Photosynthesis Research

, Volume 93, Issue 1–3, pp 55–67 | Cite as

Complete nucleotide sequence of the freshwater unicellular cyanobacterium Synechococcus elongatus PCC 6301 chromosome: gene content and organization

  • Chieko Sugita
  • Koretsugu Ogata
  • Masamitsu Shikata
  • Hiroyuki Jikuya
  • Jun Takano
  • Miho Furumichi
  • Minoru Kanehisa
  • Tatsuo Omata
  • Masahiro Sugiura
  • Mamoru SugitaEmail author
Regular Paper


The entire genome of the unicellular cyanobacterium Synechococcus elongatus PCC 6301 (formerly Anacystis nidulans Berkeley strain 6301) was sequenced. The genome consisted of a circular chromosome 2,696,255 bp long. A total of 2,525 potential protein-coding genes, two sets of rRNA genes, 45 tRNA genes representing 42 tRNA species, and several genes for small stable RNAs were assigned to the chromosome by similarity searches and computer predictions. The translated products of 56% of the potential protein-coding genes showed sequence similarities to experimentally identified and predicted proteins of known function, and the products of 35% of the genes showed sequence similarities to the translated products of hypothetical genes. The remaining 9% of genes lacked significant similarities to genes for predicted proteins in the public DNA databases. Some 139 genes coding for photosynthesis-related components were identified. Thirty-seven genes for two-component signal transduction systems were also identified. This is the smallest number of such genes identified in cyanobacteria, except for marine cyanobacteria, suggesting that only simple signal transduction systems are found in this strain. The gene arrangement and nucleotide sequence of Synechococcus elongatus PCC 6301 were nearly identical to those of a closely related strain Synechococcus elongatus PCC 7942, except for the presence of a 188.6 kb inversion. The sequences as well as the gene information shown in this paper are available in the Web database, CYORF (


Anacystis nidulans 6301 Cyanobacterial genome Large inversion Photosynthesis-related gene Synechococcus elongatus PCC 6301 Two-component signal transduction system Transcription factor 



Photosystem I


Photosystem II


Highly iterated palindrome


Insertion sequence


Open reading frame



This work was supported by Grant-in-Aid for Scientific Research on Priority Area “Genome Biology” (13206027 to MS) of the Ministry of Education, Sports, Science, Culture and Technology, Japan. We thank Tohru Matsubayashi, Takakazu Kaneko and Takahiko Tsudzuki, for valuable advises, and Nikolay Tzverkov, Makoto Suzuki, Tsuneo Fujishiro, Atsuko Tubai, Misato Ogura, Harumi Yokota, Yuriko Hara for technical assistance. We also thank Dr. Kan Tanaka, Prof. Masahiko Ikeuchi (The University of Tokyo), Prof. Ken Nishikawa, Dr. Yoshiaki Minesaki (National Institute of Genetics, Mishima), Dr. Shin-ichi Maeda, Prof. Takao Kondo (Nagoya University), Dr. Hideo Iwasaki (Wasada University) for annotation of protein-encoding genes, and an anonymous referee for valuable comments on the manuscript.


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Copyright information

© Springer Science+Business Media B.V. 2006

Authors and Affiliations

  • Chieko Sugita
    • 1
  • Koretsugu Ogata
    • 2
  • Masamitsu Shikata
    • 2
  • Hiroyuki Jikuya
    • 3
  • Jun Takano
    • 2
  • Miho Furumichi
    • 4
  • Minoru Kanehisa
    • 4
  • Tatsuo Omata
    • 5
  • Masahiro Sugiura
    • 6
  • Mamoru Sugita
    • 1
    Email author
  1. 1.Center for Gene ResearchNagoya UniversityChikusa, NagoyaJapan
  2. 2.Life Science Business UnitShimadzu Co.Nakagyo-ku, KyotoJapan
  3. 3.Bio-Architecture CenterKyushu UniversityHigashi-ku, FukuokaJapan
  4. 4.Bioinformatics Center, Institute for Chemical ResearchKyoto UniversityUji, KyotoJapan
  5. 5.Graduate School of Bioagricultural SciencesNagoya UniversityNagoyaJapan
  6. 6.Graduate School of Natural SciencesNagoya City UniversityNagoyaJapan

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