DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes最新文献_第8页

Binding of 5-bromouracil-containing S/MAR DNA to the nuclear matrix. 含5-溴酸的S/MAR DNA与核基质的结合。

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2002-01-01 DOI: 10.1093/DNARES/9.1.25

H. Ogino, M. Fujii, W. Satou, Toshikazu Suzuki, E. Michishita, D. Ayusawa

引用次数: 20

Structural analysis of a Lotus japonicus genome. II. Sequence features and mapping of sixty-five TAC clones which cover the 6.5-mb regions of the genome. 日本莲基因组的结构分析。2覆盖基因组6.5 mb区域的65个TAC克隆的序列特征和图谱。

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2002-01-01 DOI: 10.1093/dnares/9.2.63

Yasukazu Nakamura, T. Kaneko, E. Asamizu, Tomohiko Kato, Shusei Sato, S. Tabata

{"title":"Structural analysis of a Lotus japonicus genome. II. Sequence features and mapping of sixty-five TAC clones which cover the 6.5-mb regions of the genome.","authors":"Yasukazu Nakamura, T. Kaneko, E. Asamizu, Tomohiko Kato, Shusei Sato, S. Tabata","doi":"10.1093/dnares/9.2.63","DOIUrl":"https://doi.org/10.1093/dnares/9.2.63","url":null,"abstract":"Sixty-five TAC (transformation-competent artificial chromosomes) clones were selected from a genomic library of Lotus japonicus accession MG-20 based on the sequence information of expressed sequences tags (ESTs), cDNA and gene information, and their nucleotide sequences were determined. The average insert size of the TAC clone was approximately 100 kb, and the total length of the sequenced regions in this study is 6,556,100 bp. Together with the nucleotide sequences of 56 TAC clones previously reported, the regions sequenced so far total 12,029,295 bp. By comparison with the sequences in protein and EST databases and by analysis with computer programs for gene modeling, a total of 711 potential protein-encoding genes with known or predicted functions, 239 gene segments and 90 pseudogenes were identified in the newly sequenced regions. The average gene density assigned so far was 1 gene/9140 bp. The average length of the assigned genes was 2.6 kb, which is considerably larger than that assigned in the Arabidopsis thaliana genome (1.9 kb for 6451 genes). Introns were identified in approximately 73% of the potential genes, and the average number and length of the introns per gene were 3.4 and 377 bp, respectively. Simple sequence repeat length polymorphism (SSLP) or derived cleaved amplified polymorphic sequence (dCAPS) markers were generated based on the nucleotide sequences of the genomic clones obtained, and each clone was mapped onto the linkage map using the F2 mapping population derived from a cross of two accessions of L. japonicus, Gifu B-129 and Miyakojima MG-20. The sequence data, gene information and mapping information are available through the World Wide Web at http://www.kazusa.or.jp/lotus/.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"11 1","pages":"63-70"},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85213974","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 37

Biochemical examination of the potential eukaryotic-type protein kinase genes in the complete genome of the unicellular Cyanobacterium synechocystis sp. PCC 6803. 单细胞藻胞杆菌PCC 6803全基因组真核型蛋白激酶基因的生化检测。

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2002-01-01 DOI: 10.1093/DNARES/9.3.71

A. Kamei, T. Yuasa, Xiaoxing Geng, M. Ikeuchi

引用次数: 42

Conservation of translation initiation sites based on dinucleotide frequency and codon usage in Escherichia coli K-12 (W3110): non-random distribution of A/T-rich sequences immediately upstream of the translation initiation codon. 大肠杆菌K-12 (W3110)中基于二核苷酸频率和密码子使用的翻译起始位点的保护:翻译起始密码子上游的A/ t丰富序列的非随机分布

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2002-01-01 DOI: 10.1093/DNARES/9.1.19

Kazuo Yamagishi, T. Oshima, Yasushi Masuda, T. Ara, S. Kanaya, H. Mori

引用次数: 10

Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones (supplement). KIAA基因表达cDNA克隆的构建:330个KIAA cDNA克隆的人工培养(增刊)。

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2002-01-01 DOI: 10.1093/dnares/9.3.107

D. Nakajima, N. Okazaki, H. Yamakawa, R. Kikuno, O. Ohara, T. Nagase

引用次数: 4

Distribution of repetitive sequences on the leading and lagging strands of the Escherichia coli genome: comparative study of Long Direct Repeat (LDR) sequences. 大肠杆菌基因组前后链重复序列的分布:长直接重复序列(LDR)序列的比较研究。

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2002-01-01 DOI: 10.1093/DNARES/9.1.1

M. Kawano, S. Kanaya, T. Oshima, Yasushi Masuda, T. Ara, H. Mori

{"title":"Distribution of repetitive sequences on the leading and lagging strands of the Escherichia coli genome: comparative study of Long Direct Repeat (LDR) sequences.","authors":"M. Kawano, S. Kanaya, T. Oshima, Yasushi Masuda, T. Ara, H. Mori","doi":"10.1093/DNARES/9.1.1","DOIUrl":"https://doi.org/10.1093/DNARES/9.1.1","url":null,"abstract":"In the present study, we developed a method for detecting sequences whose similarity to a target sequence is statistically significant and we examined the distribution of these sequences in the E. coli K-12 genome. Target sequences examined are as follows: (i) short repeat: Crossover hot-spot instigator (Chi) sequence, replication termination (Ter) sequence, and DnaA binding sequence (DnaA box); (ii) potential stem-loop structure repeats: palindromic unit (PU), boxC sequences, and intergenic repeat unit (IRU); (iii) potential RNA coding repeats: rRNAs, PAIR, TRIP, and QUAD; and (iv) potential protein coding repeats: insertion elements (ISs) and Long Direct Repeats (LDRs). We also examined the distribution of these sequences on leading and lagging strands. We obtained another four statistically significant LDR sequences with more than 187 bp matched to LDR-A near the LDR loci, suggesting that these regions might be used as high recombination hot spots for LDR. Adaptation of individual LDRs to E. coli genome is also discussed on the basis of codon usage.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"1 1","pages":"1-10"},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83129289","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 11

Characterization of equine microsatellites and microsatellite-linked repetitive elements (eMLREs) by efficient cloning and genotyping methods. 马微卫星和微卫星链接重复元件(eMLREs)的高效克隆和基因分型研究

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2001-01-01 DOI: 10.1093/DNARES/8.1.33

T. Tozaki, S. Mashima, K. Hirota, N. Miura, N. Choi-Miura, M. Tomita

{"title":"Characterization of equine microsatellites and microsatellite-linked repetitive elements (eMLREs) by efficient cloning and genotyping methods.","authors":"T. Tozaki, S. Mashima, K. Hirota, N. Miura, N. Choi-Miura, M. Tomita","doi":"10.1093/DNARES/8.1.33","DOIUrl":"https://doi.org/10.1093/DNARES/8.1.33","url":null,"abstract":"We performed efficient cloning and genotyping methods for isolation of a large number of polymorphic microsatellites. The methods contain the time-efficient cloning method of constructing microsatellite-enriched libraries and the economic genotyping method of fluorescent labeling of PCR products. Eighty novel equine microsatellites cloned were efficiently isolated from the enrichment library and analyzed for genotype polymorphism. Of these, 72 microsatellites were analyzed with a good resolution. The average heterozygosity of all loci was 0.52, and the number of alleles ranged from one to 9 with an average of 4.5 alleles. The other eight loci showed multiple bands of PCR products, suggesting the occurrence of microsatellites in a repetitive element, in which the number of microsatellite repeats varies among different members of the repetitive element. We found five homologous groups at flanking regions in comparison with the flanking regions of microsatellites from DNA databases. One of them showed homology to equine repetitive element-2. In the other four homologous groups, the two groups were named equine microsatellite-linked repetitive element-1 (eMLRE-1) and equine microsatellite-linked repetitive element-2 (eMLRE-2) as novel equine repetitive elements identified from equine genome. These data should help the analysis of equine DNA sequences and the design of equine genome markers.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"7 1","pages":"33-45"},"PeriodicalIF":0.0,"publicationDate":"2001-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85241207","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 40

Structural analysis of a Lotus japonicus genome. I. Sequence features and mapping of fifty-six TAC clones which cover the 5.4 mb regions of the genome. 日本莲基因组的结构分析。1 .覆盖基因组5.4 mb区域的56个TAC克隆的序列特征和图谱。

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2001-01-01 DOI: 10.1093/DNARES/8.6.311

Shusei Sato, T. Kaneko, Yasukazu Nakamura, E. Asamizu, Tomohiko Kato, S. Tabata

{"title":"Structural analysis of a Lotus japonicus genome. I. Sequence features and mapping of fifty-six TAC clones which cover the 5.4 mb regions of the genome.","authors":"Shusei Sato, T. Kaneko, Yasukazu Nakamura, E. Asamizu, Tomohiko Kato, S. Tabata","doi":"10.1093/DNARES/8.6.311","DOIUrl":"https://doi.org/10.1093/DNARES/8.6.311","url":null,"abstract":"A total of 56 TAC clones with an average insert size of 100 kb were isolated from a TAC library of the Lotus japonicus genome based on the expressed sequences tags (ESTs), cDNA and gene information, and their nucleotide sequences were determined according to the shot-gun based strategy. The total length of the sequenced regions is 5,473,195 bp. By comparison with the sequences in protein and EST databases and analysis with computer programs for gene modeling, a total of 605 potential protein-encoding genes with known or predicted functions, 69 gene segments, and 172 pseudogenes were identified. The average density of the genes assigned so far is 1 gene/8120 bp. Introns were identified in approximately 78% of the potential genes. There was an average of 3.8 introns per gene and the average length of the introns was 375 bp. DNA markers were generated based on the nucleotide sequences obtained, and each clone was mapped onto the linkage map using the F2 mapping population derived from a cross of L. japonicus Gifu B-129 and Miyakojima MG-20. The sequence data, gene information and mapping information are available through the World Wide Web at http://www.kazusa.or.jp/lotus/.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"757 1","pages":"311-8"},"PeriodicalIF":0.0,"publicationDate":"2001-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77520528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 140

Complete genomic sequence of the filamentous nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120. 丝状固氮蓝藻Anabaena sp.菌株pcc7120的完整基因组序列。

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2001-01-01 DOI: 10.1093/DNARES/8.5.205

T. Kaneko, Yasukazu Nakamura, C. Wolk, T. Kuritz, S. Sasamoto, A. Watanabe, Mayumi Iriguchi, Atsuko Ishikawa, K. Kawashima, Takaharu Kimura, Y. Kishida, Mitsuyo Kohara, M. Matsumoto, A. Matsuno, A. Muraki, N. Nakazaki, Sayaka Shimpo, M. Sugimoto, Masaki Takazawa, M. Yamada, Miho Yasuda, S. Tabata

{"title":"Complete genomic sequence of the filamentous nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120.","authors":"T. Kaneko, Yasukazu Nakamura, C. Wolk, T. Kuritz, S. Sasamoto, A. Watanabe, Mayumi Iriguchi, Atsuko Ishikawa, K. Kawashima, Takaharu Kimura, Y. Kishida, Mitsuyo Kohara, M. Matsumoto, A. Matsuno, A. Muraki, N. Nakazaki, Sayaka Shimpo, M. Sugimoto, Masaki Takazawa, M. Yamada, Miho Yasuda, S. Tabata","doi":"10.1093/DNARES/8.5.205","DOIUrl":"https://doi.org/10.1093/DNARES/8.5.205","url":null,"abstract":"The nucleotide sequence of the entire genome of a filamentous cyanobacterium, Anabaena sp. strain PCC 7120, was determined. The genome of Anabaena consisted of a single chromosome (6,413,771 bp) and six plasmids, designated pCC7120alpha (408,101 bp), pCC7120beta (186,614 bp), pCC7120gamma (101,965 bp), pCC7120delta (55,414 bp), pCC7120epsilon (40,340 bp), and pCC7120zeta (5,584 bp). The chromosome bears 5368 potential protein-encoding genes, four sets of rRNA genes, 48 tRNA genes representing 42 tRNA species, and 4 genes for small structural RNAs. The predicted products of 45% of the potential protein-encoding genes showed sequence similarity to known and predicted proteins of known function, and 27% to translated products of hypothetical genes. The remaining 28% lacked significant similarity to genes for known and predicted proteins in the public DNA databases. More than 60 genes involved in various processes of heterocyst formation and nitrogen fixation were assigned to the chromosome based on their similarity to the reported genes. One hundred and ninety-five genes coding for components of two-component signal transduction systems, nearly 2.5 times as many as those in Synechocystis sp. PCC 6803, were identified on the chromosome. Only 37% of the Anabaena genes showed significant sequence similarity to those of Synechocystis, indicating a high degree of divergence of the gene information between the two cyanobacterial strains.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"180 1","pages":"205-13; 227-53"},"PeriodicalIF":0.0,"publicationDate":"2001-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75960638","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 698

The size and sequence organization of the centromeric region of Arabidopsis thaliana chromosome 4. 拟南芥4号染色体着丝区大小和序列组织。

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2001-01-01 DOI: 10.1093/DNARES/8.6.285

N. Kumekawa, T. Hosouchi, H. Tsuruoka, Hirokazu Kotani

{"title":"The size and sequence organization of the centromeric region of Arabidopsis thaliana chromosome 4.","authors":"N. Kumekawa, T. Hosouchi, H. Tsuruoka, Hirokazu Kotani","doi":"10.1093/DNARES/8.6.285","DOIUrl":"https://doi.org/10.1093/DNARES/8.6.285","url":null,"abstract":"We have determined the genome structure of the centromeric region of Arabidopsis thaliana chromosome 4 by sequence analysis of BAC clones obtained by genome walking, followed by construction of a physical map using DNA of a hypomethylated strain. The total size of the centromeric region, corresponding to the recombinant inbred (RI) markers between mi87 and mi167, was approximately 5.3 megabases (Mb). This value is over 3 Mb longer than that previously estimated by the Arabidopsis Genome Initiative (Nature, 408, 796-815, 2000). Although we could not cover the entire centromeric region by BAC clones because of the presence of highly repetitive sequences in the middle (2.7 Mb), the cloned regions spanning approximately 1 Mb at both sides of the gap were newly sequenced. These results together with the reported sequences in the adjacent regions suggest that the centromeric region is principally composed of a central domain of 2.7 Mb, consisting of mainly 180-bp repeats and Athila elements, and upper and lower flanking regions of 1.55 Mb and 1 Mb, respectively. The flanking regions were predominantly composed of various types of transposable elements, except for the upper end moiety in which a large 5S rDNA array (0.65 Mb) and central domain-like sequence are present. Such an organization is essentially identical to the centromeric region of chromosome 5 reported previously.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"2007 1","pages":"285-90"},"PeriodicalIF":0.0,"publicationDate":"2001-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86209299","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 105