Complete Genomic Structure of the Bloom-forming Toxic Cyanobacterium Microcystis aeruginosa NIES-843
Open accessAbstract
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 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.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Previous studies have shown that a large proportion of transposases and RTase constituted long repeated sequences in some cyanobacteria.
“Previous studies have shown that a large proportion of the transposases and RTase constituted the long repeated sequences in some cyanobacteria.57–60”
From Whole genomic DNA sequencing and comparative genomic analysis of<i>Arthrospira platensis</i>: high genome plasticity and genetic diversity (2016) · cites this paper as [60]
The Materials and methods section defines insertion sequences as multicopy DNA elements longer than 500 bp that can encode a transposase. The Results and discussion section reports 452 such copies in the Microcystis aeruginosa genome. These passages support the transposase-related repeat finding, but the paper passages do not identify RTase as a constituent of the repeats (page numbers unavailable). (LLM, conf=0.84)
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302 · see citing works
Bergey's Manual of Determinative Bacteriology
S., F. A., Buchanan, R. E., Gibbons, N. E., & Bergey (1975) · Taxon · doi:10.2307/1218353 · Cited by 11,334 · see citing works
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
Lowe, T. M., & Eddy, S. R. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.5.955 · Cited by 11,120 · see citing works
Report of the Ad Hoc Committee on Reconciliation of Approaches to Bacterial Systematics
Wayne, L. G., Moore, W. E., Stackebrandt, E. S., Kandler, O., Colwell, R. R., Krichevsky, M. I., Trüper, H. G., Murray, R. G. E., Grimont, P. A. D., Brenner, D. J., et al. (1987) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/00207713-37-4-463 · Cited by 7,338 · see citing works
RNAmmer: consistent and rapid annotation of ribosomal RNA genes
Lagesen, K., Hallin, P., Rødland, E., Stærfeldt, H., Rognes, T., & Ussery, D. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm160 · Cited by 5,965 · see citing works
The COG database: an updated version includes eukaryotes
Tatusov, R. L., Fedorova, N. D., Jackson, J. D., Jacobs, A. R., Kiryutin, B., Koonin, E. V., Krylov, D. M., Mazumder, R., Mekhedov, S., Nikolskaya, A. N., et al. (2003) · BMC Bioinformatics · doi:10.1186/1471-2105-4-41 · Cited by 4,410 · see citing works
Improved microbial gene identification with GLIMMER
Delcher, A. L. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.23.4636 · Cited by 2,493 · see citing works
Kaneko, T., Sato, S., Kotani, H., Tanaka, A., Asamizu, E., Nakamura, Y., Miyajima, N., Hirosawa, M., Sugiura, M., Sasamoto, S., et al. (1996) · DNA Research · doi:10.1093/dnares/3.3.185 · Cited by 2,434 · see citing works
Self-citationKaneko, T., Sato, S., Kotani, H., Tanaka, A., Asamizu, E., Nakamura, Y., Miyajima, N., Hirosawa, M., Sugiura, M., Sasamoto, S., et al. (1996) · DNA Research · doi:10.1093/dnares/3.3.109 · Cited by 2,132 · see citing works
Self-citationAsheshov, E. H., & Skalova, R. (1975) · International Journal of Systematic Bacteriology · doi:10.1099/00207713-25-2-233 · Cited by 1,681 · see citing works
Bergey's manual of determinative bacteriology
Cheng, T. C. (1975) · Journal of Invertebrate Pathology · doi:10.1016/0022-2011(75)90102-0 · Cited by 1,024 · see citing works
Tillett, D., Dittmann, E., Erhard, M., von Döhren, H., Börner, T., & Neilan, B. A. (2000) · Chemistry & Biology · doi:10.1016/s1074-5521(00)00021-1 · Cited by 996 · see citing works
Automated De Novo Identification of Repeat Sequence Families in Sequenced GenomesPreprint
Bao, Z., & Eddy, S. R. (2002) · Genome Research · doi:10.1101/gr.88502 · Cited by 995 · see citing works
Kaneko, T. (2001) · DNA Research · doi:10.1093/dnares/8.5.205 · Cited by 696 · see citing works
Self-citationNew developments in the InterPro database
Mulder, N., Apweiler, R., Attwood, T. K., Bairoch, A., Bateman, A. G., Binns, D., Peer Bork, B., Buillard, V., Cerutti, L., Copley, R. R., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkl841 · Cited by 508 · see citing works
Walsby, A. E. (1994) · Microbiological Reviews · doi:10.1128/mr.58.1.94-144.1994 · Cited by 459 · see citing works
Codd, G. A., Lindsay, J., Young, F. M., Morrison, L. F., & Metcalf, J. S. (2005) · Springer eBooks · doi:10.1007/1-4020-3022-3_1 · Cited by 387 · see citing works
Microcystin Biosynthesis in Planktothrix : Genes, Evolution, and Manipulation
Christiansen, G., Fastner, J., Erhard, M., Börner, T., & Dittmann, E. (2003) · Journal of Bacteriology · doi:10.1128/jb.185.2.564-572.2003 · Cited by 374 · see citing works
Complete Genome Structure of the Thermophilic Cyanobacterium Thermosynechococcus elongatus BP-1
Nakamura, Y. (2002) · DNA Research · doi:10.1093/dnares/9.4.123 · Cited by 352 · see citing works
Self-citationComplete Genome Structure of Gloeobacter violaceus PCC 7421, a Cyanobacterium that Lacks Thylakoids
Nakamura, Y. (2003) · DNA Research · doi:10.1093/dnares/10.4.137 · Cited by 292 · see citing works
Self-citationWalsby, A. E. (1994) · Microbiological Reviews · doi:10.1128/mmbr.58.1.94-144.1994 · Cited by 278 · see citing works
REBASE—enzymes and genes for DNA restriction and modification
Roberts, R., Vincze, T., Pósfai, J., & Macelis, D. (2007) · Nucleic Acids Res. · doi:10.1093/nar/gkl891 · Cited by 269 · see citing works
Nishizawa, T., Asayama, M., Fujii, K., et al. (1999) · The Journal of Biochemistry · doi:10.1093/oxfordjournals.jbchem.a022481 · Cited by 264 · see citing works
Nishizawa, T., Ueda, A., Asayama, M., Fujii, K., Harada, K., Ochi, K., & Shirai, M. (2000) · The Journal of Biochemistry · doi:10.1093/oxfordjournals.jbchem.a022670 · Cited by 257 · see citing works
Mikalsen, B., Boison, G., Skulberg, O. M., et al. (2003) · Journal of Bacteriology · doi:10.1128/jb.185.9.2774-2785.2003 · Cited by 241 · see citing works
Bureau, T. E., Ronald, P. C., & Wessler, S. R. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.16.8524 · Cited by 207 · see citing works
Otsuka, S., Suda, S., Li, R., et al. (1999) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.1999.tb13443.x · Cited by 201 · see citing works
An SmtB-like repressor from Synechocystis PCC 6803 regulates a zinc exporter
Thelwell, C., Robinson, N. J., & Turner-Cavet, J. S. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.18.10728 · Cited by 179 · see citing works
Otsuka, S., Suda, S., Shibata, S., Oyaizu, H., Matsumoto, S., & Watanabe, M. M. (2001) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/00207713-51-3-873 · Cited by 172 · see citing works
Self-citationSuzuki, S., Ferjani, A., Suzuki, I., & Murata, N. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m313358200 · Cited by 168 · see citing works
Self-citationMorphological variability of colonies of Microcystis morphospecies in culture.
Otsuka, S., Suda, S., Li, R., et al. (2000) · The Journal of General and Applied Microbiology · doi:10.2323/jgam.46.39 · Cited by 167 · see citing works
Mizuno, T. (1996) · DNA Research · doi:10.1093/dnares/3.6.407 · Cited by 145 · see citing works
Schneider, A., & Marahiel, M. A. (1998) · Archives of Microbiology · doi:10.1007/s002030050590 · Cited by 138 · see citing works
Kaneko, T. (2003) · DNA Research · doi:10.1093/dnares/10.5.221 · Cited by 133 · see citing works
Self-citationMcGinn, P. J., Price, G. D., Maleszka, R., & Badger, M. R. (2003) · PLANT PHYSIOLOGY · doi:10.1104/pp.019349 · Cited by 132 · see citing works
Genetic contributions to the risk assessment of microcystin in the environment
Dittmann, E., & Börner, T. (2004) · Toxicology and Applied Pharmacology · doi:10.1016/j.taap.2004.06.008 · Cited by 119 · see citing works
16S rDNA sequences and phylogenetic analyses ofMicrocystisstrains with and without phycoerythrin
Otsuka, S., Suda, S., Li, R., et al. (1998) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.1998.tb13076.x · Cited by 109 · see citing works
Vega-Palas, M. A., Madueño, F., Herrero, A., & Flores, E. (1990) · Journal of Bacteriology · doi:10.1128/jb.172.2.643-647.1990 · Cited by 103 · see citing works
A review of water bloom forming microcystis species with regard to populations from japan
Komárek, J. (1991) · Cited by 103 · see citing works
Carré‐Mlouka, A., Comte, K., Castets, A.-M., Bouchier, C., & de Marsac, N. T. (2004) · Journal of Bacteriology · doi:10.1128/jb.186.8.2355-2365.2004 · Cited by 102 · see citing works
Tanabe, Y., Kasai, F., & Watanabe, M. M. (2007) · Microbiology · doi:10.1099/mic.0.2007/010645-0 · Cited by 101 · see citing works
Self-citationTanabe, Y., Kaya, K., & Watanabe, M. M. (2004) · Journal of Molecular Evolution · doi:10.1007/s00239-004-2583-1 · Cited by 99 · see citing works
Self-citationGupta, A., Morby, A. P., Turner, J. S., Whitton, B. A., & Robinson, N. J. (1993) · Molecular Microbiology · doi:10.1111/j.1365-2958.1993.tb01110.x · Cited by 82 · see citing works
Cyanopeptolin 963A, a Chymotrypsin Inhibitor of Microcystis PCC 7806
Bister, B., Keller, S., Baumann, H., NICHOLSON, G. J., Weist, S., Jung, G., Süßmuth, R. D., & Jüttner, F. (2004) · Journal of Natural Products · doi:10.1021/np049828f · Cited by 80 · see citing works
Biosynthetic systems for nonribosomal peptide antibiotic assembly
Mootz, H. D., & Marahiel, M. A. (1997) · Current Opinion in Chemical Biology · doi:10.1016/s1367-5931(97)80051-8 · Cited by 75 · see citing works
Aichi, M., Takatani, N., & Omata, T. (2001) · Journal of Bacteriology · doi:10.1128/jb.183.20.5840-5847.2001 · Cited by 73 · see citing works
Copp, J. N., & Neilan, B. A. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.72.4.2298-2305.2006 · Cited by 71 · see citing works
The diversity of gas vesicle genes in Planktothrix rubescens from Lake Zürich
Beard, S. J., Hayes, P. K., Handley, B. A., et al. (1999) · Microbiology · doi:10.1099/00221287-145-10-2757 · Cited by 66 · see citing works
Walsby, A. E., & Hayes, P. K. (1988) · Microbiology · doi:10.1099/00221287-134-10-2647 · Cited by 62 · see citing works
Minezaki, Y., Homma, K., & Nishikawa, K. (2006) · DNA Research · doi:10.1093/dnares/dsi016 · Cited by 62 · see citing works
Targeted inactivation of the hrcA repressor gene in cyanobacteria
Nakamoto, H., Suzuki, M., & Kojima, K. (2003) · FEBS Letters · doi:10.1016/s0014-5793(03)00768-3 · Cited by 61 · see citing works
Tooming‐Klunderud, A., Rohrlack, T., Shalchian‐Tabrizi, K., Kristensen, T., & Jakobsen, K. S. (2007) · Microbiology · doi:10.1099/mic.0.2006/001123-0 · Cited by 61 · see citing works
Yoshimura, H., Hisabori, T., Yanagisawa, S., & Ohmori, M. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.275.9.6241 · Cited by 50 · see citing works
Otsuka, S., Suda, S., Li, R., et al. (1999) · Phycological Research · doi:10.1046/j.1440-1835.1999.00162.x · Cited by 49 · see citing works
A Nucleomorph-Encoded CbbX and the Phylogeny of RuBisCo Regulators
Maier, U. G., Fraunholz, M. J., Zauner, S., Penny, S. L., & Douglas, S. E. (2000) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026337 · Cited by 46 · see citing works
Juntarajumnong, W., Hirani, T. A., Simpson, J. M., et al. (2007) · Archives of Microbiology · doi:10.1007/s00203-007-0259-0 · Cited by 45 · see citing works
Kloft, N. (2005) · Microbiology · doi:10.1099/mic.0.27771-0 · Cited by 42 · see citing works
Otsuka, S., Suda, S., Li, R., et al. (1999) · Phycological Research · doi:10.1111/j.1440-1835.1999.tb00298.x · Cited by 42 · see citing works
Dunton, P. G., & Walsby, A. E. (2005) · FEMS Microbiology Letters · doi:10.1016/j.femsle.2005.04.026 · Cited by 37 · see citing works
Ashby, M. K., Houmard, J., & Mullineaux, C. W. (2002) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.2002.tb11320.x · Cited by 32 · see citing works
Ashby, M. K. (2002) · FEMS Microbiology Letters · doi:10.1016/s0378-1097(02)00834-0 · Cited by 17 · see citing works
Carré‐Mlouka, A. (2004) · FEMS Microbiology Letters · doi:10.1016/j.femsle.2004.06.011 · Cited by 12 · see citing works
Carré‐Mlouka, A., Comte, K., & de Marsac, N. T. (2004) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.2004.tb09674.x · Cited by 10 · see citing works
Flagged first, then by citations
Research works printed but not linked: 1
- [5]Watanabe M. Watanabe M. F. Harada K. Carmichael W. W. Fujiki H. Toxic Microcystis 1996 Boca Raton CRC Press 13 34
Cited by
Sorted by citations
Improving the coverage of the cyanobacterial phylum using diversity driven genome sequencing
Shih, P. M., Wu, D., Latifi, A., Axen, S. D., Fewer, D. P., Talla, E., Calteau, A., Cai, F., Tandeau de Marsac, N., Rippka, R., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1217107110 · Cited by 800 · see citing works
Frangeul, L., Quillardet, P., Castets, A.-M., Humbert, J.-F., Matthijs, H. C., Cortez, D., Tolonen, A., Zhang, C.-C., Gribaldo, S., Kehr, J.-C., et al. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-274 · Cited by 221 · see citing works
Exploitation of Oil-bearing Microalgae for Biodiesel
SONG, D., FU, J., & SHI, D. (2008) · Chinese Journal of Biotechnology · doi:10.1016/s1872-2075(08)60016-3 · Cited by 167 · see citing works
Yang, C., Lin, F., Li, Q., Li, T., & Zhao, J. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00394 · Cited by 44 · see citing works
Bench, S. R., Ilikchyan, I. N., Tripp, H. J., & Zehr, J. P. (2011) · Frontiers in Microbiology · doi:10.3389/fmicb.2011.00261 · Cited by 43 · see citing works
“…regions, phytoplankton production is often limited by nutrients, especially nitrogen (N), and in those areas, nitrogen (N2) fixation provides an important source of new N that supports primary productivity (Karl et al., 1997, 2002; Bonnet et al., 2009; Kitajima et al., 2009; Shiozaki et al., 2010).”
BackgroundXu, T., Qin, S., Hu, Y., Song, Z., Ying, J., Li, P., Dong, W., Zhao, F., Yang, H., & Bao, Q. (2016) · DNA Research · doi:10.1093/dnares/dsw023 · Cited by 37 · see citing works
- Authors
- Kaneko, T., Nakajima, N., Okamoto, S., Suzuki, I., Tanabe, Y., Tamaoki, M., Nakamura, Y., Kasai, F., Watanabe, A., Kawashima, K., Kishida, Y., Ono, A., Shimizu, Y., Takahashi, C., Minami, C., Fujishiro, T., Kohara, M., Katoh, M., Nakazaki, N., Nakayama, S., Yamada, M., Tabata, S., & Watanabe, M. M.
- Affiliations
- Kazusa DNA Research Institute (JP)
- National Institute for Environmental Studies (JP)
- University of Tsukuba (JP)
- Corresponding author
- Kaneko, Takakazu
- ORCID
- Venue
- DNA Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2007
- Volume
- 14
- Issue
- 6
- Pages
- 247-256
- ISSN
- 1340-2838 (ISSN-L)
- 1756-1663
- PMC
- PMC2779907
- OpenAlex
- W2126253234
- Cited by
- 284
- References
- 63
- Citations by year
- 2026: 5 · 2025: 9 · 2024: 14 · 2023: 6 · 2022: 6 · 2021: 21 · 2020: 7 · 2019: 16 · 2018: 16 · 2017: 10 · 2016: 17 · 2015: 22 · 2014: 12 · 2013: 22 · 2012: 31
- FWCI
- 5.29
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- DNA Research (publishedVersion)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Environmental Science › Environmental Chemistry › Aquatic Ecosystems and Phytoplankton Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Keywords
- Microcystis aeruginosa, cyanobacterial genome, genome structure, microcystin biosynthesis, cyanopeptolins, toxin gene clusters, transposable elements, insertion sequences, genome plasticity, homologous recombination, restriction-modification systems, two-component systems, cyanotoxins, bloom-forming cyanobacteria
- MeSH terms
- Bacterial Proteins, Base Composition, Base Sequence, Multigene Family, Molecular Sequence Data, Genome, Bacterial, Sequence Analysis, DNA, Protein Structure, Tertiary, Microcystis
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
