Kapitonov VV

References (4)

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 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 : Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization - Putnam_2007_Science_317_86
Author(s) : Putnam NH , Srivastava M , Hellsten U , Dirks B , Chapman J , Salamov A , Terry A , Shapiro H , Lindquist E , Kapitonov VV , Jurka J , Genikhovich G , Grigoriev IV , Lucas SM , Steele RE , Finnerty JR , Technau U , Martindale MQ , Rokhsar DS
Ref : Science , 317 :86 , 2007
Abstract : Sea anemones are seemingly primitive animals that, along with corals, jellyfish, and hydras, constitute the oldest eumetazoan phylum, the Cnidaria. Here, we report a comparative analysis of the draft genome of an emerging cnidarian model, the starlet sea anemone Nematostella vectensis. The sea anemone genome is complex, with a gene repertoire, exon-intron structure, and large-scale gene linkage more similar to vertebrates than to flies or nematodes, implying that the genome of the eumetazoan ancestor was similarly complex. Nearly one-fifth of the inferred genes of the ancestor are eumetazoan novelties, which are enriched for animal functions like cell signaling, adhesion, and synaptic transmission. Analysis of diverse pathways suggests that these gene "inventions" along the lineage leading to animals were likely already well integrated with preexisting eukaryotic genes in the eumetazoan progenitor.
ESTHER : Putnam_2007_Science_317_86
PubMedSearch : Putnam_2007_Science_317_86
PubMedID: 17615350
Gene_locus related to this paper: nemve-a7rfc6 , nemve-a7rhs0 , nemve-a7rhw2 , nemve-a7ric9 , nemve-a7riu9 , nemve-a7rk54 , nemve-a7rlg8 , nemve-a7rlv4 , nemve-a7rn07 , nemve-a7rn08 , nemve-a7rn68 , nemve-a7rnv3 , nemve-a7rpb3 , nemve-a7rpq4 , nemve-a7rqa8 , nemve-a7rqw3 , nemve-a7rwv1 , nemve-a7rxl6 , nemve-a7s1d5 , nemve-a7s3l3 , nemve-a7s3q1 , nemve-a7s5u3 , nemve-a7s6g4 , nemve-a7s6s7 , nemve-a7sa46 , nemve-a7sbd9 , nemve-a7sbe0 , nemve-a7sbm6 , nemve-a7scy7 , nemve-a7sex0 , nemve-a7sfa0 , nemve-a7sff3 , nemve-a7sgb1 , nemve-a7shf2 , nemve-a7siv4 , nemve-a7sj77 , nemve-a7sjw1 , nemve-a7skr3 , nemve-a7slm1 , nemve-a7slm2 , nemve-a7sp35 , nemve-a7sq47 , nemve-a7sq73 , nemve-a7sqk0 , nemve-a7su21 , nemve-a7su25 , nemve-a7svn0 , nemve-a7svu2 , nemve-a7sx21 , nemve-a7syk4 , nemve-a7t3e6 , nemve-a7suy2 , nemve-a7s803 , nemve-a7t3m9 , nemve-a0a1t4jh34 , nemve-a7rvd5 , nemve-a7rhu9 , nemve-a7si15

Title : The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism - Armbrust_2004_Science_306_79
Author(s) : Armbrust EV , Berges JA , Bowler C , Green BR , Martinez D , Putnam NH , Zhou S , Allen AE , Apt KE , Bechner M , Brzezinski MA , Chaal BK , Chiovitti A , Davis AK , Demarest MS , Detter JC , Glavina T , Goodstein D , Hadi MZ , Hellsten U , Hildebrand M , Jenkins BD , Jurka J , Kapitonov VV , Kroger N , Lau WW , Lane TW , Larimer FW , Lippmeier JC , Lucas S , Medina M , Montsant A , Obornik M , Parker MS , Palenik B , Pazour GJ , Richardson PM , Rynearson TA , Saito MA , Schwartz DC , Thamatrakoln K , Valentin K , Vardi A , Wilkerson FP , Rokhsar DS
Ref : Science , 306 :79 , 2004
Abstract : Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for approximately 20% of global carbon fixation. We report the 34 million-base pair draft nuclear genome of the marine diatom Thalassiosira pseudonana and its 129 thousand-base pair plastid and 44 thousand-base pair mitochondrial genomes. Sequence and optical restriction mapping revealed 24 diploid nuclear chromosomes. We identified novel genes for silicic acid transport and formation of silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes for several types of polyunsaturated fatty acids, use of a range of nitrogenous compounds, and a complete urea cycle, all attributes that allow diatoms to prosper in aquatic environments.
ESTHER : Armbrust_2004_Science_306_79
PubMedSearch : Armbrust_2004_Science_306_79
PubMedID: 15459382
Gene_locus related to this paper: thaps-b5ymy7 , thaps-b5yn04 , thaps-b5ynz7 , thaps-b8bq57 , thaps-b8bsn5 , thaps-b8bsy4 , thaps-b8bv00 , thaps-b8bxb3 , thaps-b8byx0 , thaps-b8bzg5 , thaps-b8c0a3 , thaps-b8c2d8 , thaps-b8c2k9 , thaps-b8c2s5 , thaps-b8c3p0 , thaps-b8c5l7 , thaps-b8c6y7 , thaps-b8c9k8 , thaps-b8c9t6 , thaps-b8c345 , thaps-b8c584 , thaps-b8c885 , thaps-b8c954 , thaps-b8cdd7 , thaps-b8cdt3 , thaps-b8cf07 , thaps-b8cfn8 , thaps-b8c079