1.  Introduction
With currently >4000 publications available from PubMedCentral alone, ‘Synechocystis’ is the most widely used photoautotrophic prokaryotic model organism. Synechocystis sp. PCC 6803 is a unicellular cyanobacterium that was isolated from a freshwater pond in Oakland, California.1 The high popularity of Synechocystis sp. PCC 6803 stems from the two facts that it was the first phototrophic and the third organism overall, for which a complete genome sequence was determined,2 and that it easily takes up exogenous DNA and integrates it into its chromosome by homologous recombination.3–5
Synechocystis sp. PCC6803 is known to occur in several distinct substrains, all going back to the same isolate deposited in the Pasteur Culture Collection.6 Indeed, several studies reported the differences between the genome sequence of Synechocystis sp. PCC 6803 published in 1996 (called here the ‘GT-Kazusa’ substrain) and the actual sequence found in different laboratories.7–10 A strain history has been proposed by Ikeuchi and Tabata8 with an early branching into the motile PCC strain and the non-motile ATCC 27184 strain. The latter lost motility due to a 1-bp insertion in the spkA gene coding for a eukaryotic-type Ser/Thr protein kinase11 and represents the origin of the glucose-tolerant (GT) strains5 to which also the ‘GT-Kazusa’ substrain belongs.
For decades, Synechocystis sp. PCC 6803 has served as a simple model in photosynthesis research and to solve fundamental questions in microbial and plant physiology. More recently, cyanobacteria are increasingly being recognized as a promising resource for the production of biofuels such as hydrogen,12 ethanol,13 isobutyraldehyde and isobutanol,14 ethylene15 and alkanes.16 Synechocystis sp. PCC 6803 is being developed further as a model in these biotechnology- and systems biology-oriented studies. These facts as well as the search for motility-associated genes prompted several re-sequencing studies of Synechocystis sp. PCC 6803 substrains, namely of the substrains GT-S,10 PCC-P, PCC-N, GT-I9 and YF.17 However, these studies have not included the widely used GT and motile ‘Moscow’ substrain, which we here suggest to call ‘PCC-M’. Furthermore, thus far no attention has been paid to the possible sequence variations in the seven plasmids, which constitute a total sequence length of 383 486 bp almost 10% of the total coding capacity of Synechocystis sp. PCC 6803. This analysis provides new and reliable sequence data for the Synechocystis sp. PCC 6803 substrain ‘PCC-M’, revealing several differences from the published sequence that can be interpreted as the traces of microevolution during cultivation in the laboratory.