Akiko Watanabe

Publications of Akiko Watanabe

• Characterization of active miniature inverted-repeat transposable elements in the peanut genome.

  Authors: Kenta Shirasawa, Hideki Hirakawa, Satoshi Tabata, Makoto Hasegawa, Hiroyuki Kiyoshima, Sigeru Suzuki, Sigemi Sasamoto, Akiko Watanabe, Tsunakazu Fujishiro, Sachiko Isobe

  TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik. 02/2012;

  Miniature inverted-repeat transposable elements (MITEs), some of which are known as active non-autonomous DNA transposons, are found in the genomes of plants and animals. In peanut (ArachisMiniature inverted-repeat transposable elements (MITEs), some of which are known as active non-autonomous DNA transposons, are found in the genomes of plants and animals. In peanut (Arachis hypogaea), AhMITE1 has been identified in a gene for fatty-acid desaturase, and possessed excision activity. However, the AhMITE1 distribution and frequency of excision have not been determined for the peanut genome. In order to characterize AhMITE1s, their genomic diversity and transposition ability was investigated. Southern blot analysis indicated high AhMITE1 copy number in the genomes of A. hypogaea, A. magna and A. monticola, but not in A. duranensis. A total of 504 AhMITE1s were identified from the MITE-enriched genomic libraries of A. hypogaea. The representative AhMITE1s exhibited a mean length of 205.5 bp and a GC content of 30.1%, with AT-rich, 9 bp target site duplications and 25 bp terminal inverted repeats. PCR analyses were performed using primer pairs designed against both flanking sequences of each AhMITE1. These analyses detected polymorphisms at 169 out of 411 insertional loci in the four peanut lines. In subsequent analyses of 60 gamma-irradiated mutant lines, four AhMITE1 excisions showed footprint mutations at the 109 loci tested. This study characterizes AhMITE1s in peanut and discusses their use as DNA markers and mutagens for the genetics, genomics and breeding of peanut and its relatives.

• An EST-SSR linkage map of Raphanus sativus and comparative genomics of the Brassicaceae.

  Authors: Kenta Shirasawa, Maki Oyama, Hideki Hirakawa, Shusei Sato, Satoshi Tabata, Takashi Fujioka, Chiaki Kimizuka-Takagi, Shigemi Sasamoto, Akiko Watanabe, Midori Kato, Yoshie Kishida, Mitsuyo Kohara, Chika Takahashi, Hisano Tsuruoka, Tsuyuko Wada, Takako Sakai, Sachiko Isobe

  DNA research : an international journal for rapid publication of reports on genes and genomes. 06/2011; 18(4):221-32.

  Raphanus sativus (2n = 2x = 18) is a widely cultivated member of the family Brassicaceae, for which genomic resources are available only to a limited extent in comparison to many other members of theRaphanus sativus (2n = 2x = 18) is a widely cultivated member of the family Brassicaceae, for which genomic resources are available only to a limited extent in comparison to many other members of the family. To promote more genetic and genomic studies and to enhance breeding programmes of R. sativus, we have prepared genetic resources such as complementary DNA libraries, expressed sequences tags (ESTs), simple sequence repeat (SSR) markers and a genetic linkage map. A total of 26 606 ESTs have been collected from seedlings, roots, leaves, and flowers, and clustered into 10 381 unigenes. Similarities were observed between the expression patterns of transcripts from R. sativus and those from representative members of the genera Arabidopsis and Brassica, indicating their functional relatedness. The EST sequence data were used to design 3800 SSR markers and consequently 630 polymorphic SSR loci and 213 reported marker loci have been mapped onto nine linkage groups, covering 1129.2 cM with an average distance of 1.3 cM between loci. Comparison of the mapped EST-SSR marker positions in R. sativus with the genome sequence of A. thaliana indicated that the Brassicaceae members have evolved from a common ancestor. It appears that genomic fragments corresponding to those of A. thaliana have been doubled and tripled in R. sativus. The genetic map developed here is expected to provide a standard map for the genetics, genomics, and molecular breeding of R. sativus as well as of related species. The resources are available at http://marker.kazusa.or.jp/Daikon.

• Sequence analysis of the genome of an oil-bearing tree, Jatropha curcas L.

  Authors: Shusei Sato, Hideki Hirakawa, Sachiko Isobe, Eigo Fukai, Akiko Watanabe, Midori Kato, Kumiko Kawashima, Chiharu Minami, Akiko Muraki, Naomi Nakazaki [......] Eri Makigano, Nobuko Ohmido, Nakako Shibagaki, Joyce A Cartagena, Naoki Wada, Tsutomu Kohinata, Alipour Atefeh, Shota Yuasa, Sachihiro Matsunaga, Kiichi Fukui

  DNA research : an international journal for rapid publication of reports on genes and genomes. 01/2011; 18(1):65-76.

  The whole genome of Jatropha curcas was sequenced, using a combination of the conventional Sanger method and new-generation multiplex sequencing methods. Total length of the non-redundant sequencesThe whole genome of Jatropha curcas was sequenced, using a combination of the conventional Sanger method and new-generation multiplex sequencing methods. Total length of the non-redundant sequences thus obtained was 285 858 490 bp consisting of 120 586 contigs and 29 831 singlets. They accounted for ~95% of the gene-containing regions with the average G + C content was 34.3%. A total of 40 929 complete and partial structures of protein encoding genes have been deduced. Comparison with genes of other plant species indicated that 1529 (4%) of the putative protein-encoding genes are specific to the Euphorbiaceae family. A high degree of microsynteny was observed with the genome of castor bean and, to a lesser extent, with those of soybean and Arabidopsis thaliana. In parallel with genome sequencing, cDNAs derived from leaf and callus tissues were subjected to pyrosequencing, and a total of 21 225 unigene data have been generated. Polymorphism analysis using microsatellite markers developed from the genomic sequence data obtained was performed with 12 J. curcas lines collected from various parts of the world to estimate their genetic diversity. The genomic sequence and accompanying information presented here are expected to serve as valuable resources for the acceleration of fundamental and applied research with J. curcas, especially in the fields of environment-related research such as biofuel production. Further information on the genomic sequences and DNA markers is available at http://www.kazusa.or.jp/jatropha/.

• Complete genomic structure of the cultivated rice endophyte Azospirillum sp. B510.

  Authors: Takakazu Kaneko, Kiwamu Minamisawa, Tsuyoshi Isawa, Hiroki Nakatsukasa, Hisayuki Mitsui, Yasuyuki Kawaharada, Yasukazu Nakamura, Akiko Watanabe, Kumiko Kawashima, Akiko Ono [......] Chika Takahashi, Chiharu Minami, Tsunakazu Fujishiro, Mitsuyo Kohara, Midori Katoh, Naomi Nakazaki, Shinobu Nakayama, Manabu Yamada, Satoshi Tabata, Shusei Sato

  DNA research : an international journal for rapid publication of reports on genes and genomes. 02/2010; 17(1):37-50.

  We determined the nucleotide sequence of the entire genome of a diazotrophic endophyte, Azospirillum sp. B510. Strain B510 is an endophytic bacterium isolated from stems of rice plants (Oryza sativaWe determined the nucleotide sequence of the entire genome of a diazotrophic endophyte, Azospirillum sp. B510. Strain B510 is an endophytic bacterium isolated from stems of rice plants (Oryza sativa cv. Nipponbare). The genome of B510 consisted of a single chromosome (3,311,395 bp) and six plasmids, designated as pAB510a (1,455,109 bp), pAB510b (723,779 bp), pAB510c (681,723 bp), pAB510d (628,837 bp), pAB510e (537,299 bp), and pAB510f (261,596 bp). The chromosome bears 2893 potential protein-encoding genes, two sets of rRNA gene clusters (rrns), and 45 tRNA genes representing 37 tRNA species. The genomes of the six plasmids contained a total of 3416 protein-encoding genes, seven sets of rrns, and 34 tRNAs representing 19 tRNA species. Eight genes for plasmid-specific tRNA species are located on either pAB510a or pAB510d. Two out of eight genomic islands are inserted in the plasmids, pAB510b and pAB510e, and one of the islands is inserted into trnfM-CAU in the rrn located on pAB510e. Genes other than the nif gene cluster that are involved in N(2) fixation and are homologues of Bradyrhizobium japonicum USDA110 include fixABCX, fixNOQP, fixHIS, fixG, and fixLJK. Three putative plant hormone-related genes encoding tryptophan 2-monooxytenase (iaaM) and indole-3-acetaldehyde hydrolase (iaaH), which are involved in IAA biosynthesis, and ACC deaminase (acdS), which reduces ethylene levels, were identified. Multiple gene-clusters for tripartite ATP-independent periplasmic-transport systems and a diverse set of malic enzymes were identified, suggesting that B510 utilizes C(4)-dicarboxylate during its symbiotic relationship with the host plant.

• Construction of signature-tagged mutant library in Mesorhizobium loti as a powerful tool for functional genomics.

  Authors: Yoshikazu Shimoda, Hisayuki Mitsui, Hiroko Kamimatsuse, Kiwamu Minamisawa, Eri Nishiyama, Yoshiyuki Ohtsubo, Yuji Nagata, Masataka Tsuda, Sayaka Shinpo, Akiko Watanabe, Mitsuyo Kohara, Manabu Yamada, Yasukazu Nakamura, Satoshi Tabata, Shusei Sato

  DNA research : an international journal for rapid publication of reports on genes and genomes. 10/2008; 15(5):297-308.

  Rhizobia are nitrogen-fixing soil bacteria that establish endosymbiosis with some leguminous plants. The completion of several rhizobial genome sequences provides opportunities for genome-wideRhizobia are nitrogen-fixing soil bacteria that establish endosymbiosis with some leguminous plants. The completion of several rhizobial genome sequences provides opportunities for genome-wide functional studies of the physiological roles of many rhizobial genes. In order to carry out genome-wide phenotypic screenings, we have constructed a large mutant library of the nitrogen-fixing symbiotic bacterium, Mesorhizobium loti, by transposon mutagenesis. Transposon insertion mutants were generated using the signature-tagged mutagenesis (STM) technique and a total of 29,330 independent mutants were obtained. Along with the collection of transposon mutants, we have determined the transposon insertion sites for 7892 clones, and confirmed insertions in 3680 non-redundant M. loti genes (50.5% of the total number of M. loti genes). Transposon insertions were randomly distributed throughout the M. loti genome without any bias toward G+C contents of insertion target sites and transposon plasmids used for the mutagenesis. We also show the utility of STM mutants by examining the specificity of signature tags and test screenings for growth- and nodulation-deficient mutants. This defined mutant library allows for genome-wide forward- and reverse-genetic functional studies of M. loti and will serve as an invaluable resource for researchers to further our understanding of rhizobial biology.

• Genome Structure of the Legume, Lotus japonicus.

  Authors: Shusei Sato, Yasukazu Nakamura, Takakazu Kaneko, Erika Asamizu, Tomohiko Kato, Mitsuteru Nakao, Shigemi Sasamoto, Akiko Watanabe, Akiko Ono, Kumiko Kawashima [......] Chika Takahashi, Tsuyuko Wada, Manabu Yamada, Nobuko Ohmido, Makoto Hayashi, Kiichi Fukui, Tomoya Baba, Tomoko Nakamichi, Hirotada Mori, Satoshi Tabata

  DNA research : an international journal for rapid publication of reports on genes and genomes. 06/2008;

  The legume Lotus japonicus has been widely used as a model system to investigate the genetic background of legume-specific phenomena such as symbiotic nitrogen fixation. Here, we report structuralThe legume Lotus japonicus has been widely used as a model system to investigate the genetic background of legume-specific phenomena such as symbiotic nitrogen fixation. Here, we report structural features of the L. japonicus genome. The 315.1-Mb sequences determined in this and previous studies correspond to 67% of the genome (472 Mb), and are likely to cover 91.3% of the gene space. Linkage mapping anchored 130-Mb sequences onto the six linkage groups. A total of 10 951 complete and 19 848 partial structures of protein-encoding genes were assigned to the genome. Comparative analysis of these genes revealed the expansion of several functional domains and gene families that are characteristic of L. japonicus. Synteny analysis detected traces of whole-genome duplication and the presence of synteny blocks with other plant genomes to various degrees. This study provides the first opportunity to look into the complex and unique genetic system of legumes.

• Complete genomic structure of the bloom-forming toxic cyanobacterium Microcystis aeruginosa NIES-843.

  Authors: Takakazu Kaneko, Nobuyoshi Nakajima, Shinobu Okamoto, Iwane Suzuki, Yuuhiko Tanabe, Masanori Tamaoki, Yasukazu Nakamura, Fumie Kasai, Akiko Watanabe, Kumiko Kawashima [......] Chika Takahashi, Chiharu Minami, Tsunakazu Fujishiro, Mitsuyo Kohara, Midori Katoh, Naomi Nakazaki, Shinobu Nakayama, Manabu Yamada, Satoshi Tabata, Makoto M Watanabe

  DNA research : an international journal for rapid publication of reports on genes and genomes. 01/2008; 14(6):247-56.

  The nucleotide sequence of the complete genome of a cyanobacterium, Microcystis aeruginosa NIES-843, was determined. The genome of M. aeruginosa is a single, circular chromosome of 5,842,795 baseThe nucleotide sequence of the complete genome of a cyanobacterium, Microcystis aeruginosa NIES-843, was determined. The genome of M. aeruginosa is a single, circular chromosome of 5,842,795 base pairs (bp) in length, with an average GC content of 42.3%. The chromosome comprises 6312 putative protein-encoding genes, two sets of rRNA genes, 42 tRNA genes representing 41 tRNA species, and genes for tmRNA, the B subunit of RNase P, SRP RNA, and 6Sa RNA. Forty-five percent of the putative protein-encoding sequences showed sequence similarity to genes of known function, 32% were similar to hypothetical genes, and the remaining 23% had no apparent similarity to reported genes. A total of 688 kb of the genome, equivalent to 11.8% of the entire genome, were composed of both insertion sequences and miniature inverted-repeat transposable elements. This is indicative of a plasticity of the M. aeruginosa genome, through a mechanism that involves homologous recombination mediated by repetitive DNA elements. In addition to known gene clusters related to the synthesis of microcystin and cyanopeptolin, novel gene clusters that may be involved in the synthesis and modification of toxic small polypeptides were identified. Compared with other cyanobacteria, a relatively small number of genes for two component systems and a large number of genes for restriction-modification systems were notable characteristics of the M. aeruginosa genome.

• Comprehensive structural analysis of the genome of red clover (Trifolium pratense L.).

  Authors: Shusei Sato, Sachiko Isobe, Erika Asamizu, Nobuko Ohmido, Ryohei Kataoka, Yasukazu Nakamura, Takakazu Kaneko, Nozomi Sakurai, Kenji Okumura, Irina Klimenko, Shigemi Sasamoto, Tsuyuko Wada, Akiko Watanabe, Mitsuyo Kohara, Tsunakazu Fujishiro, Satoshi Tabata

  DNA research : an international journal for rapid publication of reports on genes and genomes. 02/2005; 12(5):301-64.

  With the aim of establishing the basic knowledge and resources needed for applied genetics, we investigated the genome structure of red clover Trifolium pratense L. by a combination of cytological,With the aim of establishing the basic knowledge and resources needed for applied genetics, we investigated the genome structure of red clover Trifolium pratense L. by a combination of cytological, genomic and genetic approaches. The deduced genome size was approximately 440 Mb, as estimated by measuring the nuclear DNA content by flow cytometry. Seven chromosomes could be distinguished by microscopic observation of DAPI stained prometaphase chromosomes and fluorescence in situ hybridization using 28S and 5S rDNA probes and bacterial artificial chromosome probes containing microsatellite markers with known positions on a genetic linkage map. The average GC content of the genomes of chloroplast, mitochondrion and nucleus were shown to be 33.8, 42.9 and 34.2%, respectively, by the analysis of 1.4 Mb of random genomic sequences. A total of 26,356 expressed sequence tags (ESTs) that were grouped into 9339 non-redundant sequences were collected, and 78% of the ESTs showed sequence similarity to registered genes, mainly of Arabidopsis thaliana and rice. To facilitate basic and applied genetics in red clover, we generated a high-density genetic linkage map with gene-associated microsatellite markers. A total of 7159 primer pairs were designed to amplify simple sequence repeats (SSRs) identified in four different types of libraries. Based on sequence similarity, 82% of the SSRs were likely to be associated with genes. Polymorphism was examined using two parent plants, HR and R130, and 10 F(1) progeny by agarose gel electrophoresis, followed by genotyping for the primer pairs showing polymorphisms using 188 F(1) plants from the mapping population. The selected 1305 microsatellite markers as well as the previously developed 167 restriction fragment length polymorphism markers were subjected to linkage analysis. A total of 1434 loci detected by 1399 markers were successfully mapped onto seven linkage groups totaling 868.7 cM in length; 405 loci (28%) were bi-parental, 611 (43%) were specific to HR and 418 (29%) were specific to R130. Each genetic linkage group was linked to a corresponding chromosome by FISH analysis using seven microsatellite markers specific to each of the linkage groups as probes. Transferability of the developed microsatellite markers to other germplasms was confirmed by testing 268 selected markers on 88 red clover germplasms. Macrosynteny at the segmental level was observed between the genomes of red clover and two model legumes, Lotus japonicus and Medicago truncatula, strongly suggesting that the genome information for the model legumes is transferable to red clover for genetic investigations and experimental breeding.

• Structural analysis of four large plasmids harboring in a unicellular cyanobacterium, Synechocystis sp. PCC 6803.

  Authors: Takakazu Kaneko, Yasukazu Nakamura, Shigemi Sasamoto, Akiko Watanabe, Mitsuyo Kohara, Midori Matsumoto, Sayaka Shimpo, Manabu Yamada, Satoshi Tabata

  DNA research : an international journal for rapid publication of reports on genes and genomes. 11/2003; 10(5):221-8.

  The genome of the unicellular cyanobacterium Synechocystis sp. PCC 6803 consists of a single chromosome and several plasmids of different sizes, and the nucleotide sequences of the chromosome andThe genome of the unicellular cyanobacterium Synechocystis sp. PCC 6803 consists of a single chromosome and several plasmids of different sizes, and the nucleotide sequences of the chromosome and three small plasmids (5.2 kb, 2.4 kb, and 2.3 kb) have already been sequenced. We newly determined the nucleotide sequences of four large plasmids, which have been identified in our laboratory (pSYSM:120 kb, pSYSX:106 kb, pSYSA:103 kb, and pSYSG:44 kb). Computer-aided analysis was performed to explore the genetic information carried by these plasmids. A total of 397 potential protein-encoding genes were predicted, but little information was obtained about the functional relationship of plasmids to host cell, as a large portion of the predicted genes (77%) were of unknown function. The occurrence of the potential genes on plasmids was divergent, and parA was the only gene common to all four large plasmids. The distribution data of a Cyanobacterium-specific sequence (HIP1: 5'-GCGATCGC-3') suggested that respective plasmids could have originated from different cyanobacterial strains.

• Complete genome structure of Gloeobacter violaceus PCC 7421, a cyanobacterium that lacks thylakoids.

  Authors: Yasukazu Nakamura, Takakazu Kaneko, Shusei Sato, Mamoru Mimuro, Hideaki Miyashita, Tohru Tsuchiya, Shigemi Sasamoto, Akiko Watanabe, Kumiko Kawashima, Yoshie Kishida, Chiaki Kiyokawa, Mitsuyo Kohara, Midori Matsumoto, Ai Matsuno, Naomi Nakazaki, Sayaka Shimpo, Chie Takeuchi, Manabu Yamada, Satoshi Tabata

  DNA research : an international journal for rapid publication of reports on genes and genomes. 09/2003; 10(4):137-45.

  The nucleotide sequence of the entire genome of a cyanobacterium Gloeobacter violaceus PCC 7421 was determined. The genome of G. violaceus was a single circular chromosome 4,659,019 bp long with anThe nucleotide sequence of the entire genome of a cyanobacterium Gloeobacter violaceus PCC 7421 was determined. The genome of G. violaceus was a single circular chromosome 4,659,019 bp long with an average GC content of 62%. No plasmid was detected. The chromosome comprises 4430 potential protein-encoding genes, one set of rRNA genes, 45 tRNA genes representing 44 tRNA species and genes for tmRNA, B subunit of RNase P, SRP RNA and 6Sa RNA. Forty-one percent of the potential protein-encoding genes showed sequence similarity to genes of known function, 37% to hypothetical genes, and the remaining 22% had no apparent similarity to reported genes. Comparison of the assigned gene components with those of other cyanobacteria has unveiled distinctive features of the G. violaceus genome. Genes for PsaI, PsaJ, PsaK, and PsaX for Photosystem I and PsbY, PsbZ and Psb27 for Photosystem II were missing, and those for PsaF, PsbO, PsbU, and PsbV were poorly conserved. cpcG for a rod core linker peptide for phycobilisomes and nblA related to the degradation of phycobilisomes were also missing. Potential signal peptides of the presumptive products of petJ and petE for soluble electron transfer catalysts were less conserved than the remaining portions. These observations may be related to the fact that photosynthesis in G. violaceus takes place not in thylakoid membranes but in the cytoplasmic membrane. A large number of genes for sigma factors and transcription factors in the LuxR, LysR, PadR, TetR, and MarR families could be identified, while those for major elements for circadian clock, kaiABC were not found. These differences may reflect the phylogenetic distance between G. violaceus and other cyanobacteria.

• Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110.

  Authors: Takakazu Kaneko, Yasukazu Nakamura, Shusei Sato, Kiwamu Minamisawa, Toshiki Uchiumi, Shigemi Sasamoto, Akiko Watanabe, Kumi Idesawa, Mayumi Iriguchi, Kumiko Kawashima, Mitsuyo Kohara, Midori Matsumoto, Sayaka Shimpo, Hisae Tsuruoka, Tsuyuko Wada, Manabu Yamada, Satoshi Tabata

  DNA research : an international journal for rapid publication of reports on genes and genomes. 01/2003; 9(6):189-97.

  The complete nucleotide sequence of the genome of a symbiotic bacterium Bradyrhizobium japonicum USDA110 was determined. The genome of B. japonicum was a single circular chromosome 9,105,828 bp inThe complete nucleotide sequence of the genome of a symbiotic bacterium Bradyrhizobium japonicum USDA110 was determined. The genome of B. japonicum was a single circular chromosome 9,105,828 bp in length with an average GC content of 64.1%. No plasmid was detected. The chromosome comprises 8317 potential protein-coding genes, one set of rRNA genes and 50 tRNA genes. Fifty-two percent of the potential protein genes showed sequence similarity to genes of known function and 30% to hypothetical genes. The remaining 18% had no apparent similarity to reported genes. Thirty-four percent of the B. japonicum genes showed significant sequence similarity to those of both Mesorhizobium loti and Sinorhizobium meliloti, while 23% were unique to this species. A presumptive symbiosis island 681 kb in length, which includes a 410-kb symbiotic region previously reported by Göttfert et al., was identified. Six hundred fifty-five putative protein-coding genes were assigned in this region, and the functions of 301 genes, including those related to symbiotic nitrogen fixation and DNA transmission, were deduced. A total of 167 genes for transposases/104 copies of insertion sequences were identified in the genome. It was remarkable that 100 out of 167 transposase genes are located in the presumptive symbiotic island. DNA segments of 4 to 97 kb inserted into tRNA genes were found at 14 locations in the genome, which generates partial duplication of the target tRNA genes. These observations suggest plasticity of the B. japonicum genome, which is probably due to complex genome rearrangements such as horizontal transfer and insertion of various DNA elements, and to homologous recombination.

• Complete genome structure of the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1.

  Authors: Yasukazu Nakamura, Takakazu Kaneko, Shusei Sato, Masahiko Ikeuchi, Hiroshi Katoh, Shigemi Sasamoto, Akiko Watanabe, Mayumi Iriguchi, Kumiko Kawashima, Takaharu Kimura [......] Chiaki Kiyokawa, Mitsuyo Kohara, Midori Matsumoto, Ai Matsuno, Naomi Nakazaki, Sayaka Shimpo, Masako Sugimoto, Chie Takeuchi, Manabu Yamada, Satoshi Tabata

  DNA research : an international journal for rapid publication of reports on genes and genomes. 09/2002; 9(4):123-30.

  The entire genome of a thermophilic unicellular cyanobacterium, Thermosynechococcus elongatus BP-1, was sequenced. The genome consisted of a circular chromosome 2,593,857 bp long, and no plasmid wasThe entire genome of a thermophilic unicellular cyanobacterium, Thermosynechococcus elongatus BP-1, was sequenced. The genome consisted of a circular chromosome 2,593,857 bp long, and no plasmid was detected. A total of 2475 potential protein-encoding genes, one set of rRNA genes, 42 tRNA genes representing 42 tRNA species and 4 genes for small structural RNAs were assigned to the chromosome by similarity search and computer prediction. The translated products of 56% of the potential protein-encoding genes showed sequence similarity to experimentally identified and predicted proteins of known function, and the products of 34% of these genes showed sequence similarity to the translated products of hypothetical genes. The remaining 10% lacked significant similarity to genes for predicted proteins in the public DNA databases. Sixty-three percent of the T. elongatus genes showed significant sequence similarity to those of both Synechocystis sp. PCC 6803 and Anabaena sp. PCC 7120, while 22% of the genes were unique to this species, indicating a high degree of divergence of the gene information among cyanobacterial strains. The lack of genes for typical fatty acid desaturases and the presence of more genes for heat-shock proteins in comparison with other mesophilic cyanobacteria may be genomic features of thermophilic strains. A remarkable feature of the genome is the presence of 28 copies of group II introns, 8 of which contained a presumptive gene for maturase/reverse transcriptase. A trace of genome rearrangement mediated by the group II introns was also observed.

• Complete Genome Structure of the Nitrogen-fixing Symbiotic Bacterium Mesorhizobium loti (Supplement)

  Authors: Takakazu Kaneko, Yasukazu Nakamura, Shusei Sato, Erika Asamizu, Tomohiko Kato, Shigemi Sasamoto, Akiko Watanabe, Kumi Idesawa, Atsuko Ishikawa, Kumiko Kawashima [......] Midori Matsumoto, Ai Matsuno, Yoko Mochizuki, Shinobu Nakayama, Naomi Nakazaki, Sayaka Shimpo, Masako Sugimoto, Chie Takeuchi, Manabu Yamada, Satoshi Tabata

• Complete Genome Structure of the Nitrogen-fixing Symbiotic Bacterium Mesorhizobium loti

  Authors: Takakazu Kaneko, Yasukazu Nakamura, Shusei Sato, Erika Asamizu, Tomohiko Kato, Shigemi Sasamoto, Akiko Watanabe, Kumi Idesawa, Atsuko Ishikawa, Kumiko Kawashima [......] Midori Matsumoto, Ai Matsuno, Yoko Mochizuki, Shinobu Nakayama, Naomi Nakazaki, Sayaka Shimpo, Masako Sugimoto, Chie Takeuchi, Manabu Yamada, Satoshi Tabata

  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)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% hadno 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 islandas well as the plasmids originated andw ere transmittedfrom 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.