PMC:3514855 / 7996-11462 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/3514855","sourcedb":"PMC","sourceid":"3514855","source_url":"https://www.ncbi.nlm.nih.gov/pmc/3514855","text":"3.1. Overview\nSequencing of the Synechocystis sp. PCC 6803 ‘Moscow’ substrain ‘PCC-M’ by Illumina (Solexa) yielded an average 1100-fold coverage of the chromosome and five of the seven plasmids. The existence of the two remaining plasmids was verified individually by PCR. Following assembly of sequences, mapping to the reference strain sequences and annotation, the obtained genome and plasmid sequences were deposited in the GenBank database with the accession numbers CP003265–CP003272.\nAltogether, we found 45 differences (36 SNPs and 9 indels \u003e1 bp) between the investigated substrain ‘PCC-M’ and the published sequences of the ‘GT-Kazusa’ chromosome2 and plasmids20 used here as references (Table 1). From these differences, 41 are located in the chromosome and four in the plasmids pSYSA, pSYSM and pCA2.4. For verification, about one-third of these differences were randomly chosen and confirmed independently by PCR and Sanger sequencing of the respective regions in substrain ‘PCC-M’, but no misidentified mutations were found. These DNA regions were, in addition, amplified and compared with the sequences from substrains ‘GT-Kazusa’ and ‘GT-V’ for control and comparison, respectively. The GT ‘GT-V’ was chosen for comparison as is widely used for the dissection and analysis of photosynthetic mutants. Fully segregated PSI, PSII and Chl biosynthesis mutants were successfully generated in this genetic background21,22 and some of these mutants could not be obtained in other substrains.23\nTable 1. Location and effects of SNPs and indels found in ‘PCC-M’ compared with the nucleotide sequence of ‘GT-Kazusa’ in the database\nThe events are numbered (column #), the type of mutation (M) is indicated as S, substitution, D, deletion or I, insertion, together with the respective start and end positions in the ‘GT-Kazusa’ reference sequence. For each event the respective nucleotide change is indicated on the forward strand, together with the resulting codon modification (Ref. → Mut) and amino acid change, if any. Highlighted in italics are four instances of missing ISY203 copies and in bold all SNPs affecting intergenic spacer regions (IGR). aIndicate errors in the database.\nThe number of differences between ‘PCC-M’ and ‘GT-Kazusa’ are almost twice as many as reported by Tajima et al.10 for the GT (GT-S) ‘Kazusa’ strain, where a total of 22 differences from the published sequence were found.10 All but 3 of those 22 differences were also detected in the ‘PCC-M’ strain studied here. The three unique differences in the ‘GT-S’ and 26 differences between ‘PCC-M’ and ‘GT-Kazusa’ underline the existence of lineage splitting in the Synechocystis substrains. Moreover, we found seven SNPs (#5, 13, 15, 16, 27, 32 and 33 in Tables 1 and 2) and one larger indel (#6 in Tables 1 and 2) specifically shared between the ‘PCC-M’ and the ‘PCC-N and PCC-P’ substrains, indicating that ‘PCC-M’ belongs to the ‘PCC’ group of motile substrains.9 ‘PCC-M and PCC-P’ are strains that both exhibit the native positive phototaxis, whereas ‘PCC-N’ strain shows negative phototaxis.24\nTable 2. Comparison of SNPs and indels found in the chromosome of ‘PCC-M’ with sequences from other substrains\nAll events are numbered (column #) as in Table 1. The presence of the respective ‘PCC-M’ mutation in the different substrains is indicated by the check marks. aThe deletion of 0.6 kb in the gene slr1753 compared with the reference was also verified here in ‘GT-Kazusa’.","divisions":[{"label":"title","span":{"begin":6,"end":14}},{"label":"p","span":{"begin":15,"end":491}},{"label":"p","span":{"begin":492,"end":2194}},{"label":"table caption","span":{"begin":1504,"end":2194}},{"label":"p","span":{"begin":1513,"end":1638}},{"label":"p","span":{"begin":1640,"end":2160}},{"label":"p","span":{"begin":2161,"end":2194}},{"label":"p","span":{"begin":3095,"end":3196}},{"label":"p","span":{"begin":3198,"end":3356}}],"tracks":[{"project":"2_test","denotations":[{"id":"23069868-8905238-25970077","span":{"begin":657,"end":658},"obj":"8905238"},{"id":"23069868-14686584-25970078","span":{"begin":671,"end":673},"obj":"14686584"},{"id":"23069868-9578474-25970079","span":{"begin":1427,"end":1429},"obj":"9578474"},{"id":"23069868-8188669-25970080","span":{"begin":1430,"end":1432},"obj":"8188669"},{"id":"23069868-18625715-25970081","span":{"begin":1501,"end":1503},"obj":"18625715"},{"id":"23069868-21803841-25970082","span":{"begin":2305,"end":2307},"obj":"21803841"},{"id":"23069868-21803841-25970083","span":{"begin":2414,"end":2416},"obj":"21803841"},{"id":"23069868-22193367-25970084","span":{"begin":2952,"end":2953},"obj":"22193367"},{"id":"23069868-11158445-25970085","span":{"begin":3083,"end":3085},"obj":"11158445"}],"attributes":[{"subj":"23069868-8905238-25970077","pred":"source","obj":"2_test"},{"subj":"23069868-14686584-25970078","pred":"source","obj":"2_test"},{"subj":"23069868-9578474-25970079","pred":"source","obj":"2_test"},{"subj":"23069868-8188669-25970080","pred":"source","obj":"2_test"},{"subj":"23069868-18625715-25970081","pred":"source","obj":"2_test"},{"subj":"23069868-21803841-25970082","pred":"source","obj":"2_test"},{"subj":"23069868-21803841-25970083","pred":"source","obj":"2_test"},{"subj":"23069868-22193367-25970084","pred":"source","obj":"2_test"},{"subj":"23069868-11158445-25970085","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#ec939e","default":true}]}]}}