverse and globally distributed angiosperms in the "actinorhizal" symbioses. Three closely related clades of Frankia sp. strains are recognized; members of each clade infect a subset of plants from among eight angiosperm families. We sequenced the genomes from three strains; their sizes varied from 5.43 Mbp for a narrow host range strain (Frankia sp. strain HFPCcI3) to 7.50 Mbp for a medium host range strain (Frankia alni strain ACN14a) to 9.04 Mbp for a broad host range strain (Frankia sp. strain EAN1pec.) This size divergence is the largest yet reported for such closely related soil bacteria (97.8%-98.9% identity of 16S rRNA genes). The extent of gene deletion, duplication, and acquisition is in concert with the biogeographic history of the symbioses and host plant speciation. Host plant isolation favored genome contraction, whereas host plant diversification favored genome expansion. The results support the idea that major genome expansions as well as reductions can occur in facultative symbiotic soil bacteria as they respond to new environments in the context of their symbioses. Title: Genome sequence of the plant pathogen Ralstonia solanacearum Salanoubat M, Genin S, Artiguenave F, Gouzy J, Mangenot S, Arlat M, Billault A, Brottier P, Camus JC and Boucher CA <18 more author(s)> Salanoubat M, Genin S, Artiguenave F, Gouzy J, Mangenot S, Arlat M, Billault A, Brottier P, Camus JC, Cattolico L, Chandler M, Choisne N, Claudel-Renard C, Cunnac S, Demange N, Gaspin C, Lavie M, Moisan A, Robert C, Saurin W, Schiex T, Siguier P, Thebault P, Whalen M, Wincker P, Levy M, Weissenbach J, Boucher CA (- 18) Ref: Nature, 415:497, 2002 : PubMed ESTHER: Salanoubat_2002_Nature_415_497 PubMedSearch: Salanoubat 2002 Nature 415 497 PubMedID: 11823852 Gene_locus related to this paper: ralso-DEHH, ralso-METX, ralso-PCAD, ralso-PCAD2, ralso-PHAZ, ralso-PHBC, ralso-q8xsf9, ralso-q8xta6, ralso-q8xtf1, ralso-RSC0055, ralso-RSC0206, ralso-RSC0268, ralso-RSC0328, ralso-RSC0439, ralso-RSC0563, ralso-RSC0604, ralso-RSC0827, ralso-RSC1003, ralso-RSC1125, ralso-RSC1135, ralso-RSC1344, ralso-RSC1396, ralso-RSC1561, ralso-RSC1573, ralso-RSC1770, ralso-RSC1772, ralso-RSC1804, ralso-RSC1811, ralso-RSC1841, ralso-RSC1887, ralso-RSC2082, ralso-RSC2149, ralso-RSC2228, ralso-RSC2317, ralso-RSC2319, ralso-RSC2328, ralso-RSC2593, ralso-RSC2781, ralso-RSC3165, ralso-RSC3312, ralso-RSC3346, ralso-RSC3406, ralso-RSP0196, ralso-RSP0232, ralso-RSP0642, ralso-RSP0769, ralso-RSP0780, ralso-RSP0790, ralso-RSP0795, ralso-RSP1108, ralso-RSP1111, ralso-RSP1148, ralso-RSP1167, ralso-RSP1229, ralso-RSP1248, ralso-RSP1339, ralso-RSP1355, ralso-RSP1418, ralso-RSP1419, ralso-RSP1422, ralso-RSP1429, ralso-RSP1435, ralso-RSP1484, ralso-RSP1521, ralso-hboh, ralso-q8y0t3 Abstract Ralstonia solanacearum is a devastating, soil-borne plant pathogen with a global distribution and an unusually wide host range. It is a model system for the dissection of molecular determinants governing pathogenicity. We present here the complete genome sequence and its analysis of strain GMI1000. The 5.8-megabase (Mb) genome is organized into two replicons: a 3.7-Mb chromosome and a 2.1-Mb megaplasmid. Both replicons have a mosaic structure providing evidence for the acquisition of genes through horizontal gene transfer. Regions containing genetically mobile elements associated with the percentage of G+C bias may have an important function in genome evolution. The genome encodes many proteins potentially associated with a role in pathogenicity. In particular, many putative attachment factors were identified. The complete repertoire of type III secreted effector proteins can be studied. Over 40 candidates were identified. Comparison with other genomes suggests that bacterial plant pathogens and animal pathogens harbour distinct arrays of specialized type III-dependent effectors. Title: Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana Salanoubat M, Lemcke K, Rieger M, Ansorge W, Unseld M, Fartmann B, Valle G, Blocker H, Perez-Alonso M and Tabata S <127 more author(s)> Salanoubat M, Lemcke K, Rieger M, Ansorge W, Unseld M, Fartmann B, Valle G, Blocker H, Perez-Alonso M, Obermaier B, Delseny M, Boutry M, Grivell LA, Mache R, Puigdomenech P, de Simone V, Choisne N, Artiguenave F, Robert C, Brottier P, Wincker P, Cattolico L, Weissenbach J, Saurin W, Quetier F, Schafer M, Muller-Auer S, Gabel C, Fuchs M, Benes V, Wurmbach E, Drzonek H, Erfle H, Jordan N, Bangert S, Wiedelmann R, Kranz H, Voss H, Holland R, Brandt P, Nyakatura G, Vezzi A, D'Angelo M, Pallavicini A, Toppo S, Simionati B, Conrad A, Hornischer K, Kauer G, Lohnert TH, Nordsiek G, Reichelt J, Scharfe M, Schon O, Bargues M, Terol J, Climent J, Navarro P, Collado C, Perez-Perez A, Ottenwalder B, Duchemin D, Cooke R, Laudie M, Berger-Llauro C, Purnelle B, Masuy D, de Haan M, Maarse AC, Alcaraz JP, Cottet A, Casacuberta E, Monfort A, Argiriou A, Flores M, Liguori R, Vitale D, Mannhaupt G, Haase D, Schoof H, Rudd S, Zaccaria P, Mewes HW, Mayer KF, Kaul S, Town CD, Koo HL, Tallon LJ, Jenkins J, Rooney T, Rizzo M, Walts A, Utterback T, Fujii CY, Shea TP, Creasy TH, Haas B, Maiti R, Wu D, Peterson J, Van Aken S, Pai G, Militscher J, Sellers P, Gill JE, Feldblyum TV, Preuss D, Lin X, Nierman WC, Salzberg SL, White O, Venter JC, Fraser CM, Kaneko T, Nakamura Y, Sato S, Kato T, Asamizu E, Sasamoto S, Kimura T, Idesawa K, Kawashima K, Kishida Y, Kiyokawa C, Kohara M, Matsumoto M, Matsuno A, Muraki A, Nakayama S, Nakazaki N, Shinpo S, Takeuchi C, Wada T, Watanabe A, Yamada M, Yasuda M, Tabata S (- 127) Ref: Nature, 408:820, 2000 : PubMed ESTHER: Salanoubat_2000_Nature_408_820 PubMedSearch: Salanoubat 2000 Nature 408 820 PubMedID: 11130713 Gene_locus related to this paper: arath-MES17, arath-AT3G12150, arath-At3g61680, arath-AT3g62590, arath-CXE12, arath-eds1, arath-SCP25, arath-F1P2.110, arath-F1P2.140, arath-F11F8.28, arath-F14D17.80, arath-F16B3.4, arath-SCP27, arath-At3g50790, arath-At3g05600, arath-PAD4, arath-At3g51000, arath-SCP16, arath-gid1, arath-GID1B, arath-Q9LUG8, arath-Q84JS1, arath-Q9SFF6, arath-q9m236, arath-q9sr22, arath-q9sr23, arath-SCP7, arath-SCP14, arath-SCP15, arath-SCP17, arath-SCP36, arath-SCP37, arath-SCP39, arath-SCP40, arath-SCP49, arath-T19F11.2 Abstract Arabidopsis thaliana is an important model system for plant biologists. In 1996 an international collaboration (the Arabidopsis Genome Initiative) was formed to sequence the whole genome of Arabidopsis and in 1999 the sequence of the first two chromosomes was reported. The sequence of the last three chromosomes and an analysis of the whole genome are reported in this issue. Here we present the sequence of chromosome 3, organized into four sequence segments (contigs). The two largest (13.5 and 9.2 Mb) correspond to the top (long) and the bottom (short) arms of chromosome 3, and the two small contigs are located in the genetically defined centromere. This chromosome encodes 5,220 of the roughly 25,500 predicted protein-coding genes in the genome. About 20% of the predicted proteins have significant homology to proteins in eukaryotic genomes for which the complete sequence is available, pointing to important conserved cellular functions among eukaryotes. | |||||||
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