Genome structural variation and evolution in sub-strain of the cyanobacterium Synechocystis sp. PCC 6803.

Synechocystis sp. PCC 6803, the first photosynthetic organism, plays an important role in basic research on the mechanism and molecular genetics of the photosynthetic machinery. There are several sub-strains maintained in each laboratory, which differ in phenotypes such as phototaxis, biofilm formation, and glucose-tolerance. Recently, it has been shown that glucose-sensitive PCC-P strain accumulates specific polysaccharide sulfate, Synechan, extracellularly and forms a bloom-like cell aggregation, whereas these phenomenons not seen in another sub-strain GT-I. To date, genome resequencing using short-read sequencer revealed the SNPs and In/dels in several sub-strains, however, the genomic factor(s) responsible for those phenotypic variation are still unclear. The genome of Synechocystis 6803 consists of a main chromosome and four large plasmids, which contains a lot of duplicate sequences, such as transposons. Furthermore, it is noted that there are 18 kbp of duplicated regions in the large plasmid pSYSX. These duplication sequences make it difficult to decide precise genome sequence. In order to establish perfect sequence data and reveal the factor contributing the phenotypic differences in Synechocystis 6803, we performed resequencing of two sub-strains maintained our laboratory (GT-In and PCC-Pn) using combination of short- and long-read sequence technology. The results of comparison with the GT-I genome showed that the two large plasmids, pSYSM and pSYSX, were integrated in the PCC-Pn strain. The transcriptomic data revealed that the expression levels of pSYSM coding genes, including Synechan cluster, was significantly higher in PCC-Pn than those in GT-In, while the expression levels in pSYSX is lower. In addition, the HCO3- transporter genes encoded in chromosome were more abundantly expressed in the PCC-Pn. The deletion of HCO3- transporter genes enhanced the glucose tolerance of PCC-Pn strain, indicating that excess incorporation of HCO3- is one of the reasons for the glucose sensitivity of PCC-P strains. Further, we also found a relationship between the methyltransferase encoded in the plasmid and glucose tolerance. In summery our results suggest that the phenotypic diversity in Synechocystis 6803 is generated through plasmid rearrangement.