Asamizu E

References (17)

Title : Identification of the carotenoid modifying gene PALE YELLOW PETAL 1 as an essential factor in xanthophyll esterification and yellow flower pigmentation in tomato (Solanum lycopersicum) - Ariizumi_2014_Plant.J_79_453
Author(s) : Ariizumi T , Kishimoto S , Kakami R , Maoka T , Hirakawa H , Suzuki Y , Ozeki Y , Shirasawa K , Bernillon S , Okabe Y , Moing A , Asamizu E , Rothan C , Ohmiya A , Ezura H
Ref : Plant J , 79 :453 , 2014
Abstract : Xanthophylls, the pigments responsible for yellow to red coloration, are naturally occurring carotenoid compounds in many colored tissues of plants. These pigments are esterified within the chromoplast; however, little is known about the mechanisms underlying their accumulation in flower organs. In this study, we characterized two allelic tomato (Solanum lycopersicum L.) mutants, pale yellow petal (pyp) 1-1 and pyp1-2, that have reduced yellow color intensity in the petals and anthers due to loss-of-function mutations. Carotenoid analyses showed that the yellow flower organs of wild-type tomato contained high levels of xanthophylls that largely consisted of neoxanthin and violaxanthin esterified with myristic and/or palmitic acids. Functional disruption of PYP1 resulted in loss of xanthophyll esters, which was associated with a reduction in the total carotenoid content and disruption of normal chromoplast development. These findings suggest that xanthophyll esterification promotes the sequestration of carotenoids in the chromoplast and that accumulation of these esters is important for normal chromoplast development. Next-generation sequencing coupled with map-based positional cloning identified the mutant alleles responsible for the pyp1 phenotype. PYP1 most likely encodes a carotenoid modifying protein that plays a vital role in the production of xanthophyll esters in tomato anthers and petals. Our results provide insight into the molecular mechanism underlying the production of xanthophyll esters in higher plants, thereby shedding light on a longstanding mystery.
ESTHER : Ariizumi_2014_Plant.J_79_453
PubMedSearch : Ariizumi_2014_Plant.J_79_453
PubMedID: 24888879
Gene_locus related to this paper: pethy-XES

Title : Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence features of the regions of 4,504,864 bp covered by sixty P1 and TAC clones - Sato_2000_DNA.Res_7_131
Author(s) : Sato S , Nakamura Y , Kaneko T , Katoh T , Asamizu E , Tabata S
Ref : DNA Research , 7 :131 , 2000
Abstract : Based on the physical map of Arabidopsis thaliana chromosome 3 previously constructed with CIC YAC, TAC, P1 and BAC clones (Sato, S. et al., DNA Res., 5, 163-168, 1998), a total of 60 P1 and TAC clones were sequenced, and the sequence features of the resulting 4,504,864 bp regions were analyzed by applying various computer programs for similarity search and gene modeling. As a result, a total of 1054 potential protein-coding genes were identified. The average density of the genes identified was 1 gene per 4066 bp. Introns were observed in 77% of the genes, and the average number per gene and the average length of the introns were 3.9 and 156 bp, respectively. These sequence features are essentially identical to those of chromosome 5 in our previous reports, but the gene density was slightly higher than that observed for chromosomes 2 and 4. The regions also contained 10 tRNA genes when searched by similarity to reported tRNA genes and the tRNA scan-SE program. The sequence data and information on the potential genes are available through the World Wide Web database KAOS (Kazusa Arabidopsis data Opening Site) at http:\/\/www.kazusa.or.jp/kaos/.
ESTHER : Sato_2000_DNA.Res_7_131
PubMedSearch : Sato_2000_DNA.Res_7_131
PubMedID: 10819329
Gene_locus related to this paper: arath-At3g14360 , arath-At3g27325 , arath-Y3684 , arath-Q9LI62 , arath-Q9LUG8 , arath-Q9LUH1 , arath-Q6NKN2 , arath-Q9LW14 , arath-Q9LW28 , arath-SCP21 , arath-SCP33

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 : Structural analysis of Arabidopsis thaliana chromosome 3. II. Sequence features of the 4,251,695 bp regions covered by 90 P1, TAC and BAC clones - Kaneko_2000_DNA.Res_7_217
Author(s) : Kaneko T , Katoh T , Sato S , Nakamura A , Asamizu E , Tabata S
Ref : DNA Research , 7 :217 , 2000
Abstract : To deduce the entire sequence of the top arm of the Arabidopsis thaliana chromosome 3, the sequence determination was performed on a total of 90 P1, TAC and BAC clones chosen according to our sequencing strategy. Sequence features of the resulting 4,251,695 bp regions were analyzed with various computer programs for similarity search and gene modeling. As a result, a total of 941 potential protein-coding genes were identified. The average density of the genes identified was 1 gene per 4210 bp. Introns were observed in 73% of the genes, and the average number per gene and the average length of the introns were 3.6 and 159 bp, respectively. These sequence features are essentially identical to those of chromosomes 3 and 5 in our previous reports. The regions also contained 14 tRNA genes when searched by similarity to reported tRNA genes and the tRNA scan-SE program. The sequence data and information on the potential genes are available through the World Wide Web database KAOS (Kazusa Arabidopsis data Opening Site) at http:\/\/www.kazusa.or.jp/kaos/.
ESTHER : Kaneko_2000_DNA.Res_7_217
PubMedSearch : Kaneko_2000_DNA.Res_7_217
PubMedID: 10907853
Gene_locus related to this paper: arath-SCP16 , arath-CXE11 , arath-q9lhe8 , arath-Q9LJI1 , arath-Q9LK01 , arath-SCP15

Title : Structural analysis of Arabidopsis thaliana chromosome 5. X. Sequence features of the regions of 3,076,755 bp covered by sixty P1 and TAC clones - Sato_2000_DNA.Res_7_31
Author(s) : Sato S , Nakamura Y , Kaneko T , Katoh T , Asamizu E , Kotani H , Tabata S
Ref : DNA Research , 7 :31 , 2000
Abstract : In our ongoing project to deduce the nucleotide sequence of Arabidopsis thaliana chromosome 5, non-redundant P1 and TAC clones have been sequenced on the basis of the fine physical map, and as of January, 2000, the sequences of 16.6 Mb representing approximately 60% of chromosome 5 have been accumulated and released at our web site. Along with the sequence determination, structural features of the sequenced regions have been analyzed by applying a variety of computer programs, and we already predicted a total of 2697 potential protein coding genes in the 11,166,130 bp regions, which are covered by 159 P1 and TAC clones. In this paper, we describe the structural features of the 3,076,755 bp regions covered by newly analyzed 60 P1 and TAC clones. A total of 715 potential protein coding genes were identified, giving an average density of the genes identified of 1 gene per 4001 bp. Introns were observed in 80% of the genes, and the average number per gene and the average length of the introns were 4.5 and 147 bp, respectively. These sequence features are nearly identical to those in our latest report in which the data were compiled based on a new standard of gene assignment including the computer-predicted hypothetical genes. The regions also contained 12 tRNA genes when searched by similarity to reported tRNA genes and the tRNA scan-SE program. The sequence data and information on the potential genes are available through the World Wide Web database KAOS (Kazusa Arabidopsis data Opening Site) at http:\/\/www.kazusa.or.jp/kaos/.
ESTHER : Sato_2000_DNA.Res_7_31
PubMedSearch : Sato_2000_DNA.Res_7_31
PubMedID: 10718197
Gene_locus related to this paper: arath-At5g47330 , arath-AT5G51180 , arath-AT5G62180 , arath-At5g67050 , arath-MES18 , arath-CXE18 , arath-Q9LTX5 , arath-Q9LVS4 , arath-Q9LVS5 , arath-Q9LVU7 , arath-Q9LVX9 , arath-SCP41 , arath-SCP42

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

Title : Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti - Kaneko_2000_DNA.Res_7_331
Author(s) : Kaneko T , Nakamura Y , Sato S , Asamizu E , Kato T , Sasamoto S , Watanabe A , Idesawa K , Ishikawa A , Kawashima K , Kimura T , Kishida Y , Kiyokawa C , Kohara M , Matsumoto M , Matsuno A , Mochizuki Y , Nakayama S , Nakazaki N , Shimpo S , Sugimoto M , Takeuchi C , Yamada M , Tabata S
Ref : DNA Research , 7 :331 , 2000
Abstract : The complete nucleotide sequence of the genome of a symbiotic bacterium Mesorhizobium loti strain MAFF303099 was determined. The genome of M. loti consisted of a single chromosome (7,036,071 bp) and two plasmids, designated as pMLa (351,911 bp) and pMLb (208, 315 bp). The chromosome comprises 6752 potential protein-coding genes, two sets of rRNA genes and 50 tRNA genes representing 47 tRNA species. Fifty-four percent of the potential protein genes showed sequence similarity to genes of known function, 21% to hypothetical genes, and the remaining 25% had no apparent similarity to reported genes. A 611-kb DNA segment, a highly probable candidate of a symbiotic island, was identified, and 30 genes for nitrogen fixation and 24 genes for nodulation were assigned in this region. Codon usage analysis suggested that the symbiotic island as well as the plasmids originated and were transmitted from other genetic systems. The genomes of two plasmids, pMLa and pMLb, contained 320 and 209 potential protein-coding genes, respectively, for a variety of biological functions. These include genes for the ABC-transporter system, phosphate assimilation, two-component system, DNA replication and conjugation, but only one gene for nodulation was identified.
ESTHER : Kaneko_2000_DNA.Res_7_331
PubMedSearch : Kaneko_2000_DNA.Res_7_331
PubMedID: 11214968
Gene_locus related to this paper: meslo-acoc , meslo-EphB , meslo-est , meslo-lipest , meslo-MLL0014 , meslo-MLL0351 , meslo-MLL0537 , meslo-mll0601 , meslo-MLL0618 , meslo-MLL1209 , meslo-MLL1226 , meslo-mll1328 , meslo-MLL1329 , meslo-MLL1495 , meslo-MLL1869 , meslo-mll1900 , meslo-MLL2018 , meslo-MLL2072 , meslo-mll2481 , meslo-mll2689 , meslo-MLL2788 , meslo-MLL3556 , meslo-MLL3568 , meslo-MLL3682 , meslo-mll3776 , meslo-MLL4497 , meslo-MLL4552 , meslo-MLL5128 , meslo-mll5179 , meslo-mll5392 , meslo-MLL5717 , meslo-mll5743 , meslo-MLL6746 , meslo-MLL6752 , meslo-mll6871 , meslo-MLL7643 , meslo-mll7742 , meslo-MLL9722 , meslo-MLR0094 , meslo-mlr0145 , meslo-mlr0170 , meslo-MLR0240 , meslo-mlr0493 , meslo-MLR0937 , meslo-mlr0978 , meslo-MLR0992 , meslo-MLR1612 , meslo-mlr1789 , meslo-mlr1864 , meslo-mlr2176 , meslo-MLR2262 , meslo-mlr2612 , meslo-mlr2710 , meslo-mlr3034 , meslo-MLR3538 , meslo-mlr3816 , meslo-mlr4436 , meslo-MLR4903 , meslo-MLR5045 , meslo-MLR5063 , rhilo-dhaa , meslo-MLR6087 , meslo-MLR6657 , meslo-mlr6682 , meslo-mlr6683 , meslo-MLR6684 , meslo-MLR6787 , meslo-MLR6993 , meslo-mlr6999 , meslo-mlr7206 , meslo-mlr7232 , meslo-mlr7803 , meslo-MLR9053 , meslo-mlr9622 , meslo-mlr9641 , rhilo-MLL0076 , rhilo-MLL1824 , rhilo-MLL7123 , rhilo-MLL8374 , rhilo-MLR1247 , rhilo-MLR2444 , rhilo-MLR4383 , rhilo-MLR8175 , rhilo-q98nf6 , rhilo-q98nf8 , rhilo-q988i9

Title : Structural analysis of Arabidopsis thaliana chromosome 5. IX. Sequence features of the regions of 1,011,550 bp covered by seventeen P1 and TAC clones - Kaneko_1999_DNA.Res_6_183
Author(s) : Kaneko T , Katoh T , Sato S , Nakamura Y , Asamizu E , Kotani H , Miyajima N , Tabata S
Ref : DNA Research , 6 :183 , 1999
Abstract : In this series of projects sequencing the entire genome of Arabidopsis thaliana chromosome 5, non-redundant P1 and TAC clones have been sequenced according to the fine physical map, and as of May 7, 1999, the sequences of 16.2 Mb representing approximately 60% of chromosome 5 have been accumulated and released at our web site. In parallel, structural features of the sequenced regions have been analyzed by applying a variety of computer programs, and to date we have predicted a total of 2380 potential protein-coding genes in the 10,154,580 bp regions, which are covered by 142 P1 and TAC clones. In this paper, we newly analyzed the structural features of the 1,011,550 bp regions covered by additional 17 P1 and TAC clones, and predicted 298 protein-coding genes. The average density of the genes identified was 1 gene per 3394 bp. Introns were observed in 67% of the genes, and the average number per gene and the average length of the introns were 3.2 and 159 bp, respectively. The gene density became higher than the value estimated in the previously analyzed regions (1 gene per 4,267 bp), as the data in this paper were compiled based on a new standard of gene assignment including the computer-predicted hypothetical genes. The regions also contained 8 tRNA genes when searched by similarity to reported tRNA genes and the tRNA scan-SE program. The sequence data and information on the potential genes are available on the database KAOS (Kazusa Arabidopsis data Opening Site) at http:\/\/www.kazusa.or.jp/arabi/.
ESTHER : Kaneko_1999_DNA.Res_6_183
PubMedSearch : Kaneko_1999_DNA.Res_6_183
PubMedID: 10470850
Gene_locus related to this paper: arath-At5g37710 , arath-SCP19 , arath-Q9FI59

Title : Structural analysis of Arabidopsis thaliana chromosome 5. VIII. Sequence features of the regions of 1,081,958 bp covered by seventeen physically assigned P1 and TAC clones. -
Author(s) : Asamizu E , Sato S , Kaneko T , Nakamura Y , Kotani H , Miyajima N , Tabata S
Ref : DNA Research , 5 :379 , 1998
PubMedID: 10048488
Gene_locus related to this paper: arath-At5g14930 , arath-at5g18630 , arath-AT5G19050 , arath-At5g24180 , arath-AT5G24190 , arath-At5g24200 , arath-F2G14.100 , arath-F6H11.120 , arath-F9G14.280 , arath-F14F8.240 , arath-HNL , arath-At5g14310

Title : Structural analysis of Arabidopsis thaliana chromosome 5. VII. Sequence features of the regions of 1,013,767 bp covered by sixteen physically assigned P1 and TAC clones - Nakamura_1998_DNA.Res_5_297
Author(s) : Nakamura Y , Sato S , Asamizu E , Kaneko T , Kotani H , Miyajima N , Tabata S
Ref : DNA Research , 5 :297 , 1998
Abstract : Sixteen P1 and TAC clones assigned to Arabidopsis thaliana chromosome 5 were sequenced, and their sequence features were analyzed using various computer programs. The total length of the sequences determined was 1,013,767 bp. Together with the nucleotide sequences of 109 clones previously reported, the regions of chromosome 5 sequenced so far now total 9,072,622 bp, which presumably covers approximately one-third of the chromosome. A similarity search against the reported gene sequences predicted the presence of a total of 225 protein-coding genes and/or gene segments in the newly sequenced regions, indicating an average gene density of one gene per 4.5 kb. Introns were identified in 72.4% of the potential protein genes for which the entire gene structure was predicted, and the average number per gene and the average length of the introns were 3.3 and 163 bp, respectively. These sequence features are essentially identical to those in the previously reported sequences. The sequence data and gene information are available on the World Wide Web database KAOS (Kazusa Arabidopsis data Opening Site) at http://www.kazusa.or.jp/arabi/.
ESTHER : Nakamura_1998_DNA.Res_5_297
PubMedSearch : Nakamura_1998_DNA.Res_5_297
PubMedID: 9872454
Gene_locus related to this paper: arath-At5g41900 , arath-Q9FJ29

Title : Structural analysis of Arabidopsis thaliana chromosome 5. V. Sequence features of the regions of 1,381,565 bp covered by twenty one physically assigned P1 and TAC clones - Kaneko_1998_DNA.Res_5_131
Author(s) : Kaneko T , Kotani H , Nakamura Y , Sato S , Asamizu E , Miyajima N , Tabata S
Ref : DNA Research , 5 :131 , 1998
Abstract : The nucleotide sequences of 21 P1 and TAC clones which have been precisely localized to the fine physical map of the Arabidopsis thaliana chromosome 5, were determined, and their sequence features were analyzed. The total length of the regions sequenced in this study were 1,381,565 bp, bringing the total length of the chromosome 5 sequences determined so far to 6,691,670 bp together with the regions of the 69 clones previously reported. By computer-aided analyses including similarity search against protein and EST databases and gene modeling with computer programs, a total of 337 potential protein-coding genes and/or gene segments were identified on the basis of similarity to the reported gene sequences. An average density of the genes and/or gene segments thus assigned was 1 gene/4,100 bp. Introns were identified in 76.7% of the potential protein genes for which the entire gene structure were predicted, and the average number per gene and the average length of the introns were 3.9 and 176 bp, respectively. These sequence features are essentially identical to those in the previously reported sequences. The numbers of the Arabidopsis ESTs matched to each of the predicted genes have been counted to monitor the transcription level. The sequence data and gene information are available on the World Wide Web database KAOS (Kazusa Arabidopsis data Opening Site) at http:@www.kazusa.or.jp@arabi
ESTHER : Kaneko_1998_DNA.Res_5_131
PubMedSearch : Kaneko_1998_DNA.Res_5_131
PubMedID: 9679202
Gene_locus related to this paper: arath-AT5G39220 , arath-Q9FKP9

Title : Structural analysis of Arabidopsis thaliana chromosome 5. IV. Sequence features of the regions of 1,456,315 bp covered by nineteen physically assigned P1 and TAC clones - Sato_1998_DNA.Res_5_41
Author(s) : Sato S , Kaneko T , Kotani H , Nakamura Y , Asamizu E , Miyajima N , Tabata S
Ref : DNA Research , 5 :41 , 1998
Abstract : Nineteen P1 and TAC clones, which have been precisely localized to the fine physical map of Arabidopsis thaliana chromosome 5, were newly sequenced, and their sequence features were analysed. The total length of the clones sequenced was 1,456,315 bp. Together with the previously reported sequences, the regions of chromosome 5 that have been sequenced to date is now 5,310,105 bp. When the sequences determined in this study were subjected to similarity search against protein and expressed sequence tag (EST) databases and analysis with computer programs for gene modeling, a total of 354 potential protein-coding genes and/or gene segments were identified. The average density of the assigned genes and/or gene segments was one gene per 4,114 bp. Introns were identified in 75% of the potential protein genes, and the average number per gene and the average length of the introns were 3.7 and 194 bp, respectively. These sequence features are essentially identical to those in the previously reported sequences. The numbers of the Arabidopsis ESTs matched to each of the predicted genes have been counted to monitor the transcription level. The sequence data and gene information are available on the World Wide Web database KAOS (the Kazusa Arabidopsis data Opening Site) at http://www.kazusa.or.jp/arabi/.
ESTHER : Sato_1998_DNA.Res_5_41
PubMedSearch : Sato_1998_DNA.Res_5_41
PubMedID: 9628582
Gene_locus related to this paper: arath-AT5G41120 , arath-At5g41130 , arath-F6H11.120

Title : Structural analysis of Arabidopsis thaliana chromosome 5. VI. Sequence features of the regions of 1,367,185 bp covered by 19 physically assigned P1 and TAC clones. -
Author(s) : Kotani H , Nakamura Y , Sato S , Asamizu E , Kaneko T , Miyajima N , Tabata S
Ref : DNA Research , 5 :203 , 1998
PubMedID: 9734815
Gene_locus related to this paper: arath-At5g56750

Title : Structural analysis of Arabidopsis thaliana chromosome 5. II. Sequence features of the regions of 1,044,062 bp covered by thirteen physically assigned P1 clones - Kotani_1997_DNA.Res_4_291
Author(s) : Kotani H , Nakamura Y , Sato S , Kaneko T , Asamizu E , Miyajima N , Tabata S
Ref : DNA Research , 4 :291 , 1997
Abstract : A total of 13 P1 clones, each containing a marker(s) specifically mapped on chromosome 5, were isolated from a P1 library of the Arabidopsis thaliana Columbia genome, and their nucleotide sequences were determined according to the shot gun based strategy and precisely located on the physical map of chromosome 5. The total length of the sequenced regions was 1,044,062 bp. Since we have previously reported the sequence of 1,621,245 bp by analysis of 20 non-redundant P1 clones, the total length of the sequences of chromosome 5 determined so far reached 2,665,307 bp. The regions sequenced in this study were analysed by comparison with the sequences in protein and EST databases and analysis with computer programs for gene modeling; a total of 225 potential protein-coding genes and/or gene segments with known or predicted functions were identified. The positions of exons which do not exhibit similarity to known genes were also predicted by computer-aided analysis. An average density of the genes and/or gene was 1 gene/4,640 bp. Introns were identified in approximately 84% of the potential genes, and the average number and length of the introns per gene were 5.3 and 184 bp, respectively. These sequence features are essentially identical to those for the previously sequenced regions. The transcription level of the predicted genes has been roughly monitored by counting the numbers of matched Arabidopsis ESTs. The sequence data and gene information are available through the World Wide Web at https://www.kazusa.or.jp/kaos/.
ESTHER : Kotani_1997_DNA.Res_4_291
PubMedSearch : Kotani_1997_DNA.Res_4_291
PubMedID: 9405937
Gene_locus related to this paper: arath-At5g13640 , arath-AT5G24210 , arath-At5g24220 , arath-AT5G24230 , arath-At5g17670 , arath-Q9FN74 , arath-Q9FN79 , arath-Q9FNF6

Title : Structural analysis of Arabidopsis thaliana chromosome 5. III. Sequence features of the regions of 1,191,918 bp covered by seventeen physically assigned P1 clones - Nakamura_1997_DNA.Res_4_401
Author(s) : Nakamura Y , Sato S , Kaneko T , Kotani H , Asamizu E , Miyajima N , Tabata S
Ref : DNA Research , 4 :401 , 1997
Abstract : A total of 17 P1 and TAC clones each containing a marker(s) specifically mapped on chromosome 5 were isolated from P1 and TAC libraries of the Arabidopsis thaliana Columbia genome, and their nucleotide sequences were determined according to the shot gun-based strategy and precisely located on the physical map of chromosome 5. The total length of the clones sequenced in this study was 1,191,918 bp. As we have previously reported the sequence of 2,662,078 bp by analysis of 33 P1 clones, the total length of the sequences of chromosome 5 determined so far is now 3,853,996 bp. The sequences determined in this study were subjected to similarity search against protein and EST databases and analysis with computer programs for gene modeling, and a total of 310 potential protein-coding genes and/or gene segments with known or predicted functions were identified. The positions of exons which do not show apparent similarity to known genes were also predicted by computer-aided analysis. An average density of the assigned genes and/or gene segments was 1 gene/3,845 bp. Introns were identified in 78% of the potential protein genes, and the average number per gene and the average length of the introns were 3.7 and 185 bp, respectively. The numbers of the Arabidopsis ESTs matched to each of the predicted genes have been counted to monitor the transcription level. The sequence data and gene information are available on the World Wide Web database KAOS (Kazusa Arabidopsis data Opening Site) at http://www.kazusa.or.jp/arabi/.
ESTHER : Nakamura_1997_DNA.Res_4_401
PubMedSearch : Nakamura_1997_DNA.Res_4_401
PubMedID: 9501997
Gene_locus related to this paper: arath-AT5G22460 , arath-At5g42930 , arath-LIP2 , arath-SCPL34

Title : Structural analysis of Arabidopsis thaliana chromosome 5. I. Sequence features of the 1.6 Mb regions covered by twenty physically assigned P1 clones - Sato_1997_DNA.Res_4_215
Author(s) : Sato S , Kotani H , Nakamura Y , Kaneko T , Asamizu E , Fukami M , Miyajima N , Tabata S
Ref : DNA Research , 4 :215 , 1997
Abstract : A total of 20 P1 clones with an average insert size of 80 kb and each containing a marker(s) specifically mapped on chromosome 5 were isolated from a P1 library of the Arabidopsis thaliana genome, and their nucleotide sequences were determined according to a shotgun-based strategy and precisely located on the physical map of chromosome 5 separately constructed. The total length of the sequenced regions were summed up to 1,621,245 bp. By comparison with the sequences in protein and EST databases and analysis with computer programs for gene modeling, a total of 347 potential protein-coding genes and/or gene segments with known or predicted functions were identified. The positions of exons which do not exhibit any similarity to known genes were also predicted. An average density of the genes and/or gene segments assigned so far as 1 gene/4,672 bp. Introns were identified in approximately 78% of the potential genes, and the average number and length of the introns per gene were 3.7 and 161 bp. The transcription level of the predicted genes was roughly monitored by counting the numbers of identified Arabidopsis ESTs. The sequence data and gene information are available through the World Wide Web at http:/(/)www.kazusa.or.jp/arabi/.
ESTHER : Sato_1997_DNA.Res_4_215
PubMedSearch : Sato_1997_DNA.Res_4_215
PubMedID: 9330910
Gene_locus related to this paper: arath-AT5G38220 , arath-At5g38520 , arath-Q8LFB7 , arath-Q9FF27 , arath-q9ffg7 , arath-Q9FFZ1 , arath-SCP47 , arath-B9DFR3

Title : Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions - Kaneko_1996_DNA.Res_3_109
Author(s) : Kaneko T , Sato S , Kotani H , Tanaka A , Asamizu E , Nakamura Y , Miyajima N , Hirosawa M , Sugiura M , Sasamoto S , Kimura T , Hosouchi T , Matsuno A , Muraki A , Nakazaki N , Naruo K , Okumura S , Shimpo S , Takeuchi C , Wada T , Watanabe A , Yamada M , Yasuda M , Tabata S
Ref : DNA Research , 3 :109 , 1996
Abstract : The sequence determination of the entire genome of the Synechocystis sp. strain PCC6803 was completed. The total length of the genome finally confirmed was 3,573,470 bp, including the previously reported sequence of 1,003,450 bp from map position 64% to 92% of the genome. The entire sequence was assembled from the sequences of the physical map-based contigs of cosmid clones and of lambda clones and long PCR products which were used for gap-filling. The accuracy of the sequence was guaranteed by analysis of both strands of DNA through the entire genome. The authenticity of the assembled sequence was supported by restriction analysis of long PCR products, which were directly amplified from the genomic DNA using the assembled sequence data. To predict the potential protein-coding regions, analysis of open reading frames (ORFs), analysis by the GeneMark program and similarity search to databases were performed. As a result, a total of 3,168 potential protein genes were assigned on the genome, in which 145 (4.6%) were identical to reported genes and 1,257 (39.6%) and 340 (10.8%) showed similarity to reported and hypothetical genes, respectively. The remaining 1,426 (45.0%) had no apparent similarity to any genes in databases. Among the potential protein genes assigned, 128 were related to the genes participating in photosynthetic reactions. The sum of the sequences coding for potential protein genes occupies 87% of the genome length. By adding rRNA and tRNA genes, therefore, the genome has a very compact arrangement of protein- and RNA-coding regions. A notable feature on the gene organization of the genome was that 99 ORFs, which showed similarity to transposase genes and could be classified into 6 groups, were found spread all over the genome, and at least 26 of them appeared to remain intact. The result implies that rearrangement of the genome occurred frequently during and after establishment of this species.
ESTHER : Kaneko_1996_DNA.Res_3_109
PubMedSearch : Kaneko_1996_DNA.Res_3_109
PubMedID: 8905231
Gene_locus related to this paper: synsp-ester , synsp-PHBC , synsp-prxc , synsp-Q55130 , synsp-SLL0482 , synsp-sll0553 , synsp-SLL0992 , synsp-sll1305 , synsp-SLL1969 , synsp-SLR0825 , synsp-slr1235 , synsp-SLR1506 , synsp-SLR1771 , synsp-SLR1807 , synsp-slr1827 , synsp-slr1916 , synsp-slr1917 , synsp-slr1932 , synsp-SLR1944 , synsp-SLR2053 , synsp-todF , syny3-dlhh , syny3-P73192 , syny3-p73194 , syny3-y249 , syny3-y264