Dubchak I

References (11)

Title : The genome of Eucalyptus grandis - Myburg_2014_Nature_510_356
Author(s) : Myburg AA , Grattapaglia D , Tuskan GA , Hellsten U , Hayes RD , Grimwood J , Jenkins J , Lindquist E , Tice H , Bauer D , Goodstein DM , Dubchak I , Poliakov A , Mizrachi E , Kullan AR , Hussey SG , Pinard D , van der Merwe K , Singh P , van Jaarsveld I , Silva-Junior OB , Togawa RC , Pappas MR , Faria DA , Sansaloni CP , Petroli CD , Yang X , Ranjan P , Tschaplinski TJ , Ye CY , Li T , Sterck L , Vanneste K , Murat F , Soler M , Clemente HS , Saidi N , Cassan-Wang H , Dunand C , Hefer CA , Bornberg-Bauer E , Kersting AR , Vining K , Amarasinghe V , Ranik M , Naithani S , Elser J , Boyd AE , Liston A , Spatafora JW , Dharmwardhana P , Raja R , Sullivan C , Romanel E , Alves-Ferreira M , Kulheim C , Foley W , Carocha V , Paiva J , Kudrna D , Brommonschenkel SH , Pasquali G , Byrne M , Rigault P , Tibbits J , Spokevicius A , Jones RC , Steane DA , Vaillancourt RE , Potts BM , Joubert F , Barry K , Pappas GJ , Strauss SH , Jaiswal P , Grima-Pettenati J , Salse J , Van de Peer Y , Rokhsar DS , Schmutz J
Ref : Nature , 510 :356 , 2014
Abstract : Eucalypts are the world's most widely planted hardwood trees. Their outstanding diversity, adaptability and growth have made them a global renewable resource of fibre and energy. We sequenced and assembled >94% of the 640-megabase genome of Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest proportion thus far in plant genomes. Eucalyptus also shows the highest diversity of genes for specialized metabolites such as terpenes that act as chemical defence and provide unique pharmaceutical oils. Genome sequencing of the E. grandis sister species E. globulus and a set of inbred E. grandis tree genomes reveals dynamic genome evolution and hotspots of inbreeding depression. The E. grandis genome is the first reference for the eudicot order Myrtales and is placed here sister to the eurosids. This resource expands our understanding of the unique biology of large woody perennials and provides a powerful tool to accelerate comparative biology, breeding and biotechnology.
ESTHER : Myburg_2014_Nature_510_356
PubMedSearch : Myburg_2014_Nature_510_356
PubMedID: 24919147
Gene_locus related to this paper: eucgr-a0a059d0n8 , eucgr-a0a059cm68 , eucgr-a0a059d783 , eucgr-a0a059af93 , eucgr-a0a059awi0 , eucgr-a0a059awt4 , eucgr-a0a059ar83 , eucgr-a0a059ayw5 , eucgr-a0a059az75 , eucgr-a0a059azj1 , eucgr-a0a059azq5 , eucgr-a0a059bkm2 , eucgr-a0a059bl38 , eucgr-a0a059a7m2 , eucgr-a0a059a6p6 , eucgr-a0a059a6p1 , eucgr-a0a059a5e9 , eucgr-a0a059cpq4 , eucgr-a0a059b8v5

Title : The genome of the Western clawed frog Xenopus tropicalis - Hellsten_2010_Science_328_633
Author(s) : Hellsten U , Harland RM , Gilchrist MJ , Hendrix D , Jurka J , Kapitonov V , Ovcharenko I , Putnam NH , Shu S , Taher L , Blitz IL , Blumberg B , Dichmann DS , Dubchak I , Amaya E , Detter JC , Fletcher R , Gerhard DS , Goodstein D , Graves T , Grigoriev IV , Grimwood J , Kawashima T , Lindquist E , Lucas SM , Mead PE , Mitros T , Ogino H , Ohta Y , Poliakov AV , Pollet N , Robert J , Salamov A , Sater AK , Schmutz J , Terry A , Vize PD , Warren WC , Wells D , Wills A , Wilson RK , Zimmerman LB , Zorn AM , Grainger R , Grammer T , Khokha MK , Richardson PM , Rokhsar DS
Ref : Science , 328 :633 , 2010
Abstract : The western clawed frog Xenopus tropicalis is an important model for vertebrate development that combines experimental advantages of the African clawed frog Xenopus laevis with more tractable genetics. Here we present a draft genome sequence assembly of X. tropicalis. This genome encodes more than 20,000 protein-coding genes, including orthologs of at least 1700 human disease genes. Over 1 million expressed sequence tags validated the annotation. More than one-third of the genome consists of transposable elements, with unusually prevalent DNA transposons. Like that of other tetrapods, the genome of X. tropicalis contains gene deserts enriched for conserved noncoding elements. The genome exhibits substantial shared synteny with human and chicken over major parts of large chromosomes, broken by lineage-specific chromosome fusions and fissions, mainly in the mammalian lineage.
ESTHER : Hellsten_2010_Science_328_633
PubMedSearch : Hellsten_2010_Science_328_633
PubMedID: 20431018
Gene_locus related to this paper: xenla-q6pcj9 , xentr-a9umk0 , xentr-abhdb , xentr-ACHE , xentr-b0bm77 , xentr-b1h0y7 , xentr-b2guc4 , xentr-b7zt03 , xentr-b7ztj4 , xentr-BCHE1 , xentr-BCHE2 , xentr-cxest2 , xentr-d2x2k4 , xentr-d2x2k6 , xentr-f6rff6 , xentr-f6v0g3 , xentr-f6v2j6 , xentr-f6v3z1 , xentr-f6y4c8 , xentr-f6yve5 , xentr-f7a4y9 , xentr-f7acc5 , xentr-f7e2e2 , xentr-LOC394897 , xentr-ndrg1 , xentr-q0vfb6 , xentr-f7cpl7 , xentr-f6yj44 , xentr-f7ejk4 , xentr-f6q8j8 , xentr-f6z8f0 , xentr-f7d709 , xentr-b0bmb8 , xentr-f7af63 , xentr-a0a1b8y2w9 , xentr-f7d4k9 , xentr-f6r032 , xentr-f6yvq3 , xentr-a0a1b8y2z3 , xentr-f7afg4 , xentr-f6xb15 , xentr-f7e1r2 , xentr-a4ihf1 , xentr-f7eue5 , xentr-f6u7u3 , xentr-f172a , xentr-f7equ8 , xentr-f7dd89 , xentr-a9jtx5

Title : Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas - Worden_2009_Science_324_268
Author(s) : Worden AZ , Lee JH , Mock T , Rouze P , Simmons MP , Aerts AL , Allen AE , Cuvelier ML , Derelle E , Everett MV , Foulon E , Grimwood J , Gundlach H , Henrissat B , Napoli C , McDonald SM , Parker MS , Rombauts S , Salamov A , von Dassow P , Badger JH , Coutinho PM , Demir E , Dubchak I , Gentemann C , Eikrem W , Gready JE , John U , Lanier W , Lindquist EA , Lucas S , Mayer KF , Moreau H , Not F , Otillar R , Panaud O , Pangilinan J , Paulsen I , Piegu B , Poliakov A , Robbens S , Schmutz J , Toulza E , Wyss T , Zelensky A , Zhou K , Armbrust EV , Bhattacharya D , Goodenough UW , Van de Peer Y , Grigoriev IV
Ref : Science , 324 :268 , 2009
Abstract : Picoeukaryotes are a taxonomically diverse group of organisms less than 2 micrometers in diameter. Photosynthetic marine picoeukaryotes in the genus Micromonas thrive in ecosystems ranging from tropical to polar and could serve as sentinel organisms for biogeochemical fluxes of modern oceans during climate change. These broadly distributed primary producers belong to an anciently diverged sister clade to land plants. Although Micromonas isolates have high 18S ribosomal RNA gene identity, we found that genomes from two isolates shared only 90% of their predicted genes. Their independent evolutionary paths were emphasized by distinct riboswitch arrangements as well as the discovery of intronic repeat elements in one isolate, and in metagenomic data, but not in other genomes. Divergence appears to have been facilitated by selection and acquisition processes that actively shape the repertoire of genes that are mutually exclusive between the two isolates differently than the core genes. Analyses of the Micromonas genomes offer valuable insights into ecological differentiation and the dynamic nature of early plant evolution.
ESTHER : Worden_2009_Science_324_268
PubMedSearch : Worden_2009_Science_324_268
PubMedID: 19359590
Gene_locus related to this paper: 9chlo-c1e363 , 9chlo-c1ehp8 , 9chlo-c1fhv2 , 9chlo-c1mis3 , 9chlo-c1na62 , micpc-c1mh04 , micpc-c1mhj0 , micpc-c1mie7 , micpc-c1mj20 , micpc-c1mjh0 , micpc-c1mny7 , micpc-c1mpb2 , micpc-c1mrl2 , micpc-c1msr1 , micpc-c1mvk4 , micpc-c1mvx4 , micpc-c1n5d2 , micpc-c1n6i2 , micpc-c1n842 , micsr-c1dzu1 , micsr-c1e0v8 , micsr-c1e2u5 , micsr-c1e4q6 , micsr-c1e6z5 , micsr-c1e046 , micsr-c1e286 , micsr-c1eap0 , micsr-c1ec00 , micsr-c1edy4 , micsr-c1efl2 , micsr-c1eh15 , micsr-c1ei44 , micsr-c1eii9 , micsr-c1eiz1 , micsr-c1fft1 , micsr-c1fi89 , micsr-c1fj57 , micsr-c1e9f6 , micsr-c1e9u2 , micsr-c1fgg8 , micpc-c1mie3 , micpc-c1ms20 , micpc-c1n640 , miccc-c1e278 , micpc-c1mpa6

Title : The Sorghum bicolor genome and the diversification of grasses - Paterson_2009_Nature_457_551
Author(s) : Paterson AH , Bowers JE , Bruggmann R , Dubchak I , Grimwood J , Gundlach H , Haberer G , Hellsten U , Mitros T , Poliakov A , Schmutz J , Spannagl M , Tang H , Wang X , Wicker T , Bharti AK , Chapman J , Feltus FA , Gowik U , Grigoriev IV , Lyons E , Maher CA , Martis M , Narechania A , Otillar RP , Penning BW , Salamov AA , Wang Y , Zhang L , Carpita NC , Freeling M , Gingle AR , Hash CT , Keller B , Klein P , Kresovich S , McCann MC , Ming R , Peterson DG , Mehboob ur R , Ware D , Westhoff P , Mayer KF , Messing J , Rokhsar DS
Ref : Nature , 457 :551 , 2009
Abstract : Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the approximately 730-megabase Sorghum bicolor (L.) Moench genome, placing approximately 98% of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information. Genetic recombination is largely confined to about one-third of the sorghum genome with gene order and density similar to those of rice. Retrotransposon accumulation in recombinationally recalcitrant heterochromatin explains the approximately 75% larger genome size of sorghum compared with rice. Although gene and repetitive DNA distributions have been preserved since palaeopolyploidization approximately 70 million years ago, most duplicated gene sets lost one member before the sorghum-rice divergence. Concerted evolution makes one duplicated chromosomal segment appear to be only a few million years old. About 24% of genes are grass-specific and 7% are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum's drought tolerance.
ESTHER : Paterson_2009_Nature_457_551
PubMedSearch : Paterson_2009_Nature_457_551
PubMedID: 19189423
Gene_locus related to this paper: sorbi-b3vtb2 , sorbi-c5wp75 , sorbi-c5wts6 , sorbi-c5wu07 , sorbi-c5wvl7 , sorbi-c5ww85 , sorbi-c5ww86 , sorbi-c5wxa4 , sorbi-c5x1f6 , sorbi-c5x2x9 , sorbi-c5x5z9 , sorbi-c5x6q0 , sorbi-c5x230 , sorbi-c5x290 , sorbi-c5x345 , sorbi-c5x399 , sorbi-c5x610 , sorbi-c5xbm4 , sorbi-c5xct0 , sorbi-c5xdv0 , sorbi-c5xe87 , sorbi-c5xf40 , sorbi-c5xfu9 , sorbi-c5xh40 , sorbi-c5xh41 , sorbi-c5xh42 , sorbi-c5xh43 , sorbi-c5xh44 , sorbi-c5xh46 , sorbi-c5xhr2 , sorbi-c5xiw7 , sorbi-c5xjf0 , sorbi-c5xky2 , sorbi-c5xm54 , sorbi-c5xmb9 , sorbi-c5xmz5 , sorbi-c5xp10 , sorbi-c5xpm6 , sorbi-c5xr91 , sorbi-c5xr92 , sorbi-c5xs33 , sorbi-c5xtz0 , sorbi-c5xwd3 , sorbi-c5y0d2 , sorbi-c5y0h4 , sorbi-c5y3i5 , sorbi-c5y7x0 , sorbi-c5y517 , sorbi-c5y545 , sorbi-c5ydr3 , sorbi-c5yec0 , sorbi-c5yf71 , sorbi-c5yi32 , sorbi-c5yih2 , sorbi-c5ylw6 , sorbi-c5yn66 , sorbi-c5ynp8 , sorbi-c5yt11 , sorbi-c5yur5 , sorbi-c5ywz3 , sorbi-c5ywz4 , sorbi-c5yx73 , sorbi-c5yyn0 , sorbi-c5z2m6 , sorbi-c5z6a9 , sorbi-c5z6j1 , sorbi-c5z6s5 , sorbi-c5z177 , sorbi-Q9XE80 , sorbi-c5xyg4 , sorbi-c5z4q0 , sorbi-c5xly4 , sorbi-c5z4u8 , sorbi-c5xxg5 , sorbi-c5z9b9 , sorbi-a0a1z5r970 , sorbi-c5xhf9 , sorbi-c5yxt7 , sorbi-c5yxt6 , sorbi-c5y1m2 , sorbi-c5xdy6 , sorbi-a0a194ysf6 , sorbi-a0a1b6pnr2 , sorbi-a0a1b6qcb9 , sorbi-c5xx30 , sorbi-a0a1b6psg4 , sorbi-a0a1z5rj80 , sorbi-a0a1b6qfm2 , sorbi-a0a1b6qmu5 , sorbi-c6jru0

Title : The amphioxus genome and the evolution of the chordate karyotype - Putnam_2008_Nature_453_1064
Author(s) : Putnam NH , Butts T , Ferrier DE , Furlong RF , Hellsten U , Kawashima T , Robinson-Rechavi M , Shoguchi E , Terry A , Yu JK , Benito-Gutierrez EL , Dubchak I , Garcia-Fernandez J , Gibson-Brown JJ , Grigoriev IV , Horton AC , de Jong PJ , Jurka J , Kapitonov VV , Kohara Y , Kuroki Y , Lindquist E , Lucas S , Osoegawa K , Pennacchio LA , Salamov AA , Satou Y , Sauka-Spengler T , Schmutz J , Shin IT , Toyoda A , Bronner-Fraser M , Fujiyama A , Holland LZ , Holland PW , Satoh N , Rokhsar DS
Ref : Nature , 453 :1064 , 2008
Abstract : Lancelets ('amphioxus') are the modern survivors of an ancient chordate lineage, with a fossil record dating back to the Cambrian period. Here we describe the structure and gene content of the highly polymorphic approximately 520-megabase genome of the Florida lancelet Branchiostoma floridae, and analyse it in the context of chordate evolution. Whole-genome comparisons illuminate the murky relationships among the three chordate groups (tunicates, lancelets and vertebrates), and allow not only reconstruction of the gene complement of the last common chordate ancestor but also partial reconstruction of its genomic organization, as well as a description of two genome-wide duplications and subsequent reorganizations in the vertebrate lineage. These genome-scale events shaped the vertebrate genome and provided additional genetic variation for exploitation during vertebrate evolution.
ESTHER : Putnam_2008_Nature_453_1064
PubMedSearch : Putnam_2008_Nature_453_1064
PubMedID: 18563158
Gene_locus related to this paper: brafl-ACHE1 , brafl-ACHE2 , brafl-ACHEA , brafl-ACHEB , brafl-c3xqm2 , brafl-c3xqm5 , brafl-c3xtl0 , brafl-c3xtl1 , brafl-c3xut6 , brafl-c3xut7 , brafl-c3xvw5 , brafl-c3xx27 , brafl-c3xx28 , brafl-c3xx30 , brafl-c3xx32 , brafl-c3xx36 , brafl-c3xx38 , brafl-c3xx39 , brafl-c3xx40 , brafl-c3xx41 , brafl-c3xxt9 , brafl-c3xyd7 , brafl-c3xyd8 , brafl-c3xyd9 , brafl-c3xye0 , brafl-c3xyt7 , brafl-c3xzy1 , brafl-c3xzy2 , brafl-c3y1p9 , brafl-c3y1t3 , brafl-c3y2u3 , brafl-c3y4l1 , brafl-c3y6v9 , brafl-c3y6y4 , brafl-c3y7d7 , brafl-c3y7s1 , brafl-c3y8k5 , brafl-c3y8t3 , brafl-c3y8t4 , brafl-c3y8t5 , brafl-c3y8v8 , brafl-c3y8w1.1 , brafl-c3y8w2 , brafl-c3y9i7 , brafl-c3y9i8 , brafl-c3y9l9 , brafl-c3y9y3 , brafl-c3y087 , brafl-c3yan2 , brafl-c3yaw4 , brafl-c3ybw7 , brafl-c3yc67 , brafl-c3ydm8 , brafl-c3yfm5 , brafl-c3yfz8 , brafl-c3ygc7 , brafl-c3ygc9.1 , brafl-c3ygd0 , brafl-c3ygd1 , brafl-c3ygd2.1 , brafl-c3ygd4 , brafl-c3ygg6 , brafl-c3ygr1 , brafl-c3yi63 , brafl-c3yi64 , brafl-c3yi67 , brafl-c3yi68 , brafl-c3yi69 , brafl-c3yk61 , brafl-c3ykb2 , brafl-c3yla7 , brafl-c3ylp9 , brafl-c3ylq0 , brafl-c3ylq1 , brafl-c3ymu0 , brafl-c3yne9 , brafl-c3ypm6 , brafl-c3yr72 , brafl-c3yra8 , brafl-c3ys59 , brafl-c3yv27 , brafl-c3ywf1 , brafl-c3ywh9 , brafl-c3yx17 , brafl-c3yx19 , brafl-c3yxb9 , brafl-c3yxi7 , brafl-c3yyq5 , brafl-c3yz04 , brafl-c3z1c7 , brafl-c3z1u9 , brafl-c3z1v0 , brafl-c3z3n7 , brafl-c3z5c8 , brafl-c3z9f4 , brafl-c3z066 , brafl-c3z139 , brafl-c3z975 , brafl-c3zab8 , brafl-c3zab9 , brafl-c3zbr4 , brafl-c3zci7 , brafl-c3zcy8 , brafl-c3zd14 , brafl-c3zer1 , brafl-c3zf44 , brafl-c3zf47 , brafl-c3zf48 , brafl-c3zfs6 , brafl-c3zhm6 , brafl-c3ziv7.1 , brafl-c3ziv7.2 , brafl-c3zlg0 , brafl-c3zlg2 , brafl-c3zlg3 , brafl-c3zli5 , brafl-c3zme7 , brafl-c3zme8 , brafl-c3zmp8 , brafl-c3zmv1 , brafl-c3zmv2 , brafl-c3znd6 , brafl-c3znl2 , brafl-c3zqg7 , brafl-c3zqz2 , brafl-c3zs46 , brafl-c3zs49 , brafl-c3zs56 , brafl-c3zv54 , brafl-c3zvv1 , brafl-c3zwz6 , brafl-c3zxg2 , brafl-c3zxq3 , brafl-c3yim2 , brafl-c3zfs5 , brafl-c3zfs3 , brafl-c3xr79 , brafl-c3y7r2 , brafl-c3yj62 , brafl-c3zg22 , brafl-c3y2t9 , brafl-c3y2u0 , brafl-c3ycg1 , brafl-c3ycg2 , brafl-c3ycg4 , brafl-c3z1l3 , brafl-c3zn71 , brafl-c3zj72 , brafl-c3yf35 , brafl-c3z474 , brafl-c3zqr8 , brafl-c3yde6

Title : The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation - Palenik_2007_Proc.Natl.Acad.Sci.U.S.A_104_7705
Author(s) : Palenik B , Grimwood J , Aerts A , Rouze P , Salamov A , Putnam N , Dupont C , Jorgensen R , Derelle E , Rombauts S , Zhou K , Otillar R , Merchant SS , Podell S , Gaasterland T , Napoli C , Gendler K , Manuell A , Tai V , Vallon O , Piganeau G , Jancek S , Heijde M , Jabbari K , Bowler C , Lohr M , Robbens S , Werner G , Dubchak I , Pazour GJ , Ren Q , Paulsen I , Delwiche C , Schmutz J , Rokhsar D , Van de Peer Y , Moreau H , Grigoriev IV
Ref : Proc Natl Acad Sci U S A , 104 :7705 , 2007
Abstract : The smallest known eukaryotes, at approximately 1-mum diameter, are Ostreococcus tauri and related species of marine phytoplankton. The genome of Ostreococcus lucimarinus has been completed and compared with that of O. tauri. This comparison reveals surprising differences across orthologous chromosomes in the two species from highly syntenic chromosomes in most cases to chromosomes with almost no similarity. Species divergence in these phytoplankton is occurring through multiple mechanisms acting differently on different chromosomes and likely including acquisition of new genes through horizontal gene transfer. We speculate that this latter process may be involved in altering the cell-surface characteristics of each species. In addition, the genome of O. lucimarinus provides insights into the unique metal metabolism of these organisms, which are predicted to have a large number of selenocysteine-containing proteins. Selenoenzymes are more catalytically active than similar enzymes lacking selenium, and thus the cell may require less of that protein. As reported here, selenoenzymes, novel fusion proteins, and loss of some major protein families including ones associated with chromatin are likely important adaptations for achieving a small cell size.
ESTHER : Palenik_2007_Proc.Natl.Acad.Sci.U.S.A_104_7705
PubMedSearch : Palenik_2007_Proc.Natl.Acad.Sci.U.S.A_104_7705
PubMedID: 17460045
Gene_locus related to this paper: ostlu-a4rrl5 , ostlu-a4ruh2 , ostlu-a4rut7 , ostlu-a4ruy3 , ostlu-a4rxn1 , ostlu-a4ry37 , ostlu-a4s2e6 , ostlu-a4s2y4 , ostlu-a4s3d7 , ostlu-a4s4v4 , ostlu-a4s5e4 , ostlu-a4s5y6 , ostlu-a4s7a8 , ostlu-a4s7z5 , ostlu-a4s8g3 , ostlu-a4s8n8 , ostlu-a4s8s1 , ostlu-a4s958 , ostlu-a4sac2 , ostlu-a4saz3 , ostlu-a4sbb7 , ostlu-a4s6q5 , ostlu-a4s1q9 , ostlu-a4s8b2 , ostlu-a4s262

Title : The Chlamydomonas genome reveals the evolution of key animal and plant functions - Merchant_2007_Science_318_245
Author(s) : Merchant SS , Prochnik SE , Vallon O , Harris EH , Karpowicz SJ , Witman GB , Terry A , Salamov A , Fritz-Laylin LK , Marechal-Drouard L , Marshall WF , Qu LH , Nelson DR , Sanderfoot AA , Spalding MH , Kapitonov VV , Ren Q , Ferris P , Lindquist E , Shapiro H , Lucas SM , Grimwood J , Schmutz J , Cardol P , Cerutti H , Chanfreau G , Chen CL , Cognat V , Croft MT , Dent R , Dutcher S , Fernandez E , Fukuzawa H , Gonzalez-Ballester D , Gonzalez-Halphen D , Hallmann A , Hanikenne M , Hippler M , Inwood W , Jabbari K , Kalanon M , Kuras R , Lefebvre PA , Lemaire SD , Lobanov AV , Lohr M , Manuell A , Meier I , Mets L , Mittag M , Mittelmeier T , Moroney JV , Moseley J , Napoli C , Nedelcu AM , Niyogi K , Novoselov SV , Paulsen IT , Pazour G , Purton S , Ral JP , Riano-Pachon DM , Riekhof W , Rymarquis L , Schroda M , Stern D , Umen J , Willows R , Wilson N , Zimmer SL , Allmer J , Balk J , Bisova K , Chen CJ , Elias M , Gendler K , Hauser C , Lamb MR , Ledford H , Long JC , Minagawa J , Page MD , Pan J , Pootakham W , Roje S , Rose A , Stahlberg E , Terauchi AM , Yang P , Ball S , Bowler C , Dieckmann CL , Gladyshev VN , Green P , Jorgensen R , Mayfield S , Mueller-Roeber B , Rajamani S , Sayre RT , Brokstein P , Dubchak I , Goodstein D , Hornick L , Huang YW , Jhaveri J , Luo Y , Martinez D , Ngau WC , Otillar B , Poliakov A , Porter A , Szajkowski L , Werner G , Zhou K , Grigoriev IV , Rokhsar DS , Grossman AR
Ref : Science , 318 :245 , 2007
Abstract : Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the approximately 120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.
ESTHER : Merchant_2007_Science_318_245
PubMedSearch : Merchant_2007_Science_318_245
PubMedID: 17932292
Gene_locus related to this paper: chlre-a0a2k3e2k6 , chlre-a8hmd4 , chlre-a8hqa9 , chlre-a8htq0 , chlre-a8hus6.1 , chlre-a8hus6.2 , chlre-a8icg4 , chlre-a8iwm0 , chlre-a8ize5 , chlre-a8j2s9 , chlre-a8j5w6 , chlre-a8j7f8 , chlre-a8j8u9 , chlre-a8j8v0 , chlre-a8j9u6 , chlre-a8j143 , chlre-a8j248 , chlre-a8jd32 , chlre-a8jd42 , chlre-a8jgj2 , chlre-a8jhc8 , chlre-a8jhe5 , chlre-a8iwj1 , chlre-a8j7d5 , chlre-a0a2k3dii0

Title : The genome of black cottonwood, Populus trichocarpa (Torr. &\; Gray) - Tuskan_2006_Science_313_1596
Author(s) : Tuskan GA , Difazio S , Jansson S , Bohlmann J , Grigoriev I , Hellsten U , Putnam N , Ralph S , Rombauts S , Salamov A , Schein J , Sterck L , Aerts A , Bhalerao RR , Bhalerao RP , Blaudez D , Boerjan W , Brun A , Brunner A , Busov V , Campbell M , Carlson J , Chalot M , Chapman J , Chen GL , Cooper D , Coutinho PM , Couturier J , Covert S , Cronk Q , Cunningham R , Davis J , Degroeve S , Dejardin A , dePamphilis C , Detter J , Dirks B , Dubchak I , Duplessis S , Ehlting J , Ellis B , Gendler K , Goodstein D , Gribskov M , Grimwood J , Groover A , Gunter L , Hamberger B , Heinze B , Helariutta Y , Henrissat B , Holligan D , Holt R , Huang W , Islam-Faridi N , Jones S , Jones-Rhoades M , Jorgensen R , Joshi C , Kangasjarvi J , Karlsson J , Kelleher C , Kirkpatrick R , Kirst M , Kohler A , Kalluri U , Larimer F , Leebens-Mack J , Leple JC , Locascio P , Lou Y , Lucas S , Martin F , Montanini B , Napoli C , Nelson DR , Nelson C , Nieminen K , Nilsson O , Pereda V , Peter G , Philippe R , Pilate G , Poliakov A , Razumovskaya J , Richardson P , Rinaldi C , Ritland K , Rouze P , Ryaboy D , Schmutz J , Schrader J , Segerman B , Shin H , Siddiqui A , Sterky F , Terry A , Tsai CJ , Uberbacher E , Unneberg P , Vahala J , Wall K , Wessler S , Yang G , Yin T , Douglas C , Marra M , Sandberg G , Van de Peer Y , Rokhsar D
Ref : Science , 313 :1596 , 2006
Abstract : We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.
ESTHER : Tuskan_2006_Science_313_1596
PubMedSearch : Tuskan_2006_Science_313_1596
PubMedID: 16973872
Gene_locus related to this paper: burvg-a4jw31 , delas-a9c1v9 , poptr-a9pfp5 , poptr-a9ph43 , poptr-a9ph71 , poptr-a9pha7 , poptr-b9giq0 , poptr-b9gjs0 , poptr-b9gl72 , poptr-b9gmx8 , poptr-b9gnp9 , poptr-b9gny4 , poptr-b9grg2 , poptr-b9gsc2 , poptr-b9gvp3 , poptr-b9gvs3 , poptr-b9gwn9 , poptr-b9gy32 , poptr-b9gyq1 , poptr-b9gys8 , poptr-b9h0h0 , poptr-b9h4j2 , poptr-b9h6c2 , poptr-b9h6c5 , poptr-b9h6l8 , poptr-b9h8c9 , poptr-b9h301 , poptr-b9h579 , poptr-b9hbl2 , poptr-b9hbw5 , poptr-b9hcn9 , poptr-b9hee0 , poptr-b9hee2 , poptr-b9hee5 , poptr-b9hee6 , poptr-b9hef3 , poptr-b9hfa7 , poptr-b9hfd3 , poptr-b9hfi6 , poptr-b9hft8 , poptr-b9hg83 , poptr-b9hif5 , poptr-b9hll5 , poptr-b9hmd0 , poptr-b9hnv3 , poptr-b9hqr6 , poptr-b9hqr7 , poptr-b9hrv7 , poptr-b9hs66 , poptr-b9huf0 , poptr-b9hur3 , poptr-b9hux1 , poptr-b9hwp2 , poptr-b9hxr7 , poptr-b9hyk8 , poptr-b9hyx2 , poptr-b9i2q8 , poptr-b9i5b8 , poptr-b9i5j8 , poptr-b9i5j9 , poptr-b9i5k0 , poptr-b9i6b6 , poptr-b9i7b7 , poptr-b9i9p8 , poptr-b9i484 , poptr-b9i994 , poptr-b9ial3 , poptr-b9ial4 , poptr-b9ib28 , poptr-b9ibr8 , poptr-b9id97 , poptr-b9idr4 , poptr-b9iid9 , poptr-b9iip0 , poptr-b9ik80 , poptr-b9ik90 , poptr-b9il63 , poptr-b9ink7 , poptr-b9iqa0 , poptr-b9iqd5 , poptr-b9mwf1 , poptr-b9mwi8 , poptr-b9n0c6 , poptr-b9n0n1 , poptr-b9n0n4 , poptr-b9n0z5 , poptr-b9n1t8 , poptr-b9n1z3 , poptr-b9n3m7 , poptr-b9n233 , poptr-b9n236 , poptr-b9n395 , poptr-b9nd33 , poptr-b9nd34 , poptr-b9ndi6 , poptr-b9ndj5 , poptr-b9p9i8 , poptr-a9pfa7 , poptr-b9hdp2 , poptr-b9inj0 , poptr-b9n5g7 , poptr-b9i8q4 , poptr-u5g0r4 , poptr-u5gf59 , poptr-u7e1l9 , poptr-b9hj61 , poptr-b9hwd0 , poptr-u5fz17 , poptr-a0a2k2brq1 , poptr-a0a2k2b9i6 , poptr-a0a2k1x9y8 , poptr-a9pch4 , poptr-a0a2k1wwt1 , poptr-a0a2k1wv10 , poptr-a0a2k2a850 , poptr-a0a2k2asj6 , poptr-a0a2k1x6k1 , poptr-u5fv96 , poptr-a0a2k2blg2 , poptr-a0a2k1xpi3 , poptr-a0a2k1xpj0 , poptr-a0a2k2b331 , poptr-a0a2k2byl7 , poptr-b9iek5 , poptr-a9pfg4 , poptr-a0a2k1xzs5 , poptr-b9gga9 , poptr-b9guw6 , poptr-b9hff2

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