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  • Computational Biology  (6)
  • American Association for the Advancement of Science (AAAS)  (6)
  • American Chemical Society (ACS)
  • American Physical Society (APS)
  • Molecular Diversity Preservation International
  • 2015-2019
  • 2005-2009  (3)
  • 2000-2004  (3)
Collection
Keywords
Publisher
  • American Association for the Advancement of Science (AAAS)  (6)
  • American Chemical Society (ACS)
  • American Physical Society (APS)
  • Molecular Diversity Preservation International
Years
  • 2015-2019
  • 2005-2009  (3)
  • 2000-2004  (3)
Year
  • 1
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    The composite genome of the legume symbiont Sinorhizobium meliloti (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-07-28
    Description: The scarcity of usable nitrogen frequently limits plant growth. A tight metabolic association with rhizobial bacteria allows legumes to obtain nitrogen compounds by bacterial reduction of dinitrogen (N2) to ammonium (NH4+). We present here the annotated DNA sequence of the alpha-proteobacterium Sinorhizobium meliloti, the symbiont of alfalfa. The tripartite 6.7-megabase (Mb) genome comprises a 3.65-Mb chromosome, and 1.35-Mb pSymA and 1.68-Mb pSymB megaplasmids. Genome sequence analysis indicates that all three elements contribute, in varying degrees, to symbiosis and reveals how this genome may have emerged during evolution. The genome sequence will be useful in understanding the dynamics of interkingdom associations and of life in soil environments.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Galibert, F -- Finan, T M -- Long, S R -- Puhler, A -- Abola, P -- Ampe, F -- Barloy-Hubler, F -- Barnett, M J -- Becker, A -- Boistard, P -- Bothe, G -- Boutry, M -- Bowser, L -- Buhrmester, J -- Cadieu, E -- Capela, D -- Chain, P -- Cowie, A -- Davis, R W -- Dreano, S -- Federspiel, N A -- Fisher, R F -- Gloux, S -- Godrie, T -- Goffeau, A -- Golding, B -- Gouzy, J -- Gurjal, M -- Hernandez-Lucas, I -- Hong, A -- Huizar, L -- Hyman, R W -- Jones, T -- Kahn, D -- Kahn, M L -- Kalman, S -- Keating, D H -- Kiss, E -- Komp, C -- Lelaure, V -- Masuy, D -- Palm, C -- Peck, M C -- Pohl, T M -- Portetelle, D -- Purnelle, B -- Ramsperger, U -- Surzycki, R -- Thebault, P -- Vandenbol, M -- Vorholter, F J -- Weidner, S -- Wells, D H -- Wong, K -- Yeh, K C -- Batut, J -- GM30962/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Jul 27;293(5530):668-72.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉UMR6061-CNRS, Laboratoire de Genetique et Developpement, Faculte de Medecine, 2 avenue du Pr. Leon Bernard, F-35043 Rennes cedex, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11474104" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Adhesion ; Bacterial Proteins/genetics ; Carrier Proteins/genetics ; Chromosomes, Bacterial/genetics ; Computational Biology ; DNA Transposable Elements ; Energy Metabolism/genetics ; Evolution, Molecular ; Gene Duplication ; Genes, Bacterial ; Genes, Essential ; Genes, Regulator ; *Genome, Bacterial ; Medicago sativa/microbiology ; Nitrogen/metabolism ; Nitrogen Fixation/genetics ; Plasmids ; Polysaccharides, Bacterial/genetics ; Replicon ; Rhizobiaceae/genetics ; *Sequence Analysis, DNA ; Sinorhizobium meliloti/*genetics/physiology ; Symbiosis/*genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Empirical analysis of transcriptional activity in the Arabidopsis genome (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-11-01
    Description: Functional analysis of a genome requires accurate gene structure information and a complete gene inventory. A dual experimental strategy was used to verify and correct the initial genome sequence annotation of the reference plant Arabidopsis. Sequencing full-length cDNAs and hybridizations using RNA populations from various tissues to a set of high-density oligonucleotide arrays spanning the entire genome allowed the accurate annotation of thousands of gene structures. We identified 5817 novel transcription units, including a substantial amount of antisense gene transcription, and 40 genes within the genetically defined centromeres. This approach resulted in completion of approximately 30% of the Arabidopsis ORFeome as a resource for global functional experimentation of the plant proteome.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yamada, Kayoko -- Lim, Jun -- Dale, Joseph M -- Chen, Huaming -- Shinn, Paul -- Palm, Curtis J -- Southwick, Audrey M -- Wu, Hank C -- Kim, Christopher -- Nguyen, Michelle -- Pham, Paul -- Cheuk, Rosa -- Karlin-Newmann, George -- Liu, Shirley X -- Lam, Bao -- Sakano, Hitomi -- Wu, Troy -- Yu, Guixia -- Miranda, Molly -- Quach, Hong L -- Tripp, Matthew -- Chang, Charlie H -- Lee, Jeong M -- Toriumi, Mitsue -- Chan, Marie M H -- Tang, Carolyn C -- Onodera, Courtney S -- Deng, Justine M -- Akiyama, Kenji -- Ansari, Yasser -- Arakawa, Takahiro -- Banh, Jenny -- Banno, Fumika -- Bowser, Leah -- Brooks, Shelise -- Carninci, Piero -- Chao, Qimin -- Choy, Nathan -- Enju, Akiko -- Goldsmith, Andrew D -- Gurjal, Mani -- Hansen, Nancy F -- Hayashizaki, Yoshihide -- Johnson-Hopson, Chanda -- Hsuan, Vickie W -- Iida, Kei -- Karnes, Meagan -- Khan, Shehnaz -- Koesema, Eric -- Ishida, Junko -- Jiang, Paul X -- Jones, Ted -- Kawai, Jun -- Kamiya, Asako -- Meyers, Cristina -- Nakajima, Maiko -- Narusaka, Mari -- Seki, Motoaki -- Sakurai, Tetsuya -- Satou, Masakazu -- Tamse, Racquel -- Vaysberg, Maria -- Wallender, Erika K -- Wong, Cecilia -- Yamamura, Yuki -- Yuan, Shiaulou -- Shinozaki, Kazuo -- Davis, Ronald W -- Theologis, Athanasios -- Ecker, Joseph R -- New York, N.Y. -- Science. 2003 Oct 31;302(5646):842-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Plant Gene Expression Center, Albany, CA 94710, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14593172" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/*genetics ; Chromosome Mapping ; Chromosomes, Plant/genetics ; Cloning, Molecular ; Computational Biology ; DNA, Complementary/genetics ; DNA, Intergenic ; Expressed Sequence Tags ; Gene Expression Profiling ; Genes, Plant ; *Genome, Plant ; Genomics ; Nucleic Acid Hybridization ; Oligonucleotide Array Sequence Analysis ; Open Reading Frames ; RNA, Messenger/*genetics ; RNA, Plant/*genetics ; Reverse Transcriptase Polymerase Chain Reaction ; *Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Niemann-Pick C1 Like 1 protein is critical for intestinal cholesterol absorption (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-02-21
    Description: Dietary cholesterol consumption and intestinal cholesterol absorption contribute to plasma cholesterol levels, a risk factor for coronary heart disease. The molecular mechanism of sterol uptake from the lumen of the small intestine is poorly defined. We show that Niemann-Pick C1 Like 1(NPC1L1) protein plays a critical role in the absorption of intestinal cholesterol. NPC1L1 expression is enriched in the small intestine and is in the brush border membrane of enterocytes. Although otherwise phenotypically normal, NPC1L1-deficient mice exhibit a substantial reduction in absorbed cholesterol, which is unaffected by dietary supplementation of bile acids. Ezetimibe, a drug that inhibits cholesterol absorption, had no effect in NPC1L1 knockout mice, suggesting that NPC1L1 resides in an ezetimibe-sensitive pathway responsible for intestinal cholesterol absorption.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Altmann, Scott W -- Davis, Harry R Jr -- Zhu, Li-Ji -- Yao, Xiaorui -- Hoos, Lizbeth M -- Tetzloff, Glen -- Iyer, Sai Prasad N -- Maguire, Maureen -- Golovko, Andrei -- Zeng, Ming -- Wang, Luquan -- Murgolo, Nicholas -- Graziano, Michael P -- New York, N.Y. -- Science. 2004 Feb 20;303(5661):1201-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cardiovascular/Endocrine Research, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ, 07033-0539, USA. scott.altmann@spcorp.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14976318" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Anticholesteremic Agents/pharmacology ; Azetidines/pharmacology ; Cholesterol/*metabolism ; Cholesterol, Dietary/*metabolism ; Cholic Acid/administration & dosage/pharmacology ; Computational Biology ; Enterocytes/*metabolism ; Ezetimibe ; Female ; Gene Expression Profiling ; Humans ; *Intestinal Absorption/drug effects ; Intestine, Small/metabolism ; Jejunum/metabolism ; Liver/metabolism ; Male ; Membrane Proteins/chemistry/genetics/*metabolism ; Membrane Transport Proteins/chemistry/genetics/*metabolism ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; Proteins/chemistry/genetics/*metabolism ; Rats ; Rats, Sprague-Dawley
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-01-18
    Description: Cryptococcus neoformans is a basidiomycetous yeast ubiquitous in the environment, a model for fungal pathogenesis, and an opportunistic human pathogen of global importance. We have sequenced its approximately 20-megabase genome, which contains approximately 6500 intron-rich gene structures and encodes a transcriptome abundant in alternatively spliced and antisense messages. The genome is rich in transposons, many of which cluster at candidate centromeric regions. The presence of these transposons may drive karyotype instability and phenotypic variation. C. neoformans encodes unique genes that may contribute to its unusual virulence properties, and comparison of two phenotypically distinct strains reveals variation in gene content in addition to sequence polymorphisms between the genomes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3520129/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3520129/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Loftus, Brendan J -- Fung, Eula -- Roncaglia, Paola -- Rowley, Don -- Amedeo, Paolo -- Bruno, Dan -- Vamathevan, Jessica -- Miranda, Molly -- Anderson, Iain J -- Fraser, James A -- Allen, Jonathan E -- Bosdet, Ian E -- Brent, Michael R -- Chiu, Readman -- Doering, Tamara L -- Donlin, Maureen J -- D'Souza, Cletus A -- Fox, Deborah S -- Grinberg, Viktoriya -- Fu, Jianmin -- Fukushima, Marilyn -- Haas, Brian J -- Huang, James C -- Janbon, Guilhem -- Jones, Steven J M -- Koo, Hean L -- Krzywinski, Martin I -- Kwon-Chung, June K -- Lengeler, Klaus B -- Maiti, Rama -- Marra, Marco A -- Marra, Robert E -- Mathewson, Carrie A -- Mitchell, Thomas G -- Pertea, Mihaela -- Riggs, Florenta R -- Salzberg, Steven L -- Schein, Jacqueline E -- Shvartsbeyn, Alla -- Shin, Heesun -- Shumway, Martin -- Specht, Charles A -- Suh, Bernard B -- Tenney, Aaron -- Utterback, Terry R -- Wickes, Brian L -- Wortman, Jennifer R -- Wye, Natasja H -- Kronstad, James W -- Lodge, Jennifer K -- Heitman, Joseph -- Davis, Ronald W -- Fraser, Claire M -- Hyman, Richard W -- AI47087/AI/NIAID NIH HHS/ -- AI48594/AI/NIAID NIH HHS/ -- R01 AI050184/AI/NIAID NIH HHS/ -- R01 AI050184-05/AI/NIAID NIH HHS/ -- R01 HL088905/HL/NHLBI NIH HHS/ -- R01 HL088905-04A2/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2005 Feb 25;307(5713):1321-4. Epub 2005 Jan 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA. bjloftus@tigr.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15653466" target="_blank"〉PubMed〈/a〉
    Keywords: Alternative Splicing ; Cell Wall/metabolism ; Chromosomes, Fungal/genetics ; Computational Biology ; Cryptococcus neoformans/*genetics/pathogenicity/physiology ; DNA Transposable Elements ; Fungal Proteins/metabolism ; Gene Library ; Genes, Fungal ; *Genome, Fungal ; Humans ; Introns ; Molecular Sequence Data ; Phenotype ; Polymorphism, Genetic ; Polymorphism, Single Nucleotide ; Polysaccharides/metabolism ; RNA, Antisense ; Sequence Analysis, DNA ; Transcription, Genetic ; Virulence ; Virulence Factors/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
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    The genome of the sea urchin Strongylocentrotus purpuratus (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-11-11
    Description: We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159423/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159423/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sea Urchin Genome Sequencing Consortium -- Sodergren, Erica -- Weinstock, George M -- Davidson, Eric H -- Cameron, R Andrew -- Gibbs, Richard A -- Angerer, Robert C -- Angerer, Lynne M -- Arnone, Maria Ina -- Burgess, David R -- Burke, Robert D -- Coffman, James A -- Dean, Michael -- Elphick, Maurice R -- Ettensohn, Charles A -- Foltz, Kathy R -- Hamdoun, Amro -- Hynes, Richard O -- Klein, William H -- Marzluff, William -- McClay, David R -- Morris, Robert L -- Mushegian, Arcady -- Rast, Jonathan P -- Smith, L Courtney -- Thorndyke, Michael C -- Vacquier, Victor D -- Wessel, Gary M -- Wray, Greg -- Zhang, Lan -- Elsik, Christine G -- Ermolaeva, Olga -- Hlavina, Wratko -- Hofmann, Gretchen -- Kitts, Paul -- Landrum, Melissa J -- Mackey, Aaron J -- Maglott, Donna -- Panopoulou, Georgia -- Poustka, Albert J -- Pruitt, Kim -- Sapojnikov, Victor -- Song, Xingzhi -- Souvorov, Alexandre -- Solovyev, Victor -- Wei, Zheng -- Whittaker, Charles A -- Worley, Kim -- Durbin, K James -- Shen, Yufeng -- Fedrigo, Olivier -- Garfield, David -- Haygood, Ralph -- Primus, Alexander -- Satija, Rahul -- Severson, Tonya -- Gonzalez-Garay, Manuel L -- Jackson, Andrew R -- Milosavljevic, Aleksandar -- Tong, Mark -- Killian, Christopher E -- Livingston, Brian T -- Wilt, Fred H -- Adams, Nikki -- Belle, Robert -- Carbonneau, Seth -- Cheung, Rocky -- Cormier, Patrick -- Cosson, Bertrand -- Croce, Jenifer -- Fernandez-Guerra, Antonio -- Geneviere, Anne-Marie -- Goel, Manisha -- Kelkar, Hemant -- Morales, Julia -- Mulner-Lorillon, Odile -- Robertson, Anthony J -- Goldstone, Jared V -- Cole, Bryan -- Epel, David -- Gold, Bert -- Hahn, Mark E -- Howard-Ashby, Meredith -- Scally, Mark -- Stegeman, John J -- Allgood, Erin L -- Cool, Jonah -- Judkins, Kyle M -- McCafferty, Shawn S -- Musante, Ashlan M -- Obar, Robert A -- Rawson, Amanda P -- Rossetti, Blair J -- Gibbons, Ian R -- Hoffman, Matthew P -- Leone, Andrew -- Istrail, Sorin -- Materna, Stefan C -- Samanta, Manoj P -- Stolc, Viktor -- Tongprasit, Waraporn -- Tu, Qiang -- Bergeron, Karl-Frederik -- Brandhorst, Bruce P -- Whittle, James -- Berney, Kevin -- Bottjer, David J -- Calestani, Cristina -- Peterson, Kevin -- Chow, Elly -- Yuan, Qiu Autumn -- Elhaik, Eran -- Graur, Dan -- Reese, Justin T -- Bosdet, Ian -- Heesun, Shin -- Marra, Marco A -- Schein, Jacqueline -- Anderson, Michele K -- Brockton, Virginia -- Buckley, Katherine M -- Cohen, Avis H -- Fugmann, Sebastian D -- Hibino, Taku -- Loza-Coll, Mariano -- Majeske, Audrey J -- Messier, Cynthia -- Nair, Sham V -- Pancer, Zeev -- Terwilliger, David P -- Agca, Cavit -- Arboleda, Enrique -- Chen, Nansheng -- Churcher, Allison M -- Hallbook, F -- Humphrey, Glen W -- Idris, Mohammed M -- Kiyama, Takae -- Liang, Shuguang -- Mellott, Dan -- Mu, Xiuqian -- Murray, Greg -- Olinski, Robert P -- Raible, Florian -- Rowe, Matthew -- Taylor, John S -- Tessmar-Raible, Kristin -- Wang, D -- Wilson, Karen H -- Yaguchi, Shunsuke -- Gaasterland, Terry -- Galindo, Blanca E -- Gunaratne, Herath J -- Juliano, Celina -- Kinukawa, Masashi -- Moy, Gary W -- Neill, Anna T -- Nomura, Mamoru -- Raisch, Michael -- Reade, Anna -- Roux, Michelle M -- Song, Jia L -- Su, Yi-Hsien -- Townley, Ian K -- Voronina, Ekaterina -- Wong, Julian L -- Amore, Gabriele -- Branno, Margherita -- Brown, Euan R -- Cavalieri, Vincenzo -- Duboc, Veronique -- Duloquin, Louise -- Flytzanis, Constantin -- Gache, Christian -- Lapraz, Francois -- Lepage, Thierry -- Locascio, Annamaria -- Martinez, Pedro -- Matassi, Giorgio -- Matranga, Valeria -- Range, Ryan -- Rizzo, Francesca -- Rottinger, Eric -- Beane, Wendy -- Bradham, Cynthia -- Byrum, Christine -- Glenn, Tom -- Hussain, Sofia -- Manning, Gerard -- Miranda, Esther -- Thomason, Rebecca -- Walton, Katherine -- Wikramanayke, Athula -- Wu, Shu-Yu -- Xu, Ronghui -- Brown, C Titus -- Chen, Lili -- Gray, Rachel F -- Lee, Pei Yun -- Nam, Jongmin -- Oliveri, Paola -- Smith, Joel -- Muzny, Donna -- Bell, Stephanie -- Chacko, Joseph -- Cree, Andrew -- Curry, Stacey -- Davis, Clay -- Dinh, Huyen -- Dugan-Rocha, Shannon -- Fowler, Jerry -- Gill, Rachel -- Hamilton, Cerrissa -- Hernandez, Judith -- Hines, Sandra -- Hume, Jennifer -- Jackson, Laronda -- Jolivet, Angela -- Kovar, Christie -- Lee, Sandra -- Lewis, Lora -- Miner, George -- Morgan, Margaret -- Nazareth, Lynne V -- Okwuonu, Geoffrey -- Parker, David -- Pu, Ling-Ling -- Thorn, Rachel -- Wright, Rita -- 2P42 ESO7381/PHS HHS/ -- 5 U54 HG003273/HG/NHGRI NIH HHS/ -- EY11930/EY/NEI NIH HHS/ -- F32 ESO12794/PHS HHS/ -- F32 HD047136/HD/NICHD NIH HHS/ -- F32 HD047136-02/HD/NICHD NIH HHS/ -- F32 HD047136-03/HD/NICHD NIH HHS/ -- F32-HD47136/HD/NICHD NIH HHS/ -- GM058231/GM/NIGMS NIH HHS/ -- GM070840/GM/NIGMS NIH HHS/ -- GM61005/GM/NIGMS NIH HHS/ -- GM61464/GM/NIGMS NIH HHS/ -- HD-37105/HD/NICHD NIH HHS/ -- HD039948/HD/NICHD NIH HHS/ -- HD14483/HD/NICHD NIH HHS/ -- HD66219/HD/NICHD NIH HHS/ -- P30-CA14051/CA/NCI NIH HHS/ -- R01 ES006272/ES/NIEHS NIH HHS/ -- R01 ES006272-13/ES/NIEHS NIH HHS/ -- R01 GM070840/GM/NIGMS NIH HHS/ -- R01 HD028152/HD/NICHD NIH HHS/ -- R01ES006272/ES/NIEHS NIH HHS/ -- R37-HD12896/HD/NICHD NIH HHS/ -- RR-15044/RR/NCRR NIH HHS/ -- S19916/Biotechnology and Biological Sciences Research Council/United Kingdom -- T32 GM007601/GM/NIGMS NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2006 Nov 10;314(5801):941-52.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17095691" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Calcification, Physiologic ; Cell Adhesion Molecules/genetics/physiology ; Complement Activation/genetics ; Computational Biology ; Embryonic Development/genetics ; Evolution, Molecular ; Gene Expression Regulation, Developmental ; Genes ; *Genome ; Immunity, Innate/genetics ; Immunologic Factors/genetics/physiology ; Male ; Nervous System Physiological Phenomena ; Proteins/genetics/physiology ; *Sequence Analysis, DNA ; Signal Transduction ; Strongylocentrotus purpuratus/embryology/*genetics/immunology/physiology ; Transcription Factors/genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
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    The genome of black cottonwood, Populus trichocarpa (Torr. & Gray) (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-09-16
    Description: 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.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tuskan, G A -- 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, R R -- Bhalerao, R P -- Blaudez, D -- Boerjan, W -- Brun, A -- Brunner, A -- Busov, V -- Campbell, M -- Carlson, J -- Chalot, M -- Chapman, J -- Chen, G-L -- Cooper, D -- Coutinho, P M -- 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, J-C -- Locascio, P -- Lou, Y -- Lucas, S -- Martin, F -- Montanini, B -- Napoli, C -- Nelson, D R -- 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, C-J -- 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 -- New York, N.Y. -- Science. 2006 Sep 15;313(5793):1596-604.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA. gtk@ornl.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16973872" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/genetics ; Chromosome Mapping ; Computational Biology ; Evolution, Molecular ; Expressed Sequence Tags ; *Gene Duplication ; Gene Expression ; Genes, Plant ; *Genome, Plant ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; Plant Proteins/chemistry/genetics ; Polymorphism, Single Nucleotide ; Populus/*genetics/growth & development/metabolism ; Protein Structure, Tertiary ; RNA, Plant/analysis ; RNA, Untranslated/analysis ; *Sequence Analysis, DNA
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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