Couronne O

References (4)

Title : Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution - Richards_2005_Genome.Res_15_1
Author(s) : Richards S , Liu Y , Bettencourt BR , Hradecky P , Letovsky S , Nielsen R , Thornton K , Hubisz MJ , Chen R , Meisel RP , Couronne O , Hua S , Smith MA , Zhang P , Liu J , Bussemaker HJ , van Batenburg MF , Howells SL , Scherer SE , Sodergren E , Matthews BB , Crosby MA , Schroeder AJ , Ortiz-Barrientos D , Rives CM , Metzker ML , Muzny DM , Scott G , Steffen D , Wheeler DA , Worley KC , Havlak P , Durbin KJ , Egan A , Gill R , Hume J , Morgan MB , Miner G , Hamilton C , Huang Y , Waldron L , Verduzco D , Clerc-Blankenburg KP , Dubchak I , Noor MA , Anderson W , White KP , Clark AG , Schaeffer SW , Gelbart W , Weinstock GM , Gibbs RA
Ref : Genome Res , 15 :1 , 2005
Abstract : We have sequenced the genome of a second Drosophila species, Drosophila pseudoobscura, and compared this to the genome sequence of Drosophila melanogaster, a primary model organism. Throughout evolution the vast majority of Drosophila genes have remained on the same chromosome arm, but within each arm gene order has been extensively reshuffled, leading to a minimum of 921 syntenic blocks shared between the species. A repetitive sequence is found in the D. pseudoobscura genome at many junctions between adjacent syntenic blocks. Analysis of this novel repetitive element family suggests that recombination between offset elements may have given rise to many paracentric inversions, thereby contributing to the shuffling of gene order in the D. pseudoobscura lineage. Based on sequence similarity and synteny, 10,516 putative orthologs have been identified as a core gene set conserved over 25-55 million years (Myr) since the pseudoobscura/melanogaster divergence. Genes expressed in the testes had higher amino acid sequence divergence than the genome-wide average, consistent with the rapid evolution of sex-specific proteins. Cis-regulatory sequences are more conserved than random and nearby sequences between the species--but the difference is slight, suggesting that the evolution of cis-regulatory elements is flexible. Overall, a pattern of repeat-mediated chromosomal rearrangement, and high coadaptation of both male genes and cis-regulatory sequences emerges as important themes of genome divergence between these species of Drosophila.
ESTHER : Richards_2005_Genome.Res_15_1
PubMedSearch : Richards_2005_Genome.Res_15_1
PubMedID: 15632085
Gene_locus related to this paper: drome-BEM46 , drome-GH02439 , drops-ACHE , drops-b5dhd2 , drops-b5di70 , drops-b5djn7 , drops-b5dk96 , drops-b5dm12 , drops-b5dpe3 , drops-b5drp9 , drops-b5du62 , drops-b5dud8 , drops-b5dwa7 , drops-b5dwa8 , drops-b5dy09 , drops-b5dz85 , drops-b5dz86 , drops-b5e1k7 , drops-CG4390 , drops-est5a , drops-est5b , drops-est5c , drops-nrtac , drops-q2lyp3 , drops-q2lyp4 , drops-q2lyu3 , drops-q2lz68 , drops-q2m0u9 , drops-q2m169 , drops-q28wj5 , drops-q28wt2 , drops-q28wt8 , drops-q28zi3 , drops-q28zz1 , drops-q29a22 , drops-q29ad8 , drops-q29ad9 , drops-q29ae0 , drops-q29ae1 , drops-q29ay7 , drops-q29ay8 , drops-q29ay9 , drops-q29bq2 , drops-q29br3 , drops-q29d59 , drops-q29dc9 , drops-q29dd7 , drops-q29dp4 , drops-q29dw3 , drops-q29dw4 , drops-q29e16 , drops-q29ew0 , drops-q29f35 , drops-q29f66 , drops-q29fi0 , drops-q29fw0 , drops-q29fw9 , drops-q29g93 , drops-q29gb0 , drops-q29gs6 , drops-q29h54 , drops-b5dmp7 , drops-q29hd2 , drops-q29hu2 , drops-q29hu3 , drops-q29hv0 , drops-q29i09 , drops-q29js9 , drops-q29jt5 , drops-q29jt6 , drops-q29jy5 , drops-q29k25 , drops-q29kd5 , drops-q29kd6 , drops-q29ke5 , drops-q29kq9 , drops-q29kr1 , drops-q29kr3 , drops-q29kr5 , drops-q29kr8 , drops-q29kr9 , drops-q29ks6 , drops-q29kz0 , drops-q29kz1 , drops-q29l31 , drops-q29lf8 , drops-q29lv0 , drops-q29m07 , drops-q29m08 , drops-q29m27 , drops-q29m66 , drops-q29m81 , drops-q29mj7 , drops-q29mv2 , drops-q29mx0 , drops-q29n87 , drops-q29na5 , drops-q29na6 , drops-q29pe4 , drops-q29pk4 , drops-q290i1 , drops-q290k3 , drops-q290v8 , drops-q290v9 , drops-q290w0 , drops-q290z8 , drops-q291d5 , drops-q291e8 , drops-q291y3 , drops-q292f5 , drops-q292g6 , drops-q293n1 , drops-q293n4 , drops-q293n5 , drops-q293n6 , drops-q293y7 , drops-q294n3 , drops-q294n6 , drops-q294n7 , drops-q294n9 , drops-q294p0 , drops-q294p1 , drops-q294p3 , drops-q294p4 , drops-q294u9 , drops-q295h3 , drops-q296h2 , drops-q296x1 , drops-q296x2 , drops-q297h5 , drops-q298u8 , drope-b4gkk1

Title : The DNA sequence and biology of human chromosome 19 - Grimwood_2004_Nature_428_529
Author(s) : Grimwood J , Gordon LA , Olsen A , Terry A , Schmutz J , Lamerdin J , Hellsten U , Goodstein D , Couronne O , Tran-Gyamfi M , Aerts A , Altherr M , Ashworth L , Bajorek E , Black S , Branscomb E , Caenepeel S , Carrano A , Caoile C , Chan YM , Christensen M , Cleland CA , Copeland A , Dalin E , Dehal P , Denys M , Detter JC , Escobar J , Flowers D , Fotopulos D , Garcia C , Georgescu AM , Glavina T , Gomez M , Gonzales E , Groza M , Hammon N , Hawkins T , Haydu L , Ho I , Huang W , Israni S , Jett J , Kadner K , Kimball H , Kobayashi A , Larionov V , Leem SH , Lopez F , Lou Y , Lowry S , Malfatti S , Martinez D , McCready P , Medina C , Morgan J , Nelson K , Nolan M , Ovcharenko I , Pitluck S , Pollard M , Popkie AP , Predki P , Quan G , Ramirez L , Rash S , Retterer J , Rodriguez A , Rogers S , Salamov A , Salazar A , She X , Smith D , Slezak T , Solovyev V , Thayer N , Tice H , Tsai M , Ustaszewska A , Vo N , Wagner M , Wheeler J , Wu K , Xie G , Yang J , Dubchak I , Furey TS , DeJong P , Dickson M , Gordon D , Eichler EE , Pennacchio LA , Richardson P , Stubbs L , Rokhsar DS , Myers RM , Rubin EM , Lucas SM
Ref : Nature , 428 :529 , 2004
Abstract : Chromosome 19 has the highest gene density of all human chromosomes, more than double the genome-wide average. The large clustered gene families, corresponding high G + C content, CpG islands and density of repetitive DNA indicate a chromosome rich in biological and evolutionary significance. Here we describe 55.8 million base pairs of highly accurate finished sequence representing 99.9% of the euchromatin portion of the chromosome. Manual curation of gene loci reveals 1,461 protein-coding genes and 321 pseudogenes. Among these are genes directly implicated in mendelian disorders, including familial hypercholesterolaemia and insulin-resistant diabetes. Nearly one-quarter of these genes belong to tandemly arranged families, encompassing more than 25% of the chromosome. Comparative analyses show a fascinating picture of conservation and divergence, revealing large blocks of gene orthology with rodents, scattered regions with more recent gene family expansions and deletions, and segments of coding and non-coding conservation with the distant fish species Takifugu.
ESTHER : Grimwood_2004_Nature_428_529
PubMedSearch : Grimwood_2004_Nature_428_529
PubMedID: 15057824

Title : Genome sequence of the Brown Norway rat yields insights into mammalian evolution - Gibbs_2004_Nature_428_493
Author(s) : Gibbs RA , Weinstock GM , Metzker ML , Muzny DM , Sodergren EJ , Scherer S , Scott G , Steffen D , Worley KC , Burch PE , Okwuonu G , Hines S , Lewis L , DeRamo C , Delgado O , Dugan-Rocha S , Miner G , Morgan M , Hawes A , Gill R , Celera , Holt RA , Adams MD , Amanatides PG , Baden-Tillson H , Barnstead M , Chin S , Evans CA , Ferriera S , Fosler C , Glodek A , Gu Z , Jennings D , Kraft CL , Nguyen T , Pfannkoch CM , Sitter C , Sutton GG , Venter JC , Woodage T , Smith D , Lee HM , Gustafson E , Cahill P , Kana A , Doucette-Stamm L , Weinstock K , Fechtel K , Weiss RB , Dunn DM , Green ED , Blakesley RW , Bouffard GG , de Jong PJ , Osoegawa K , Zhu B , Marra M , Schein J , Bosdet I , Fjell C , Jones S , Krzywinski M , Mathewson C , Siddiqui A , Wye N , McPherson J , Zhao S , Fraser CM , Shetty J , Shatsman S , Geer K , Chen Y , Abramzon S , Nierman WC , Havlak PH , Chen R , Durbin KJ , Egan A , Ren Y , Song XZ , Li B , Liu Y , Qin X , Cawley S , Cooney AJ , D'Souza LM , Martin K , Wu JQ , Gonzalez-Garay ML , Jackson AR , Kalafus KJ , McLeod MP , Milosavljevic A , Virk D , Volkov A , Wheeler DA , Zhang Z , Bailey JA , Eichler EE , Tuzun E , Birney E , Mongin E , Ureta-Vidal A , Woodwark C , Zdobnov E , Bork P , Suyama M , Torrents D , Alexandersson M , Trask BJ , Young JM , Huang H , Wang H , Xing H , Daniels S , Gietzen D , Schmidt J , Stevens K , Vitt U , Wingrove J , Camara F , Mar Alba M , Abril JF , Guigo R , Smit A , Dubchak I , Rubin EM , Couronne O , Poliakov A , Hubner N , Ganten D , Goesele C , Hummel O , Kreitler T , Lee YA , Monti J , Schulz H , Zimdahl H , Himmelbauer H , Lehrach H , Jacob HJ , Bromberg S , Gullings-Handley J , Jensen-Seaman MI , Kwitek AE , Lazar J , Pasko D , Tonellato PJ , Twigger S , Ponting CP , Duarte JM , Rice S , Goodstadt L , Beatson SA , Emes RD , Winter EE , Webber C , Brandt P , Nyakatura G , Adetobi M , Chiaromonte F , Elnitski L , Eswara P , Hardison RC , Hou M , Kolbe D , Makova K , Miller W , Nekrutenko A , Riemer C , Schwartz S , Taylor J , Yang S , Zhang Y , Lindpaintner K , Andrews TD , Caccamo M , Clamp M , Clarke L , Curwen V , Durbin R , Eyras E , Searle SM , Cooper GM , Batzoglou S , Brudno M , Sidow A , Stone EA , Payseur BA , Bourque G , Lopez-Otin C , Puente XS , Chakrabarti K , Chatterji S , Dewey C , Pachter L , Bray N , Yap VB , Caspi A , Tesler G , Pevzner PA , Haussler D , Roskin KM , Baertsch R , Clawson H , Furey TS , Hinrichs AS , Karolchik D , Kent WJ , Rosenbloom KR , Trumbower H , Weirauch M , Cooper DN , Stenson PD , Ma B , Brent M , Arumugam M , Shteynberg D , Copley RR , Taylor MS , Riethman H , Mudunuri U , Peterson J , Guyer M , Felsenfeld A , Old S , Mockrin S , Collins F
Ref : Nature , 428 :493 , 2004
Abstract : The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.
ESTHER : Gibbs_2004_Nature_428_493
PubMedSearch : Gibbs_2004_Nature_428_493
PubMedID: 15057822
Gene_locus related to this paper: rat-abhea , rat-abheb , rat-cd029 , rat-d3zaw4 , rat-dpp9 , rat-d3zhq1 , rat-d3zkp8 , rat-d3zuq1 , rat-d3zxw8 , rat-d4a4w4 , rat-d4a7w1 , rat-d4a9l7 , rat-d4a071 , rat-d4aa31 , rat-d4aa33 , rat-d4aa61 , rat-dglb , rat-f1lz91 , rat-Kansl3 , rat-nceh1 , rat-Tex30 , ratno-1hlip , ratno-1neur , ratno-1plip , ratno-2neur , ratno-3neur , ratno-3plip , ratno-ABH15 , ratno-ACHE , ratno-balip , ratno-BCHE , ratno-cauxin , ratno-Ces1d , ratno-Ces1e , ratno-Ces2f , ratno-d3ze31 , ratno-d3zp14 , ratno-d3zxi3 , ratno-d3zxq0 , ratno-d3zxq1 , ratno-d4a3d4 , ratno-d4aa05 , ratno-dpp4 , ratno-dpp6 , ratno-est8 , ratno-FAP , ratno-hyep , ratno-hyes , ratno-kmcxe , ratno-lmcxe , ratno-LOC246252 , ratno-MGLL , ratno-pbcxe , ratno-phebest , ratno-Ppgb , ratno-q4qr68 , ratno-q6ayr2 , ratno-q6q629 , ratno-SPG21 , ratno-thyro , rat-m0rc77 , rat-a0a0g2k9y7 , rat-a0a0g2kb83 , rat-d3zba8 , rat-d3zbj1 , rat-d3zcr8 , rat-d3zxw5 , rat-d4a340 , rat-f1lvg7 , rat-m0r509 , rat-m0r5d4 , rat-b5den3 , rat-d3zxk4 , rat-d4a1b6 , rat-d3zmg4 , rat-ab17c

Title : The sequence and analysis of duplication-rich human chromosome 16 - Martin_2004_Nature_432_988
Author(s) : Martin J , Han C , Gordon LA , Terry A , Prabhakar S , She X , Xie G , Hellsten U , Chan YM , Altherr M , Couronne O , Aerts A , Bajorek E , Black S , Blumer H , Branscomb E , Brown NC , Bruno WJ , Buckingham JM , Callen DF , Campbell CS , Campbell ML , Campbell EW , Caoile C , Challacombe JF , Chasteen LA , Chertkov O , Chi HC , Christensen M , Clark LM , Cohn JD , Denys M , Detter JC , Dickson M , Dimitrijevic-Bussod M , Escobar J , Fawcett JJ , Flowers D , Fotopulos D , Glavina T , Gomez M , Gonzales E , Goodstein D , Goodwin LA , Grady DL , Grigoriev I , Groza M , Hammon N , Hawkins T , Haydu L , Hildebrand CE , Huang W , Israni S , Jett J , Jewett PB , Kadner K , Kimball H , Kobayashi A , Krawczyk MC , Leyba T , Longmire JL , Lopez F , Lou Y , Lowry S , Ludeman T , Manohar CF , Mark GA , McMurray KL , Meincke LJ , Morgan J , Moyzis RK , Mundt MO , Munk AC , Nandkeshwar RD , Pitluck S , Pollard M , Predki P , Parson-Quintana B , Ramirez L , Rash S , Retterer J , Ricke DO , Robinson DL , Rodriguez A , Salamov A , Saunders EH , Scott D , Shough T , Stallings RL , Stalvey M , Sutherland RD , Tapia R , Tesmer JG , Thayer N , Thompson LS , Tice H , Torney DC , Tran-Gyamfi M , Tsai M , Ulanovsky LE , Ustaszewska A , Vo N , White PS , Williams AL , Wills PL , Wu JR , Wu K , Yang J , DeJong P , Bruce D , Doggett NA , Deaven L , Schmutz J , Grimwood J , Richardson P , Rokhsar DS , Eichler EE , Gilna P , Lucas SM , Myers RM , Rubin EM , Pennacchio LA
Ref : Nature , 432 :988 , 2004
Abstract : Human chromosome 16 features one of the highest levels of segmentally duplicated sequence among the human autosomes. We report here the 78,884,754 base pairs of finished chromosome 16 sequence, representing over 99.9% of its euchromatin. Manual annotation revealed 880 protein-coding genes confirmed by 1,670 aligned transcripts, 19 transfer RNA genes, 341 pseudogenes and three RNA pseudogenes. These genes include metallothionein, cadherin and iroquois gene families, as well as the disease genes for polycystic kidney disease and acute myelomonocytic leukaemia. Several large-scale structural polymorphisms spanning hundreds of kilobase pairs were identified and result in gene content differences among humans. Whereas the segmental duplications of chromosome 16 are enriched in the relatively gene-poor pericentromere of the p arm, some are involved in recent gene duplication and conversion events that are likely to have had an impact on the evolution of primates and human disease susceptibility.
ESTHER : Martin_2004_Nature_432_988
PubMedSearch : Martin_2004_Nature_432_988
PubMedID: 15616553
Gene_locus related to this paper: human-CES1 , human-CES2 , human-CES3 , human-CES4A , human-CES5A