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.

Takakazu Kaneko1, Shusei Sato1, Hirokazu Kotani1, Ayako Tanaka1, Erika Asamizu1, Yasukazu Nakamura1, Nobuyuki Miyajima1, Makoto Hirosawa1, Masahiro Sugiura2, Shigemi Sasamoto1, Takaharu Kimura1, Tsutomu Hosouchi1, Ai Matsuno1, Akiko Muraki1, Naomi Nakazaki1, Kaoru Naruo1, Satomi Okumura1, Sayaka Shimpo1, Chie Takeuchi1, Tsuyuko Wada1, Akiko Watanabe1, Manabu Yamada1, Miho Yasuda1 and Satoshi Tabata1,*

1Kazusa DNA Research Institute 1532-3 Yana, Kisarazu, Chiba 292, Japan
2Center for Gene Research, Nagoya University Furho-cho, Nagoya 464-01, Japan

• To whom correspondence should be addressed. Tel. +81-438-52-3933, Fax. +81-438-52-3934, E-mail: tabata@kazusa.or.jp
  

Received June 19, 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 λ 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.

 

 

http://dnaresearch.oxfordjournals.org/content/3/3/109.abstract