Author Report for: Himmelbauer HNo contact information in database for Himmelbauer H
Dohm JC, Minoche AE, Holtgrawe D, Capella-Gutierrez S, Zakrzewski F, Tafer H, Rupp O, Sorensen TR, Stracke R and Himmelbauer H <9 more author(s)> Dohm JC, Minoche AE, Holtgrawe D, Capella-Gutierrez S, Zakrzewski F, Tafer H, Rupp O, Sorensen TR, Stracke R, Reinhardt R, Goesmann A, Kraft T, Schulz B, Stadler PF, Schmidt T, Gabaldon T, Lehrach H, Weisshaar B, Himmelbauer H (- 9) Ref: Nature, 505:546, 2014 : PubMed ESTHER: Dohm_2014_Nature_505_546 PubMedSearch: Dohm 2014 Nature 505 546 PubMedID: 24352233 Gene_locus related to this paper: betvu-a0a0j8bcg5, betvu-a0a0j8fqe7, spiol-a0a0k9r9x3, spiol-a0a0k9rit5, spiol-a0a0k9riw3, spiol-a0a0k9rub8, spiol-a0a0k9rxl0, spiol-a0a0k9qau1, spiol-a0a0k9rrd8, spiol-a0a0k9qe58, spiol-a0a0k9r322, betvv-a0a0j8b442, spiol-a0a0k9qnw2, spiol-a0a0k9ri52, spiol-a0a0k9r6e9 Abstract Sugar beet (Beta vulgaris ssp. vulgaris) is an important crop of temperate climates which provides nearly 30% of the world's annual sugar production and is a source for bioethanol and animal feed. The species belongs to the order of Caryophylalles, is diploid with 2n = 18 chromosomes, has an estimated genome size of 714-758 megabases and shares an ancient genome triplication with other eudicot plants. Leafy beets have been cultivated since Roman times, but sugar beet is one of the most recently domesticated crops. It arose in the late eighteenth century when lines accumulating sugar in the storage root were selected from crosses made with chard and fodder beet. Here we present a reference genome sequence for sugar beet as the first non-rosid, non-asterid eudicot genome, advancing comparative genomics and phylogenetic reconstructions. The genome sequence comprises 567 megabases, of which 85% could be assigned to chromosomes. The assembly covers a large proportion of the repetitive sequence content that was estimated to be 63%. We predicted 27,421 protein-coding genes supported by transcript data and annotated them on the basis of sequence homology. Phylogenetic analyses provided evidence for the separation of Caryophyllales before the split of asterids and rosids, and revealed lineage-specific gene family expansions and losses. We sequenced spinach (Spinacia oleracea), another Caryophyllales species, and validated features that separate this clade from rosids and asterids. Intraspecific genomic variation was analysed based on the genome sequences of sea beet (Beta vulgaris ssp. maritima; progenitor of all beet crops) and four additional sugar beet accessions. We identified seven million variant positions in the reference genome, and also large regions of low variability, indicating artificial selection. The sugar beet genome sequence enables the identification of genes affecting agronomically relevant traits, supports molecular breeding and maximizes the plant's potential in energy biotechnology. Title: Genome sequence of the Brown Norway rat yields insights into mammalian evolution Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC and Collins F <218 more 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 (- 218) Ref: Nature, 428:493, 2004 : PubMed 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 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. Title: The genomic sequence and comparative analysis of the rat major histocompatibility complex Hurt P, Walter L, Sudbrak R, Klages S, Muller I, Shiina T, Inoko H, Lehrach H, Gunther E and Himmelbauer H <1 more author(s)> Hurt P, Walter L, Sudbrak R, Klages S, Muller I, Shiina T, Inoko H, Lehrach H, Gunther E, Reinhardt R, Himmelbauer H (- 1) Ref: Genome Res, 14:631, 2004 : PubMed ESTHER: Hurt_2004_Genome.Res_14_631 PubMedSearch: Hurt 2004 Genome.Res 14 631 PubMedID: 15060004 Gene_locus related to this paper: ratno-PPT2, ratno-q6mg55 Abstract We have determined the sequence of a 4-Mb interval on rat chromosome 20p12 that encompasses the rat major histocompatibility complex (MHC). This is the first report of a finished sequence for a segment of the rat genome and constitutes one of the largest contiguous sequences thus far for rodent genomes in general. The rat MHC is, next to the human MHC, the second mammalian MHC sequenced to completion. Our analysis has resulted in the identification of at least 220 genes located within the sequenced interval. Although gene content and order are well conserved in the class II and class III gene intervals as well as the framework gene regions, profound rat-specific features were encountered within the class I gene regions, in comparison to human and mouse. Class I region-associated differences were found both at the structural level, the number, and organization of class I genes and gene families, and, in a more global context, in the way that evolution worked to shape the present-day rat MHC. | |||||||
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