Author Report for: Wong GKNo contact information in database for Wong GK
Lang D, Ullrich KK, Murat F, Fuchs J, Jenkins J, Haas FB, Piednoel M, Gundlach H, Van Bel M and Rensing SA <46 more author(s)> Lang D, Ullrich KK, Murat F, Fuchs J, Jenkins J, Haas FB, Piednoel M, Gundlach H, Van Bel M, Meyberg R, Vives C, Morata J, Symeonidi A, Hiss M, Muchero W, Kamisugi Y, Saleh O, Blanc G, Decker EL, van Gessel N, Grimwood J, Hayes RD, Graham SW, Gunter LE, McDaniel SF, Hoernstein SNW, Larsson A, Li FW, Perroud PF, Phillips J, Ranjan P, Rokshar DS, Rothfels CJ, Schneider L, Shu S, Stevenson DW, Thummler F, Tillich M, Villarreal Aguilar JC, Widiez T, Wong GK, Wymore A, Zhang Y, Zimmer AD, Quatrano RS, Mayer KFX, Goodstein D, Casacuberta JM, Vandepoele K, Reski R, Cuming AC, Tuskan GA, Maumus F, Salse J, Schmutz J, Rensing SA (- 46) Ref: Plant J, 93:515, 2018 : PubMed ESTHER: Lang_2018_Plant.J_93_515 PubMedSearch: Lang 2018 Plant.J 93 515 PubMedID: 29237241 Gene_locus related to this paper: phypa-a9tc36, phypa-a0a2k1kfe3, phypa-a9sqk3, phypa-a0a2k1ie71, phypa-a0a2k1kg29, phypa-a0a2k1iji3 Abstract The draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene- and TE-rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono-centric with peaks of a class of Copia elements potentially coinciding with centromeres. Gene body methylation is evident in 5.7% of the protein-coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via siRNA mediated silencing. Structure-based detection methods show that the genome evolved via two rounds of whole genome duplications (WGDs), apparently common in mosses but not in liverworts and hornworts. Several hundred genes are present in colinear regions conserved since the last common ancestor of plants. These syntenic regions are enriched for functions related to plant-specific cell growth and tissue organization. The P. patens genome lacks the TE-rich pericentromeric and gene-rich distal regions typical for most flowering plant genomes. More non-seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes. Title: Evolution of strigolactone receptors by gradual neo-functionalization of KAI2 paralogues Bythell-Douglas R, Rothfels CJ, Stevenson DWD, Graham SW, Wong GK, Nelson DC, Bennett T Ref: BMC Biol, 15:52, 2017 : PubMed ESTHER: Bythell-Douglas_2017_BMC.Biol_15_52 PubMedSearch: Bythell-Douglas 2017 BMC.Biol 15 52 PubMedID: 28662667 Abstract BACKGROUND: Strigolactones (SLs) are a class of plant hormones that control many aspects of plant growth. The SL signalling mechanism is homologous to that of karrikins (KARs), smoke-derived compounds that stimulate seed germination. In angiosperms, the SL receptor is an alpha/beta-hydrolase known as DWARF14 (D14); its close homologue, KARRIKIN INSENSITIVE2 (KAI2), functions as a KAR receptor and likely recognizes an uncharacterized, endogenous signal ('KL'). Previous phylogenetic analyses have suggested that the KAI2 lineage is ancestral in land plants, and that canonical D14-type SL receptors only arose in seed plants; this is paradoxical, however, as non-vascular plants synthesize and respond to SLs. Title: Algal ancestor of land plants was preadapted for symbiosis Delaux PM, Radhakrishnan GV, Jayaraman D, Cheema J, Malbreil M, Volkening JD, Sekimoto H, Nishiyama T, Melkonian M and Ane JM <12 more author(s)> Delaux PM, Radhakrishnan GV, Jayaraman D, Cheema J, Malbreil M, Volkening JD, Sekimoto H, Nishiyama T, Melkonian M, Pokorny L, Rothfels CJ, Sederoff HW, Stevenson DW, Surek B, Zhang Y, Sussman MR, Dunand C, Morris RJ, Roux C, Wong GK, Oldroyd GE, Ane JM (- 12) Ref: Proc Natl Acad Sci U S A, 112:13390, 2015 : PubMed ESTHER: Delaux_2015_Proc.Natl.Acad.Sci.U.S.A_112_13390 PubMedSearch: Delaux 2015 Proc.Natl.Acad.Sci.U.S.A 112 13390 PubMedID: 26438870 Abstract Colonization of land by plants was a major transition on Earth, but the developmental and genetic innovations required for this transition remain unknown. Physiological studies and the fossil record strongly suggest that the ability of the first land plants to form symbiotic associations with beneficial fungi was one of these critical innovations. In angiosperms, genes required for the perception and transduction of diffusible fungal signals for root colonization and for nutrient exchange have been characterized. However, the origin of these genes and their potential correlation with land colonization remain elusive. A comprehensive phylogenetic analysis of 259 transcriptomes and 10 green algal and basal land plant genomes, coupled with the characterization of the evolutionary path leading to the appearance of a key regulator, a calcium- and calmodulin-dependent protein kinase, showed that the symbiotic signaling pathway predated the first land plants. In contrast, downstream genes required for root colonization and their specific expression pattern probably appeared subsequent to the colonization of land. We conclude that the most recent common ancestor of extant land plants and green algae was preadapted for symbiotic associations. Subsequent improvement of this precursor stage in early land plants through rounds of gene duplication led to the acquisition of additional pathways and the ability to form a fully functional arbuscular mycorrhizal symbiosis. Title: The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads Wang Z, Hobson N, Galindo L, Zhu S, Shi D, McDill J, Yang L, Hawkins S, Neutelings G and Deyholos MK <13 more author(s)> Wang Z, Hobson N, Galindo L, Zhu S, Shi D, McDill J, Yang L, Hawkins S, Neutelings G, Datla R, Lambert G, Galbraith DW, Grassa CJ, Geraldes A, Cronk QC, Cullis C, Dash PK, Kumar PA, Cloutier S, Sharpe AG, Wong GK, Wang J, Deyholos MK (- 13) Ref: Plant J, 72:461, 2012 : PubMed ESTHER: Wang_2012_Plant.J_72_461 PubMedSearch: Wang 2012 Plant.J 72 461 PubMedID: 22757964 Gene_locus related to this paper: linus-i6xnh8 Abstract Flax (Linum usitatissimum) is an ancient crop that is widely cultivated as a source of fiber, oil and medicinally relevant compounds. To accelerate crop improvement, we performed whole-genome shotgun sequencing of the nuclear genome of flax. Seven paired-end libraries ranging in size from 300 bp to 10 kb were sequenced using an Illumina genome analyzer. A de novo assembly, comprised exclusively of deep-coverage (approximately 94x raw, approximately 69x filtered) short-sequence reads (44-100 bp), produced a set of scaffolds with N(50) =694 kb, including contigs with N(50)=20.1 kb. The contig assembly contained 302 Mb of non-redundant sequence representing an estimated 81% genome coverage. Up to 96% of published flax ESTs aligned to the whole-genome shotgun scaffolds. However, comparisons with independently sequenced BACs and fosmids showed some mis-assembly of regions at the genome scale. A total of 43384 protein-coding genes were predicted in the whole-genome shotgun assembly, and up to 93% of published flax ESTs, and 86% of A. thaliana genes aligned to these predicted genes, indicating excellent coverage and accuracy at the gene level. Analysis of the synonymous substitution rates (K(s) ) observed within duplicate gene pairs was consistent with a recent (5-9 MYA) whole-genome duplication in flax. Within the predicted proteome, we observed enrichment of many conserved domains (Pfam-A) that may contribute to the unique properties of this crop, including agglutinin proteins. Together these results show that de novo assembly, based solely on whole-genome shotgun short-sequence reads, is an efficient means of obtaining nearly complete genome sequence information for some plant species. Title: The sequence and de novo assembly of the giant panda genome Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B and Yang H <103 more author(s)> Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y, Zhang Z, Zhang Y, Wang W, Li J, Wei F, Li H, Jian M, Nielsen R, Li D, Gu W, Yang Z, Xuan Z, Ryder OA, Leung FC, Zhou Y, Cao J, Sun X, Fu Y, Fang X, Guo X, Wang B, Hou R, Shen F, Mu B, Ni P, Lin R, Qian W, Wang G, Yu C, Nie W, Wang J, Wu Z, Liang H, Min J, Wu Q, Cheng S, Ruan J, Wang M, Shi Z, Wen M, Liu B, Ren X, Zheng H, Dong D, Cook K, Shan G, Zhang H, Kosiol C, Xie X, Lu Z, Li Y, Steiner CC, Lam TT, Lin S, Zhang Q, Li G, Tian J, Gong T, Liu H, Zhang D, Fang L, Ye C, Zhang J, Hu W, Xu A, Ren Y, Zhang G, Bruford MW, Li Q, Ma L, Guo Y, An N, Hu Y, Zheng Y, Shi Y, Li Z, Liu Q, Chen Y, Zhao J, Qu N, Zhao S, Tian F, Wang X, Wang H, Xu L, Liu X, Vinar T, Wang Y, Lam TW, Yiu SM, Liu S, Huang Y, Yang G, Jiang Z, Qin N, Li L, Bolund L, Kristiansen K, Wong GK, Olson M, Zhang X, Li S, Yang H (- 103) Ref: Nature, 463:311, 2010 : PubMed ESTHER: Li_2010_Nature_463_311 PubMedSearch: Li 2010 Nature 463 311 PubMedID: 20010809 Gene_locus related to this paper: ailme-ABH15, ailme-ACHE, ailme-BCHE, ailme-d2gtv3, ailme-d2gty9, ailme-d2gu87, ailme-d2gu97, ailme-d2gve7, ailme-d2gwu1, ailme-d2gx08, ailme-d2gyt0, ailme-d2gz36, ailme-d2gz37, ailme-d2gz38, ailme-d2gz39, ailme-d2gz40, ailme-d2h5r9, ailme-d2h7b7, ailme-d2h9c9, ailme-d2h794, ailme-d2hau7, ailme-d2hau8, ailme-d2hcd9, ailme-d2hdi6, ailme-d2heu6, ailme-d2hga4, ailme-d2hqw5, ailme-d2hs98, ailme-d2hsx4, ailme-d2hti6, ailme-d2htv3, ailme-d2htz6, ailme-d2huc7, ailme-d2hwj8, ailme-d2hwy7, ailme-d2hxm1, ailme-d2hyc8, ailme-d2hyv2, ailme-d2hz11, ailme-d2hza3, ailme-d2hzr4, ailme-d2i1l4, ailme-d2i2g8, ailme-g1l7m3, ailme-g1lu36, ailme-g1m769, ailme-g1mc29, ailme-g1mdj8, ailme-g1mdr5, ailme-g1mfp4, ailme-g1mfx5, ailme-g1lj41, ailme-g1lm28, ailme-g1l3u1, ailme-g1l7l1, ailme-g1m5i3, ailme-g1l2f6, ailme-g1lji5, ailme-g1lqk3, ailme-g1l8s9, ailme-d2h717, ailme-d2h718, ailme-d2h719, ailme-d2h720, ailme-g1m5v0, ailme-g1m5y7, ailme-g1lkt7, ailme-g1l2a1, ailme-g1lsc8, ailme-g1lrp4, ailme-d2gv02, ailme-g1mik5, ailme-g1ljr1, ailme-g1lxw7, ailme-d2h8b5, ailme-d2h2r2, ailme-d2h9w7, ailme-g1meh3, ailme-g1m719 Abstract Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes. Title: The complete genome and proteome of Laribacter hongkongensis reveal potential mechanisms for adaptations to different temperatures and habitats Woo PC, Lau SK, Tse H, Teng JL, Curreem SO, Tsang AK, Fan RY, Wong GK, Huang Y and Yuen KY <7 more author(s)> Woo PC, Lau SK, Tse H, Teng JL, Curreem SO, Tsang AK, Fan RY, Wong GK, Huang Y, Loman NJ, Snyder LA, Cai JJ, Huang JD, Mak W, Pallen MJ, Lok S, Yuen KY (- 7) Ref: PLoS Genet, 5:e1000416, 2009 : PubMed ESTHER: Woo_2009_PLoS.Genet_5_E1000416 PubMedSearch: Woo 2009 PLoS.Genet 5 E1000416 PubMedID: 19283063 Gene_locus related to this paper: larhh-c1d5s6, larhh-c1d7j8, larhh-c1d8b4, larhh-c1d8q3, larhh-c1db23, larhh-metx, larhh-c1d9y5 Abstract Laribacter hongkongensis is a newly discovered Gram-negative bacillus of the Neisseriaceae family associated with freshwater fish-borne gastroenteritis and traveler's diarrhea. The complete genome sequence of L. hongkongensis HLHK9, recovered from an immunocompetent patient with severe gastroenteritis, consists of a 3,169-kb chromosome with G+C content of 62.35%. Genome analysis reveals different mechanisms potentially important for its adaptation to diverse habitats of human and freshwater fish intestines and freshwater environments. The gene contents support its phenotypic properties and suggest that amino acids and fatty acids can be used as carbon sources. The extensive variety of transporters, including multidrug efflux and heavy metal transporters as well as genes involved in chemotaxis, may enable L. hongkongensis to survive in different environmental niches. Genes encoding urease, bile salts efflux pump, adhesin, catalase, superoxide dismutase, and other putative virulence factors-such as hemolysins, RTX toxins, patatin-like proteins, phospholipase A1, and collagenases-are present. Proteomes of L. hongkongensis HLHK9 cultured at 37 degrees C (human body temperature) and 20 degrees C (freshwater habitat temperature) showed differential gene expression, including two homologous copies of argB, argB-20, and argB-37, which encode two isoenzymes of N-acetyl-L-glutamate kinase (NAGK)-NAGK-20 and NAGK-37-in the arginine biosynthesis pathway. NAGK-20 showed higher expression at 20 degrees C, whereas NAGK-37 showed higher expression at 37 degrees C. NAGK-20 also had a lower optimal temperature for enzymatic activities and was inhibited by arginine probably as negative-feedback control. Similar duplicated copies of argB are also observed in bacteria from hot springs such as Thermus thermophilus, Deinococcus geothermalis, Deinococcus radiodurans, and Roseiflexus castenholzii, suggesting that similar mechanisms for temperature adaptation may be employed by other bacteria. Genome and proteome analysis of L. hongkongensis revealed novel mechanisms for adaptations to survival at different temperatures and habitats. Title: Large-insert genome analysis technology detects structural variation in Pseudomonas aeruginosa clinical strains from cystic fibrosis patients Hayden HS, Gillett W, Saenphimmachak C, Lim R, Zhou Y, Jacobs MA, Chang J, Rohmer L, D'Argenio DA and Kaul R <8 more author(s)> Hayden HS, Gillett W, Saenphimmachak C, Lim R, Zhou Y, Jacobs MA, Chang J, Rohmer L, D'Argenio DA, Palmieri A, Levy R, Haugen E, Wong GK, Brittnacher MJ, Burns JL, Miller SI, Olson MV, Kaul R (- 8) Ref: Genomics, 91:530, 2008 : PubMed ESTHER: Hayden_2008_Genomics_91_530 PubMedSearch: Hayden 2008 Genomics 91 530 PubMedID: 18445516 Abstract Large-insert genome analysis (LIGAN) is a broadly applicable, high-throughput technology designed to characterize genome-scale structural variation. Fosmid paired-end sequences and DNA fingerprints from a query genome are compared to a reference sequence using the Genomic Variation Analysis (GenVal) suite of software tools to pinpoint locations of insertions, deletions, and rearrangements. Fosmids spanning regions that contain new structural variants can then be sequenced. Clonal pairs of Pseudomonas aeruginosa isolates from four cystic fibrosis patients were used to validate the LIGAN technology. Approximately 1.5 Mb of inserted sequences were identified, including 743 kb containing 615 ORFs that are absent from published P. aeruginosa genomes. Six rearrangement breakpoints and 220 kb of deleted sequences were also identified. Our study expands the "genome universe" of P. aeruginosa and validates a technology that complements emerging, short-read sequencing methods that are better suited to characterizing single-nucleotide polymorphisms than structural variation. Title: Evolution of genes and genomes on the Drosophila phylogeny Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W and MacCallum I <405 more author(s)> Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW, Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D, Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK, Caggese C, Calvi BR, Bernardo de Carvalho A, Caspi A, Castrezana S, Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A, Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD, Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia AC, Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S, Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL, Halter GM, Han MV, Heger A, Hillier L, Hinrichs AS, Holmes I, Hoskins RA, Hubisz MJ, Hultmark D, Huntley MA, Jaffe DB, Jagadeeshan S, Jeck WR, Johnson J, Jones CD, Jordan WC, Karpen GH, Kataoka E, Keightley PD, Kheradpour P, Kirkness EF, Koerich LB, Kristiansen K, Kudrna D, Kulathinal RJ, Kumar S, Kwok R, Lander E, Langley CH, Lapoint R, Lazzaro BP, Lee SJ, Levesque L, Li R, Lin CF, Lin MF, Lindblad-Toh K, Llopart A, Long M, Low L, Lozovsky E, Lu J, Luo M, Machado CA, Makalowski W, Marzo M, Matsuda M, Matzkin L, McAllister B, McBride CS, McKernan B, McKernan K, Mendez-Lago M, Minx P, Mollenhauer MU, Montooth K, Mount SM, Mu X, Myers E, Negre B, Newfeld S, Nielsen R, Noor MA, O'Grady P, Pachter L, Papaceit M, Parisi MJ, Parisi M, Parts L, Pedersen JS, Pesole G, Phillippy AM, Ponting CP, Pop M, Porcelli D, Powell JR, Prohaska S, Pruitt K, Puig M, Quesneville H, Ram KR, Rand D, Rasmussen MD, Reed LK, Reenan R, Reily A, Remington KA, Rieger TT, Ritchie MG, Robin C, Rogers YH, Rohde C, Rozas J, Rubenfield MJ, Ruiz A, Russo S, Salzberg SL, Sanchez-Gracia A, Saranga DJ, Sato H, Schaeffer SW, Schatz MC, Schlenke T, Schwartz R, Segarra C, Singh RS, Sirot L, Sirota M, Sisneros NB, Smith CD, Smith TF, Spieth J, Stage DE, Stark A, Stephan W, Strausberg RL, Strempel S, Sturgill D, Sutton G, Sutton GG, Tao W, Teichmann S, Tobari YN, Tomimura Y, Tsolas JM, Valente VL, Venter E, Venter JC, Vicario S, Vieira FG, Vilella AJ, Villasante A, Walenz B, Wang J, Wasserman M, Watts T, Wilson D, Wilson RK, Wing RA, Wolfner MF, Wong A, Wong GK, Wu CI, Wu G, Yamamoto D, Yang HP, Yang SP, Yorke JA, Yoshida K, Zdobnov E, Zhang P, Zhang Y, Zimin AV, Baldwin J, Abdouelleil A, Abdulkadir J, Abebe A, Abera B, Abreu J, Acer SC, Aftuck L, Alexander A, An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A, Bayul T, Berlin A, Bessette D, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y, Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M, Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D, Fisher S, Foley CD, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin CR, Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard MD, Hughes L, Hurhula B, Husby ME, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P, Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu X, Liu J, Liu S, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, Macdonald P, Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T, Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V, Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N, Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E, Oyono OL, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S, Rege F, Reyes R, Rise C, Rogov P, Ross K, Ryan E, Settipalli S, Shea T, Sherpa N, Shi L, Shih D, Sparrow T, Spaulding J, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Strader C, Tesfaye S, Thomson T, Thoulutsang Y, Thoulutsang D, Topham K, Topping I, Tsamla T, Vassiliev H, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Young G, Yu Q, Zembek L, Zhong D, Zimmer A, Zwirko Z, Alvarez P, Brockman W, Butler J, Chin C, Grabherr M, Kleber M, Mauceli E, MacCallum I (- 405) Ref: Nature, 450:203, 2007 : PubMed ESTHER: Clark_2007_Nature_450_203 PubMedSearch: Clark 2007 Nature 450 203 PubMedID: 17994087 Gene_locus related to this paper: droan-ACHE, droan-b3lx10, droan-b3lx75, droan-b3lxv7, droan-b3ly87, droan-b3lyh4, droan-b3lyh5, droan-b3lyh7, droan-b3lyh9, droan-b3lyi0, droan-b3lyi2, droan-b3lyi3, droan-b3lyi4, droan-b3lyj8, droan-b3lyj9, droan-b3lyx4, droan-b3lyx5, droan-b3lyx6, droan-b3lyx7, droan-b3lyx9, droan-b3lz72, droan-b3m1x3, droan-b3m2d4, droan-b3m3d9, droan-b3m4e3, droan-b3m5w1, droan-b3m6i7, droan-b3m7v2, droan-b3m9a5, droan-b3m9f4, droan-b3m9p3, droan-b3m254, droan-b3m259, droan-b3m260, droan-b3m262, droan-b3m524, droan-b3m635, droan-b3m845, droan-b3m846, droan-b3md01, droan-b3mdh7, droan-b3mdm6, droan-b3mdw8, droan-b3mee1, droan-b3mf47, droan-b3mf48, droan-b3mg94, droan-b3mgk2, droan-b3mgn6, droan-b3mii3, droan-b3mjk2, droan-b3mjk3, droan-b3mjk4, droan-b3mjk5, droan-b3mjl2, droan-b3mjl4, droan-b3mjl7, droan-b3mjl9, droan-b3mjm8, droan-b3mjm9, droan-b3mjs6, droan-b3mkr0, droan-b3ml20, droan-b3mly4, droan-b3mly5, droan-b3mly6, droan-b3mmm8, droan-b3mnb5, droan-b3mny9, droan-b3mtj5, droan-b3muw4, droan-b3muw8, droan-b3n0e7, droan-b3n2j7, droan-b3n247, droan-c5idb2, droer-ACHE, droer-b3n5c7, droer-b3n5d0, droer-b3n5d8, droer-b3n5d9, droer-b3n5t7, droer-b3n5y4, droer-b3n7d2, droer-b3n7d3, droer-b3n7d4, droer-b3n7k8, droer-b3n8e4, droer-b3n8f7, droer-b3n8f8, droer-b3n9e1, droer-b3n319, droer-b3n547, droer-b3n549, droer-b3n558, droer-b3n560, droer-b3n577, droer-b3n612, droer-b3nar5, droer-b3nb91, droer-b3nct9, droer-b3nd53, droer-b3ndh9, droer-b3ndq8, droer-b3ne66, droer-b3ne67, droer-b3ne97, droer-b3nfk3, droer-b3nfq9, droer-b3nim7, droer-b3nkn2, droer-b3nm11, droer-b3nmh4, droer-b3nmy2, droer-b3npx2, droer-b3npx3, droer-b3nq76, droer-b3nqg9, droer-b3nqm8, droer-b3nr28, droer-b3nrd3, droer-b3nst4, droer-b3nwa7, droer-b3nyp5.1, droer-b3nyp5.2, droer-b3nyp6, droer-b3nyp7, droer-b3nyp8, droer-b3nyp9, droer-b3nyq3, droer-b3nz06, droer-b3nz14, droer-b3nzj0, droer-b3p0c0, droer-b3p0c1, droer-b3p0c2, droer-b3p2x6, droer-b3p2x7, droer-b3p2x9, droer-b3p2y1, droer-b3p2y2, droer-b3p6d4, droer-b3p6d5, droer-b3p6w3, droer-b3p7b4, droer-b3p7h9, droer-b3p152, droer-b3p486, droer-b3p487, droer-b3p488, droer-b3p489, droer-EST6, droer-q670j5, drogr-ACHE, drogr-b4iwp3, drogr-b4iww3, drogr-b4iwy3, drogr-b4ixf7, drogr-b4ixh4, drogr-b4iyz5, drogr-b4j2s2, drogr-b4j2u8, drogr-b4j3u1, drogr-b4j3v3, drogr-b4j4g7, drogr-b4j4x9, drogr-b4j6e6, drogr-b4j9c9, drogr-b4j9y4, drogr-b4j156, drogr-b4j384, drogr-b4j605, drogr-b4j685, drogr-b4ja76, drogr-b4jay5, drogr-b4jcf0, drogr-b4jcf1, drogr-b4jdg6, drogr-b4jdg7, drogr-b4jdh6, drogr-b4jdz1, drogr-b4jdz2, drogr-b4jdz4, drogr-b4je66, drogr-b4je79, drogr-b4je82, drogr-b4je88, drogr-b4je89, drogr-b4je90, drogr-b4je91, drogr-b4jf76, drogr-b4jf79, drogr-b4jf80, drogr-b4jf81, drogr-b4jf82, drogr-b4jf83, drogr-b4jf84, drogr-b4jf85, drogr-b4jf87, drogr-b4jf91, drogr-b4jf92, drogr-b4jg66, drogr-b4jgh0, drogr-b4jgh1, drogr-b4jgr9, drogr-b4ji67, drogr-b4jls2, drogr-b4jnh9, drogr-b4jpc6, drogr-b4jpq3, drogr-b4jpx9, drogr-b4jql2, drogr-b4jrh5, drogr-b4jsb2, drogr-b4jth3, drogr-b4jti1, drogr-b4jul5, drogr-b4jur4, drogr-b4jvh3, drogr-b4jz00, drogr-b4jz03, drogr-b4jz04, drogr-b4jz05, drogr-b4jzh2, drogr-b4k0u2, drogr-b4k2r1, drogr-b4k234, drogr-b4k235, drome-BEM46, drome-CG3734, drome-CG9953, drome-CG11626, drome-GH02439, dromo-ACHE, dromo-b4k6a7, dromo-b4k6a8, dromo-b4k6q8, dromo-b4k6q9, dromo-b4k6r1, dromo-b4k6r3, dromo-b4k6r4, dromo-b4k6r5, dromo-b4k6r6, dromo-b4k6r7, dromo-b4k6r8, dromo-b4k6r9, dromo-b4k6s0, dromo-b4k6s1, dromo-b4k6s2, dromo-b4k9c7, dromo-b4k9d3, dromo-b4k571, dromo-b4k721, dromo-b4ka74, dromo-b4ka89, dromo-b4kaj4, dromo-b4kc20, dromo-b4kcl2, dromo-b4kcl3, dromo-b4kd55.1, dromo-b4kd55.2, dromo-b4kd56, dromo-b4kd57, dromo-b4kde1, dromo-b4kdg2, dromo-b4kdh4, dromo-b4kdh5, dromo-b4kdh6, dromo-A0A0Q9XDF2, dromo-b4kdh8.1, dromo-b4kdh8.2, dromo-b4kg04, dromo-b4kg05, dromo-b4kg06, dromo-b4kg16, dromo-b4kg44, dromo-b4kg90, dromo-b4kh20, dromo-b4kh21, dromo-b4kht7, dromo-b4kid3, dromo-b4kik0, dromo-b4kjx0, dromo-b4kki1, dromo-b4kkp6, dromo-b4kkp8, dromo-b4kkq8, dromo-b4kkr0, dromo-b4kkr3, dromo-b4kkr4, dromo-b4kks0, dromo-b4kks1, dromo-b4kks2, dromo-b4kla1, dromo-b4klv8, dromo-b4knt4, dromo-b4kp08, dromo-b4kp16, dromo-b4kqa6, dromo-b4kqa7, dromo-b4kqa8, dromo-b4kqh1, dromo-b4kst4, dromo-b4ksy6, dromo-b4kt84, dromo-b4ktf5, dromo-b4ktf6, dromo-b4kvl3, dromo-b4kvw2, dromo-b4kwv4, dromo-b4kwv5, dromo-b4kxz6, dromo-b4ky12, dromo-b4ky36, dromo-b4ky44, dromo-b4kzu7, dromo-b4l0n8, dromo-b4l4u5, dromo-b4l6l9, dromo-b4l084, drope-ACHE, drope-b4g3s6, drope-b4g4p7, drope-b4g6v4, drope-b4g8m0, drope-b4g8n6, drope-b4g8n7, drope-b4g9p2, drope-b4g815, drope-b4g816, drope-b4gat7, drope-b4gav5, drope-b4gb05, drope-b4gc08, drope-b4gcr3, drope-b4gdk2, drope-b4gdl9, drope-b4gdv9, drope-b4gei8, drope-b4gei9, drope-b4gej0, drope-b4ghz9, drope-b4gj62, drope-b4gj64, drope-b4gj74, drope-b4gkf4, drope-b4gkv2, drope-b4gky9, drope-b4gl76, drope-b4glf3, drope-b4gmt3, drope-b4gmt7, drope-b4gmt9, drope-b4gmu2, drope-b4gmu3, drope-b4gmu4, drope-b4gmu5, drope-b4gmu6, drope-b4gmu7, drope-b4gmv1, drope-b4gn08, drope-b4gpa7, drope-b4gq13, drope-b4grh7, drope-b4gsf9, drope-b4gsw4, drope-b4gsw5, drope-b4gsx2, drope-b4gsx7, drope-b4gsy6, drope-b4gsy7, drope-b4guj8, drope-b4gw36, drope-b4gzc2, drope-b4gzc6, drope-b4gzc7, drope-b4h4p9, drope-b4h5l3, drope-b4h6a0, drope-b4h6a8, drope-b4h6a9, drope-b4h6b0, drope-b4h7m7, drope-b4h462, drope-b4h601, drope-b4h602, drope-b4hay1, drope-b4hb18, drope-est5a, drope-est5b, drope-est5c, drops-ACHE, drops-b5dhd2, drops-b5dk96, drops-b5dpe3, drops-b5drp9, drops-b5dwa7, drops-b5dwa8, drops-b5dz85, drops-b5dz86, drops-est5a, drops-est5b, drops-q29bq2, drops-q29dd7, drops-q29ew0, drops-q291d5, drops-q291e8, drops-q293n1, drops-q293n4, drops-q293n5, drops-q293n6, drops-q294n6, drops-q294n7, drops-q294n9, drops-q294p4, drose-b4he97, drose-b4hfu2, drose-b4hg54, drose-b4hga0, drose-b4hgu9, drose-b4hgv0, drose-b4hgv3, drose-b4hgv4, drose-b4hhm8, drose-b4hhs6, drose-b4hie4, drose-b4him9, drose-b4hk63, drose-b4hkj5, drose-b4hr07, drose-b4hr81, drose-b4hre7, drose-b4hs13, drose-b4hsj9, drose-b4hsk0, drose-b4hsm8, drose-b4hvr5, drose-b4hwr7, drose-b4hwr8, drose-b4hwr9, drose-b4hws6, drose-b4hws7, drose-b4hwt0, drose-b4hwt2, drose-b4hwu1, drose-b4hwu2, drose-b4hxs9, drose-b4hxu4, drose-b4hxz1, drose-b4hyp8, drose-b4hyp9, drose-b4hyq0, drose-b4hyz4, drose-b4hyz5, drose-b4i1k8, drose-b4i2f3, drose-b4i2w5, drose-b4i4u3, drose-b4i4u7, drose-b4i4u9, drose-b4i4v0, drose-b4i4v1, drose-b4i4v4, drose-b4i4v5, drose-b4i4v6, drose-b4i4v7, drose-b4i4v8, drose-b4i4w0, drose-b4i7s6, drose-b4i133, drose-b4i857, drose-b4iam7, drose-b4iam9, drose-b4iaq6, drose-b4icf6, drose-b4icf7, drose-b4id80, drose-b4ifc5, drose-b4ihv9, drose-b4iie9, drose-b4ilj8, drose-b4in13, drose-b4inj9, drosi-ACHE, drosi-aes04a, drosi-b4nsh8, drosi-b4q3d7, drosi-b4q4w5, drosi-b4q4y7, drosi-b4q6h6, drosi-b4q7u2, drosi-b4q7u3, drosi-b4q9c6, drosi-b4q9c7, drosi-b4q9d3, drosi-b4q9d4, drosi-b4q9r0, drosi-b4q9r1, drosi-b4q9r3, drosi-b4q9s2, drosi-b4q9s3, drosi-b4q429, drosi-b4q530, drosi-b4q734, drosi-b4q782, drosi-b4q783, drosi-b4q942, drosi-b4qet1, drosi-b4qfv6, drosi-b4qge5, drosi-b4qgh5, drosi-b4qgs5, drosi-b4qhf3, drosi-b4qhf4, drosi-b4qhi5, drosi-b4qjr2, drosi-b4qjr3, drosi-b4qjv6, drosi-b4qk23, drosi-b4qk51, drosi-b4qlt1, drosi-b4qlz9, drosi-b4qmn9, drosi-b4qrq7, drosi-b4qs01, drosi-b4qs57, drosi-b4qs82, drosi-b4qs83, drosi-b4qs84, drosi-b4qs85, drosi-b4qs86, drosi-b4qsq1, drosi-b4quk6, drosi-b4qvg5, drosi-b4qvg6, drosi-b4qzn2, drosi-b4qzn3, drosi-b4qzn5, drosi-b4qzn7, drosi-b4qzn8, drosi-b4qzp2, drosi-b4qzp3, drosi-b4qzp4, drosi-b4qzp5, drosi-b4qzp6, drosi-b4qzp7, drosi-b4r1a4, drosi-b4r025, drosi-b4r207, drosi-b4r662, drosi-este6, drosi-q670k8, drovi-ACHE, drovi-b4lev2, drovi-b4lf33, drovi-b4lf51, drovi-b4lg54, drovi-b4lg72, drovi-b4lgc6, drovi-b4lgd5, drovi-b4lgg0, drovi-b4lgk5, drovi-b4lgn2, drovi-b4lh17, drovi-b4lh18, drovi-b4lk43, drovi-b4ll59, drovi-b4ll60, drovi-b4llm5, drovi-b4lln3, drovi-b4lmk4, drovi-b4lmp0, drovi-b4lnr4, drovi-b4lp47, drovi-b4lpd0, drovi-b4lps0, drovi-b4lqc6, drovi-b4lr00, drovi-b4lrp6, drovi-b4lrw2, drovi-b4lse7, drovi-b4lse9, drovi-b4lsf0, drovi-b4lsn0, drovi-b4lsq5, drovi-b4lt32, drovi-b4ltr1, drovi-b4lui7, drovi-b4lui9, drovi-b4luj8, drovi-b4luk0, drovi-b4luk3, drovi-b4luk8, drovi-b4luk9, drovi-b4lul0, drovi-b4lve2, drovi-b4lxi9, drovi-b4lxj8, drovi-b4lyf3, drovi-b4lyq2, drovi-b4lyq3, drovi-b4lz07, drovi-b4lz13, drovi-b4lz14, drovi-b4lz15, drovi-b4m0j7, drovi-b4m0s0, drovi-b4m2b6, drovi-b4m4h7, drovi-b4m4h8, drovi-b4m4i0, drovi-b4m4i2, drovi-b4m4i3.A, drovi-b4m4i3.B, drovi-b4m4i4, drovi-b4m4i5, drovi-b4m4i6, drovi-b4m4i7, drovi-b4m4i8, drovi-b4m4i9, drovi-b4m4j2, drovi-b4m5a0, drovi-b4m5a1, drovi-b4m5a2, drovi-b4m6b9, drovi-b4m7k9, drovi-b4m9g9, drovi-b4m9h0, drovi-b4m564, drovi-b4m599, drovi-b4m918, drovi-b4mb87, drovi-b4mc71, drovi-b4mfa4, drowi-ACHE, drowi-b4mjb9, drowi-b4mkt7, drowi-b4mlc1, drowi-b4mp68, drowi-b4mqe9, drowi-b4mqf0.2, drowi-b4mqf1, drowi-b4mqf3, drowi-b4mqf4, drowi-b4mqf5, drowi-b4mqq6, drowi-b4mrd1, drowi-b4mrk3, drowi-b4mtl5, drowi-b4mug2, drowi-b4muj8, drowi-b4mv18, drowi-b4mw32, drowi-b4mw85, drowi-b4mwp2, drowi-b4mwp6, drowi-b4mwq5, drowi-b4mwr0, drowi-b4mwr8, drowi-b4mwr9, drowi-b4mwt1, drowi-b4mwz7, drowi-b4mxn5, drowi-b4my54, drowi-b4myg1, drowi-b4myh5, drowi-b4n0d4, drowi-b4n1a7, drowi-b4n1c8, drowi-b4n3s9, drowi-b4n3x7, drowi-b4n4x9, drowi-b4n4y0, drowi-b4n6m1, drowi-b4n6n0, drowi-b4n6n7, drowi-b4n6u6, drowi-b4n7s6, drowi-b4n7s7, drowi-b4n7s8, drowi-b4n899.1, drowi-b4n8a1, drowi-b4n8a2, drowi-b4n8a3, drowi-b4n8a4, drowi-b4n8a9, drowi-b4n023, drowi-b4n075, drowi-b4n543, drowi-b4n888, drowi-b4n889, drowi-b4n891, drowi-b4n893, drowi-b4n895, drowi-b4n897, drowi-b4n898, drowi-b4n899.2, drowi-b4nae3, drowi-b4ner8, drowi-b4ng76, drowi-b4nga7, drowi-b4ngb5, drowi-b4nhz9, drowi-b4nj18, drowi-b4nj19, drowi-b4nja7, drowi-b4nja8, drowi-b4nja9, drowi-b4njk8, drowi-b4nkc8, drowi-b4nky0, drowi-b4nl36, drowi-b4nm27, drowi-b4nn59, drowi-b4nnc1, drowi-b4nng1, drowi-b4nng2, droya-ACHE, droya-aes04, droya-b4itg2, droya-b4itg6, droya-b4itu9, droya-b4iuv4, droya-b4iuv5, droya-b4nxe6, droya-b4nxg5, droya-b4nxg6, droya-b4nxg8, droya-b4nxw4, droya-b4ny57, droya-b4ny58, droya-b4ny86, droya-b4nzz8, droya-b4p0b5, droya-b4p0q9, droya-b4p0r0, droya-b4p0r7, droya-b4p0r8, droya-b4p0r9, droya-b4p0s0, droya-b4p0s2, droya-b4p0t0, droya-b4p0t1, droya-b4p3h4, droya-b4p3x8, droya-b4p5g8, droya-b4p6c9, droya-b4p6l9, droya-b4p6r1, droya-b4p6r2, droya-b4p7u4, droya-b4p8w7, droya-b4p023, droya-b4p241, droya-b4p774, droya-b4pat9, droya-b4pbl1, droya-b4pd22, droya-b4pd70, droya-b4pdm8, droya-b4pet9, droya-b4pff9, droya-b4pga7, droya-b4pgu0, droya-b4pig3, droya-b4pjt8, droya-b4pka2, droya-b4plh2, droya-b4pma3, droya-b4pmv3, droya-b4pmv4, droya-b4pmv5, droya-b4pn92, droya-b4pp65, droya-b4ppc5, droya-b4ppc6, droya-b4ppc7, droya-b4ppc8, droya-b4pq03, droya-b4prg6B, droya-b4prg9, droya-b4prh3, droya-b4prh4, droya-b4prh6, droya-b4prh7, droya-b4psz8, droya-b4psz9, droya-b4pv22, droya-b4q0g5, droya-b4q246, droya-EST6, droya-q71d76, drowi-b4n7m9, drope-b4gkk1, droer-b3n5s3, drose-b4i1w5, drowi-a0a0q9x0t3, drogr-b4jvm7, dromo-b4ku70, drovi-b4mcn9, drovi-b4lty2, drogr-b4jdu1, drovi-a0a0q9wiq8, dromo-b4kf70, drosi-b2zi86, droya-b4p2y4, drose-b2zic5, droer-b3n895 Abstract Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species. Title: The DNA sequence, annotation and analysis of human chromosome 3 Muzny DM, Scherer SE, Kaul R, Wang J, Yu J, Sudbrak R, Buhay CJ, Chen R, Cree A and Gibbs RA <100 more author(s)> Muzny DM, Scherer SE, Kaul R, Wang J, Yu J, Sudbrak R, Buhay CJ, Chen R, Cree A, Ding Y, Dugan-Rocha S, Gill R, Gunaratne P, Harris RA, Hawes AC, Hernandez J, Hodgson AV, Hume J, Jackson A, Khan ZM, Kovar-Smith C, Lewis LR, Lozado RJ, Metzker ML, Milosavljevic A, Miner GR, Morgan MB, Nazareth LV, Scott G, Sodergren E, Song XZ, Steffen D, Wei S, Wheeler DA, Wright MW, Worley KC, Yuan Y, Zhang Z, Adams CQ, Ansari-Lari MA, Ayele M, Brown MJ, Chen G, Chen Z, Clendenning J, Clerc-Blankenburg KP, Davis C, Delgado O, Dinh HH, Dong W, Draper H, Ernst S, Fu G, Gonzalez-Garay ML, Garcia DK, Gillett W, Gu J, Hao B, Haugen E, Havlak P, He X, Hennig S, Hu S, Huang W, Jackson LR, Jacob LS, Kelly SH, Kube M, Levy R, Li Z, Liu B, Liu J, Liu W, Lu J, Maheshwari M, Nguyen BV, Okwuonu GO, Palmeiri A, Pasternak S, Perez LM, Phelps KA, Plopper FJ, Qiang B, Raymond C, Rodriguez R, Saenphimmachak C, Santibanez J, Shen H, Shen Y, Subramanian S, Tabor PE, Verduzco D, Waldron L, Wang Q, Williams GA, Wong GK, Yao Z, Zhang J, Zhang X, Zhao G, Zhou J, Zhou Y, Nelson D, Lehrach H, Reinhardt R, Naylor SL, Yang H, Olson M, Weinstock G, Gibbs RA (- 100) Ref: Nature, 440:1194, 2006 : PubMed ESTHER: Muzny_2006_Nature_440_1194 PubMedSearch: Muzny 2006 Nature 440 1194 PubMedID: 16641997 Gene_locus related to this paper: human-AADAC, human-AADACL2, human-ABHD5, human-ABHD6, human-ABHD10, human-ABHD14A, human-APEH, human-BCHE, human-CIB, human-LIPH, human-MGLL, human-NLGN1, human-PLA1A Abstract After the completion of a draft human genome sequence, the International Human Genome Sequencing Consortium has proceeded to finish and annotate each of the 24 chromosomes comprising the human genome. Here we describe the sequencing and analysis of human chromosome 3, one of the largest human chromosomes. Chromosome 3 comprises just four contigs, one of which currently represents the longest unbroken stretch of finished DNA sequence known so far. The chromosome is remarkable in having the lowest rate of segmental duplication in the genome. It also includes a chemokine receptor gene cluster as well as numerous loci involved in multiple human cancers such as the gene encoding FHIT, which contains the most common constitutive fragile site in the genome, FRA3B. Using genomic sequence from chimpanzee and rhesus macaque, we were able to characterize the breakpoints defining a large pericentric inversion that occurred some time after the split of Homininae from Ponginae, and propose an evolutionary history of the inversion. Title: The Genomes of Oryza sativa: a history of duplications Yu J, Wang J, Lin W, Li S, Li H, Zhou J, Ni P, Dong W, Hu S and Yang H <88 more author(s)> Yu J, Wang J, Lin W, Li S, Li H, Zhou J, Ni P, Dong W, Hu S, Zeng C, Zhang J, Zhang Y, Li R, Xu Z, Li X, Zheng H, Cong L, Lin L, Yin J, Geng J, Li G, Shi J, Liu J, Lv H, Li J, Deng Y, Ran L, Shi X, Wang X, Wu Q, Li C, Ren X, Li D, Liu D, Zhang X, Ji Z, Zhao W, Sun Y, Zhang Z, Bao J, Han Y, Dong L, Ji J, Chen P, Wu S, Xiao Y, Bu D, Tan J, Yang L, Ye C, Xu J, Zhou Y, Yu Y, Zhang B, Zhuang S, Wei H, Liu B, Lei M, Yu H, Li Y, Xu H, Wei S, He X, Fang L, Huang X, Su Z, Tong W, Tong Z, Ye J, Wang L, Lei T, Chen C, Chen H, Huang H, Zhang F, Li N, Zhao C, Huang Y, Li L, Xi Y, Qi Q, Li W, Hu W, Tian X, Jiao Y, Liang X, Jin J, Gao L, Zheng W, Hao B, Liu S, Wang W, Yuan L, Cao M, McDermott J, Samudrala R, Wong GK, Yang H (- 88) Ref: PLoS Biol, 3:e38, 2005 : PubMed ESTHER: Yu_2005_PLoS.Biol_3_e38 PubMedSearch: Yu 2005 PLoS.Biol 3 e38 PubMedID: 15685292 Gene_locus related to this paper: orysa-Q7XTC5, orysa-Q852M6, orysa-Q8GSE8, orysa-Q9S7P1, orysa-Q9FYP7, orysa-Q5ZBH3, orysa-Q5ZA26, orysa-Q5JLP6, orysa-Q8H5P9, orysa-Q8H5P5, orysa-Q7F1Y5, orysa-Q949C9, orysa-cbp1, orysa-cbp3, orysa-cbpx, orysa-Q33B71, orysa-Q8GSJ3, orysa-LPL1, orysa-Q6YSZ8, orysa-Q8S5X5, orysa-Q8LIG3, orysa-Q6K7F5, orysa-Q7F1B1, orysa-Q8H4S9, orysa-Q69UB1, orysa-Q9FW17, orysa-Q337C3, orysa-Q7F959, orysa-Q84QZ6, orysa-Q84QY7, orysa-Q851E3, orysa-Q6YTH5, orysa-Q0JK71, orysa-Q8S1D9, orysa-Q5N8V4, orysa-Q0JCY4, orysa-Q8GTK2, orysa-B9EWJ8, orysa-Q8H3K6, orysa-Q6ZDG8, orysa-Q6ZDG6, orysa-Q6ZDG5, orysa-Q6ZDG4, orysa-Q5NAI4, orysa-Q658B2, orysa-Q5JMQ8, orysa-Q5QMD9, orysa-Q5N7L1, orysa-Q8RYV9, orysa-Q8H3R3, orysa-Q5SNH3, orysa-Q8W0F0, orysa-pir7a, orysa-pir7b, orysa-q2qlm4, orysa-q2qm78, orysa-q2qm82, orysa-q2qn31, orysa-q2qnj4, orysa-q2qnt9, orysa-q2qur1, orysa-q2qx94, orysa-q2qyi1, orysa-q2qyj1, orysa-q2r051, orysa-q2r077, orysa-q2ram0, orysa-q2rat1, orysa-q2rbb3, orysa-Q4VWY7, orysa-q5na00, orysa-q5nbu1, orysa-Q5QLC0, orysa-q5smv5, orysa-Q5VP27, orysa-q5vrt2, orysa-q5w6c5, orysa-q5z5a3, orysa-q5z9i2, orysa-q5z417, orysa-q5z901, orysa-Q5ZAM8, orysa-Q5ZBI5, orysa-Q5ZCR3, orysa-q6atz0, orysa-q6ave2, orysa-q6f358, orysa-q6h6s1, orysa-q6h7i6, orysa-q6i5q3, orysa-q6i5u7, orysa-q6j657, orysa-q6k3d9, orysa-q6k4q2, orysa-q6k880, orysa-q6l5b6, orysa-Q6L5F5, orysa-q6l556, orysj-q6yse8, orysa-q6yy42, orysa-q6yzk1, orysa-q6z8b1, orysa-q6z995, orysa-q6zc62, orysa-q6zia4, orysa-q6zjq6, orysa-q7x7y5, orysa-Q7XC50, orysa-q7xej4, orysa-q7xem8, orysa-q7xkj9, orysa-q7xr62, orysa-q7xr63, orysa-q7xr64, orysa-q7xsg1, orysa-q7xsq2, orysa-q7xts6, orysa-q7xv53, orysa-Q7XVB5, orysa-Q8L562, orysa-Q8LQS5, orysa-Q8RZ40, orysa-Q8RZ79, orysa-Q8S0U8, orysa-Q8S0V0, orysa-Q8S125, orysa-Q8SAY7, orysa-Q8SAY9, orysa-Q8W3C6, orysa-Q8W3F2, orysa-Q8W3F4, orysa-Q8W3F6, orysa-Q9LHX5, orysa-q33aq0, orysa-q53lh1, orysa-q53m20, orysa-q53nd8, orysa-q60e79, orysa-q60ew8, orysa-q67iz2, orysa-q67iz3, orysa-q67iz7, orysa-q67iz8, orysa-q67j02, orysa-q67j05, orysa-q67j07, orysa-q67j09, orysa-q67j10, orysa-q67tr6, orysa-q67tv0, orysa-q67uz1, orysa-q67v34, orysa-q67wz5, orysa-q69j38, orysa-q69k08, orysa-q69md7, orysa-q69me0, orysa-q69pf3, orysa-q69ti3, orysa-q69xr2, orysa-q69y12, orysa-q69y21, orysa-q75hy2, orysa-q75i01, orysa-Q94JD7, orysa-Q0J0A4, orysa-q651a8, orysa-q651z3, orysa-q652g4, orysa-q688m0, orysa-q688m8, orysa-q688m9, orysa-Q6H8G1, orysi-a2wn01, orysi-a2xc83, orysi-a2yh83, orysi-a2z179, orysi-a2zef2, orysi-b8a7e6, orysi-b8a7e7, orysi-b8bfe5, orysi-b8bhp9, orysj-a3b9l8, orysj-b9eub8, orysj-b9eya5, orysj-b9fi05, orysj-b9fkb0, orysj-b9fn42, orysj-b9gbb7, orysj-cgep, orysj-PLA7, orysj-q0d4u5, orysj-q0djj0, orysj-q0jaf0, orysj-q5jl22, orysj-q5jlw7, orysj-q5z419, orysj-q6h7q9, orysj-q6yvk6, orysj-q6z6i1, orysj-q7f8x1, orysj-q7xcx3, orysj-q9fwm6, orysj-q10j20, orysj-q10ss2, orysj-q69uw6, orysj-q94d71, orysj-q338c0, orysi-b8bly4, orysj-b9gbs4, orysi-a2zb88, orysj-b9gbs1, orysi-b8b698, orysj-pla4, orysj-pla1 Abstract We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000-40,000. Only 2%-3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family. Title: Apolipoprotein E4 inhibits, and apolipoprotein E3 promotes neurite outgrowth in cultured adult mouse cortical neurons through the low-density lipoprotein receptor-related protein Nathan BP, Jiang Y, Wong GK, Shen F, Brewer GJ, Struble RG Ref: Brain Research, 928:96, 2002 : PubMed ESTHER: Nathan_2002_Brain.Res_928_96 PubMedSearch: Nathan 2002 Brain.Res 928 96 PubMedID: 11844476 Abstract The apolipoprotein E4 (apoE4) genotype is a major risk factor for Alzheimer's disease (AD); however, the mechanism is unknown. We previously demonstrated that apoE isoforms differentially modulated neurite outgrowth in embryonic neurons and in neuronal cell lines. ApoE3 increased neurite outgrowth whereas apoE4 decreased outgrowth, suggesting that apoE4 may directly affect neurons in the brain. In the present study we examined the effects of apoE on neurite outgrowth from cultured adult mouse cortical neurons to examine if adult neurons respond the same way that embryonic cells do. The results from this study demonstrated that (1) cortical neurons derived from adult apoE-gene knockout (apoE KO) mice have significantly shorter neurites than neurons from adult wild-type (WT) mice; (2) incubation of cortical neurons from adult apoE KO mice with human apoE3 increased neurite outgrowth, whereas human apoE4 decreased outgrowth in a dose-dependent fashion; (3) the isoform specific effects were abolished by incubation of the neurons with either receptor associated protein (RAP) or lactoferrin, both of which block the interaction of apoE-containing lipoproteins with the low-density lipoprotein receptor-related protein (LRP). These data suggest a potential mechanism whereby apoE4 may play a role in regenerative failure and accelerate the development of AD. Title: Apolipoprotein E is upregulated in olfactory bulb glia following peripheral receptor lesion in mice Nathan BP, Nisar R, Randall S, Short J, Sherrow M, Wong GK, Struble RG Ref: Experimental Neurology, 172:128, 2001 : PubMed ESTHER: Nathan_2001_Exp.Neurol_172_128 PubMedSearch: Nathan 2001 Exp.Neurol 172 128 PubMedID: 11681846 Abstract Apolipoprotein E (apoE), a lipid transporting protein, has been postulated to participate in nerve regeneration. To better clarify apoE function in the olfactory system, we evaluated the amount and distribution of apoE in the olfactory bulb following olfactory nerve lesion in mice. Olfactory nerve was lesioned in 2- to 4-month-old mice by intranasal irrigation with Triton X-100. Olfactory bulbs were collected at 0, 3, 7, 21, 42, and 56 days postlesion, and both apoE concentrations and apoE distribution were determined. ApoE levels, as determined by immunoblot analysis, were twofold greater than normal during nerve degeneration at 3 days. ApoE levels remained elevated by approximately 1.5 times normal levels at 7 through 21 days after injury and returned to baseline by 56 days. Immunocytochemical studies supported these observations. ApoE immunoreactivity was prominent on the olfactory nerve at 3 days after lesion and decreased to baseline levels at later time periods. Double-labeling immunocytochemical studies confirmed that both reactive astroglia and microglia produced detectable amounts of apoE following the lesion. Return of apoE expression to baseline paralleled measures of olfactory nerve maturation as measured by olfactory marker protein. These data suggest that apoE increases concurrent with nerve degeneration. ApoE may facilitate efficient regeneration perhaps by recycling lipids from degenerating fibers for use by growing axons. The association of apoE genotype with dementing illnesses may represent a diminished ability to support a lifetime of nerve regeneration. Title: Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen Stover CK, Pham XQ, Erwin AL, Mizoguchi SD, Warrener P, Hickey MJ, Brinkman FS, Hufnagle WO, Kowalik DJ and Olson MV <21 more author(s)> Stover CK, Pham XQ, Erwin AL, Mizoguchi SD, Warrener P, Hickey MJ, Brinkman FS, Hufnagle WO, Kowalik DJ, Lagrou M, Garber RL, Goltry L, Tolentino E, Westbrock-Wadman S, Yuan Y, Brody LL, Coulter SN, Folger KR, Kas A, Larbig K, Lim R, Smith K, Spencer D, Wong GK, Wu Z, Paulsen IT, Reizer J, Saier MH, Hancock RE, Lory S, Olson MV (- 21) Ref: Nature, 406:959, 2000 : PubMed ESTHER: Stover_2000_Nature_406_959 PubMedSearch: Stover 2000 Nature 406 959 PubMedID: 10984043 Gene_locus related to this paper: pseae-clipa, pseae-CPO, pseae-metx, pseae-PA0201, pseae-PA0231, pseae-PA0308, pseae-PA0368, pseae-PA0480, pseae-PA0502, pseae-PA0543, pseae-PA0599, pseae-PA0829, pseae-PA1166, pseae-PA1211, pseae-PA1239, pseae-PA1291, pseae-PA1304, pseae-PA1510, pseae-PA1558, pseae-PA1597, pseae-PA1621, pseae-PA1622, pseae-PA1680, pseae-PA1771, pseae-PA1888, pseae-PA1907, pseae-PA1990, pseae-PA2086, pseae-PA2098, pseae-PA2168, pseae-PA2302, pseae-PA2411, pseae-PA2425, pseae-PA2451, pseae-PA2540, pseae-PA2682, pseae-PA2689, pseae-PA2745, pseae-PA2764, pseae-PA2927, pseae-PA2934, pseae-PA2949, pseae-PA3053, pseae-PA3132, pseae-PA3226, pseae-PA3301, pseae-PA3324, pseae-PA3327, pseae-PA3429, pseae-PA3509, pseae-PA3586, pseae-PA3628, pseae-PA3695, pseae-PA3734, pseae-PA3829, pseae-PA3859, pseae-PA3994, pseae-PA4008, pseae-PA4152, pseae-PA4440, pseae-PA4968, pseae-PA5080, pseae-PA5384, pseae-PA5513, pseae-PCHC, pseae-PCHF, pseae-PHAC1, pseae-PHAC2, pseae-phaD, pseae-phag, pseae-PVDD, pseae-q9i4b9, pseae-q9i538, pseae-rhla, pseae-Y2218, pseae-q9hyv3, pseae-q9i252, pseae-q9i6m9 Abstract Pseudomonas aeruginosa is a ubiquitous environmental bacterium that is one of the top three causes of opportunistic human infections. A major factor in its prominence as a pathogen is its intrinsic resistance to antibiotics and disinfectants. Here we report the complete sequence of P. aeruginosa strain PAO1. At 6.3 million base pairs, this is the largest bacterial genome sequenced, and the sequence provides insights into the basis of the versatility and intrinsic drug resistance of P. aeruginosa. Consistent with its larger genome size and environmental adaptability, P. aeruginosa contains the highest proportion of regulatory genes observed for a bacterial genome and a large number of genes involved in the catabolism, transport and efflux of organic compounds as well as four potential chemotaxis systems. We propose that the size and complexity of the P. aeruginosa genome reflect an evolutionary adaptation permitting it to thrive in diverse environments and resist the effects of a variety of antimicrobial substances. | |||||||
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