Rudd S

References (4)

Title : Draft genome sequences of Helicobacter pylori isolates from Malaysia, cultured from patients with functional dyspepsia and gastric cancer - Gunaletchumy_2012_J.Bacteriol_194_5695
Author(s) : Gunaletchumy SP , Teh X , Khosravi Y , Ramli NS , Chua EG , Kavitha T , Mason JN , Lee HT , Alias H , Zaidan NZ , Yassin NB , Tay LC , Rudd S , Mitchell HM , Kaakoush NO , Loke MF , Goh KL , Vadivelu J
Ref : Journal of Bacteriology , 194 :5695 , 2012
Abstract : Helicobacter pylori is the main bacterial causative agent of gastroduodenal disorders and a risk factor for gastric adenocarcinoma and mucosa-associated lymphoid tissue (MALT) lymphoma. The draft genomes of 10 closely related H. pylori isolates from the multiracial Malaysian population will provide an insight into the genetic diversity of isolates in Southeast Asia. These isolates were cultured from gastric biopsy samples from patients with functional dyspepsia and gastric cancer. The availability of this genomic information will provide an opportunity for examining the evolution and population structure of H. pylori isolates from Southeast Asia, where the East meets the West.
ESTHER : Gunaletchumy_2012_J.Bacteriol_194_5695
PubMedSearch : Gunaletchumy_2012_J.Bacteriol_194_5695
PubMedID: 23012278

Title : The genome sequence of the filamentous fungus Neurospora crassa - Galagan_2003_Nature_422_859
Author(s) : Galagan JE , Calvo SE , Borkovich KA , Selker EU , Read ND , Jaffe D , FitzHugh W , Ma LJ , Smirnov S , Purcell S , Rehman B , Elkins T , Engels R , Wang S , Nielsen CB , Butler J , Endrizzi M , Qui D , Ianakiev P , Bell-Pedersen D , Nelson MA , Werner-Washburne M , Selitrennikoff CP , Kinsey JA , Braun EL , Zelter A , Schulte U , Kothe GO , Jedd G , Mewes W , Staben C , Marcotte E , Greenberg D , Roy A , Foley K , Naylor J , Stange-Thomann N , Barrett R , Gnerre S , Kamal M , Kamvysselis M , Mauceli E , Bielke C , Rudd S , Frishman D , Krystofova S , Rasmussen C , Metzenberg RL , Perkins DD , Kroken S , Cogoni C , Macino G , Catcheside D , Li W , Pratt RJ , Osmani SA , DeSouza CP , Glass L , Orbach MJ , Berglund JA , Voelker R , Yarden O , Plamann M , Seiler S , Dunlap J , Radford A , Aramayo R , Natvig DO , Alex LA , Mannhaupt G , Ebbole DJ , Freitag M , Paulsen I , Sachs MS , Lander ES , Nusbaum C , Birren B
Ref : Nature , 422 :859 , 2003
Abstract : Neurospora crassa is a central organism in the history of twentieth-century genetics, biochemistry and molecular biology. Here, we report a high-quality draft sequence of the N. crassa genome. The approximately 40-megabase genome encodes about 10,000 protein-coding genes--more than twice as many as in the fission yeast Schizosaccharomyces pombe and only about 25% fewer than in the fruitfly Drosophila melanogaster. Analysis of the gene set yields insights into unexpected aspects of Neurospora biology including the identification of genes potentially associated with red light photobiology, genes implicated in secondary metabolism, and important differences in Ca2+ signalling as compared with plants and animals. Neurospora possesses the widest array of genome defence mechanisms known for any eukaryotic organism, including a process unique to fungi called repeat-induced point mutation (RIP). Genome analysis suggests that RIP has had a profound impact on genome evolution, greatly slowing the creation of new genes through genomic duplication and resulting in a genome with an unusually low proportion of closely related genes.
ESTHER : Galagan_2003_Nature_422_859
PubMedSearch : Galagan_2003_Nature_422_859
PubMedID: 12712197
Gene_locus related to this paper: neucr-5E6.090 , neucr-64C2.080 , neucr-90C4.300 , neucr-a7uw78 , neucr-a7uwh6 , neucr-a7uwy7 , neucr-apth1 , neucr-ATG15 , neucr-B7H23.190 , neucr-B11O8.160 , neucr-B13B3.090 , neucr-B14D6.130 , neucr-B18E6.050 , neucr-B19A17.360 , neucr-B23G1.090 , neucr-CBPYA , neucr-MET5 , neucr-NCU00292.1 , neucr-NCU00350.1 , neucr-NCU00536.1 , neucr-NCU00825.1 , neucr-NCU02148.1 , neucr-NCU02679.1 , neucr-NCU02904.1 , neucr-NCU02924.1 , neucr-NCU03158.1 , neucr-NCU04930.1 , neucr-NCU06332.1 , neucr-NCU06573.1 , neucr-NCU07081.1 , neucr-NCU07415.1 , neucr-NCU07909.1 , neucr-NCU08752.1 , neucr-NCU09575.1 , neucr-NCU10022.1 , neucr-ppme1 , neucr-q6mfs7 , neucr-q7rxb4 , neucr-q7rxv5 , neucr-q7ry06 , neucr-q7ryd2 , neucr-q7rzk2 , neucr-q7s0g7 , neucr-q7s1x0 , neucr-q7s2b3 , neucr-q7s2c5 , neucr-q7s2p4 , neucr-q7s2u9 , neucr-q7s3c6 , neucr-q7s3c8 , neucr-q7s3m2 , neucr-q7s4e3 , neucr-q7s4f8 , neucr-q7s4j4 , neucr-q7s5d6 , neucr-q7s5m2 , neucr-q7s5v8 , neucr-q7s6c5 , neucr-q7s8h2 , neucr-q7s070 , neucr-q7s082 , neucr-q7s134 , neucr-q7s216 , neucr-q7s259 , neucr-q7s260 , neucr-q7s283 , neucr-q7s512 , neucr-q7s736 , neucr-q7s828 , neucr-q7s897 , neucr-q7sbf9 , neucr-q7sbn0 , neucr-q7scr4 , neucr-q7sdw5 , neucr-q7sdx9 , neucr-q7se51 , neucr-q7sea3 , neucr-q7sez8 , neucr-q7sff7 , neucr-q7sga3 , neucr-q7sgj0 , neucr-q7sgp3 , neucr-q7sha3 , neucr-q7sha5 , neucr-q7shu8 , neucr-q9p6a7 , neucr-q872l1 , neucr-f5hbr2 , neucr-q7ry64

Title : Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana - Tabata_2000_Nature_408_823
Author(s) : Tabata S , Kaneko T , Nakamura Y , Kotani H , Kato T , Asamizu E , Miyajima N , Sasamoto S , Kimura T , Hosouchi T , Kawashima K , Kohara M , Matsumoto M , Matsuno A , Muraki A , Nakayama S , Nakazaki N , Naruo K , Okumura S , Shinpo S , Takeuchi C , Wada T , Watanabe A , Yamada M , Yasuda M , Sato S , de la Bastide M , Huang E , Spiegel L , Gnoj L , O'Shaughnessy A , Preston R , Habermann K , Murray J , Johnson D , Rohlfing T , Nelson J , Stoneking T , Pepin K , Spieth J , Sekhon M , Armstrong J , Becker M , Belter E , Cordum H , Cordes M , Courtney L , Courtney W , Dante M , Du H , Edwards J , Fryman J , Haakensen B , Lamar E , Latreille P , Leonard S , Meyer R , Mulvaney E , Ozersky P , Riley A , Strowmatt C , Wagner-McPherson C , Wollam A , Yoakum M , Bell M , Dedhia N , Parnell L , Shah R , Rodriguez M , See LH , Vil D , Baker J , Kirchoff K , Toth K , King L , Bahret A , Miller B , Marra M , Martienssen R , McCombie WR , Wilson RK , Murphy G , Bancroft I , Volckaert G , Wambutt R , Dusterhoft A , Stiekema W , Pohl T , Entian KD , Terryn N , Hartley N , Bent E , Johnson S , Langham SA , McCullagh B , Robben J , Grymonprez B , Zimmermann W , Ramsperger U , Wedler H , Balke K , Wedler E , Peters S , van Staveren M , Dirkse W , Mooijman P , Lankhorst RK , Weitzenegger T , Bothe G , Rose M , Hauf J , Berneiser S , Hempel S , Feldpausch M , Lamberth S , Villarroel R , Gielen J , Ardiles W , Bents O , Lemcke K , Kolesov G , Mayer K , Rudd S , Schoof H , Schueller C , Zaccaria P , Mewes HW , Bevan M , Fransz P
Ref : Nature , 408 :823 , 2000
Abstract : The genome of the model plant Arabidopsis thaliana has been sequenced by an international collaboration, The Arabidopsis Genome Initiative. Here we report the complete sequence of chromosome 5. This chromosome is 26 megabases long; it is the second largest Arabidopsis chromosome and represents 21% of the sequenced regions of the genome. The sequence of chromosomes 2 and 4 have been reported previously and that of chromosomes 1 and 3, together with an analysis of the complete genome sequence, are reported in this issue. Analysis of the sequence of chromosome 5 yields further insights into centromere structure and the sequence determinants of heterochromatin condensation. The 5,874 genes encoded on chromosome 5 reveal several new functions in plants, and the patterns of gene organization provide insights into the mechanisms and extent of genome evolution in plants.
ESTHER : Tabata_2000_Nature_408_823
PubMedSearch : Tabata_2000_Nature_408_823
PubMedID: 11130714
Gene_locus related to this paper: arath-At5g11650 , arath-At5g16120 , arath-at5g18630 , arath-AT5G20520 , arath-At5g21950 , arath-AT5G27320 , arath-CXE15 , arath-F1N13.220 , arath-F14F8.240 , arath-q3e9e4 , arath-q8lae9 , arath-Q8LFB7 , arath-q9ffg7 , arath-q9fij5 , arath-Q9LVU7 , arath-q66gm8 , arath-SCPL34 , arath-B9DFR3 , arath-a0a1p8bcz0

Title : Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana - Salanoubat_2000_Nature_408_820
Author(s) : Salanoubat M , Lemcke K , Rieger M , Ansorge W , Unseld M , Fartmann B , Valle G , Blocker H , Perez-Alonso M , Obermaier B , Delseny M , Boutry M , Grivell LA , Mache R , Puigdomenech P , de Simone V , Choisne N , Artiguenave F , Robert C , Brottier P , Wincker P , Cattolico L , Weissenbach J , Saurin W , Quetier F , Schafer M , Muller-Auer S , Gabel C , Fuchs M , Benes V , Wurmbach E , Drzonek H , Erfle H , Jordan N , Bangert S , Wiedelmann R , Kranz H , Voss H , Holland R , Brandt P , Nyakatura G , Vezzi A , D'Angelo M , Pallavicini A , Toppo S , Simionati B , Conrad A , Hornischer K , Kauer G , Lohnert TH , Nordsiek G , Reichelt J , Scharfe M , Schon O , Bargues M , Terol J , Climent J , Navarro P , Collado C , Perez-Perez A , Ottenwalder B , Duchemin D , Cooke R , Laudie M , Berger-Llauro C , Purnelle B , Masuy D , de Haan M , Maarse AC , Alcaraz JP , Cottet A , Casacuberta E , Monfort A , Argiriou A , Flores M , Liguori R , Vitale D , Mannhaupt G , Haase D , Schoof H , Rudd S , Zaccaria P , Mewes HW , Mayer KF , Kaul S , Town CD , Koo HL , Tallon LJ , Jenkins J , Rooney T , Rizzo M , Walts A , Utterback T , Fujii CY , Shea TP , Creasy TH , Haas B , Maiti R , Wu D , Peterson J , Van Aken S , Pai G , Militscher J , Sellers P , Gill JE , Feldblyum TV , Preuss D , Lin X , Nierman WC , Salzberg SL , White O , Venter JC , Fraser CM , Kaneko T , Nakamura Y , Sato S , Kato T , Asamizu E , Sasamoto S , Kimura T , Idesawa K , Kawashima K , Kishida Y , Kiyokawa C , Kohara M , Matsumoto M , Matsuno A , Muraki A , Nakayama S , Nakazaki N , Shinpo S , Takeuchi C , Wada T , Watanabe A , Yamada M , Yasuda M , Tabata S
Ref : Nature , 408 :820 , 2000
Abstract : Arabidopsis thaliana is an important model system for plant biologists. In 1996 an international collaboration (the Arabidopsis Genome Initiative) was formed to sequence the whole genome of Arabidopsis and in 1999 the sequence of the first two chromosomes was reported. The sequence of the last three chromosomes and an analysis of the whole genome are reported in this issue. Here we present the sequence of chromosome 3, organized into four sequence segments (contigs). The two largest (13.5 and 9.2 Mb) correspond to the top (long) and the bottom (short) arms of chromosome 3, and the two small contigs are located in the genetically defined centromere. This chromosome encodes 5,220 of the roughly 25,500 predicted protein-coding genes in the genome. About 20% of the predicted proteins have significant homology to proteins in eukaryotic genomes for which the complete sequence is available, pointing to important conserved cellular functions among eukaryotes.
ESTHER : Salanoubat_2000_Nature_408_820
PubMedSearch : Salanoubat_2000_Nature_408_820
PubMedID: 11130713
Gene_locus related to this paper: arath-MES17 , arath-AT3G12150 , arath-At3g61680 , arath-AT3g62590 , arath-CXE12 , arath-eds1 , arath-SCP25 , arath-F1P2.110 , arath-F1P2.140 , arath-F11F8.28 , arath-F14D17.80 , arath-F16B3.4 , arath-SCP27 , arath-At3g50790 , arath-At3g05600 , arath-PAD4 , arath-At3g51000 , arath-SCP16 , arath-gid1 , arath-GID1B , arath-Q9LUG8 , arath-Q84JS1 , arath-Q9SFF6 , arath-q9m236 , arath-q9sr22 , arath-q9sr23 , arath-SCP7 , arath-SCP14 , arath-SCP15 , arath-SCP17 , arath-SCP36 , arath-SCP37 , arath-SCP39 , arath-SCP40 , arath-SCP49 , arath-T19F11.2