Phylogenetic analyses of Synechococcus strains (cyanobacteria) using sequences of 16S rDNA and part of the phycocyanin operon reveal multiple evolutionary lines and reflect phycobilin content

Int J Syst Evol Microbiol. 2001 May;51(Pt 3):861-871. doi: 10.1099/00207713-51-3-861.


The genus Synechococcus (cyanobacteria), while containing morphologically similar isolates, is polyphyletic and organisms presently classified as such require reclassification into several independent genera. Studies based on analysis of 16S rRNA gene sequences have shown that members of the genus Synechococcus are affiliated to three of seven deeply branching cyanobacterial lineages. In addition, some strains do not appear to be associated with any of these lineages and may represent novel clades. In this report, a cyanobacterial phylogeny based on 16S rDNA sequences, including 14 newly sequenced Synechococcus isolates, is presented. One newly sequenced Synechococcus strain (PCC 7902) did not have any close relatives amongst cyanobacterial isolates currently contained in 16S rDNA sequence databases and was only loosely affiliated to a cyanobacterial lineage in which no other Synechococcus strains were found. Three hot-spring Synechococcus isolates, including two that were newly sequenced in this study (PCC 6716 and PCC 6717), formed an additional cyanobacterial lineage. These results indicated that Synechococcus species are affiliated to five of eight deeply branching cyanobacterial lineages. Part of the phycocyanin (PC) gene sequence (cpc), including the intergenic spacer (IGS) between cpcB and cpcA and the corresponding flanking regions (cpcBA-IGS), was used to investigate relationships between closely related Synechococcus isolates. Previously described PCR primers did not amplify this region from the majority of strains under investigation, so a new set of primers was designed that allowed amplification and sequencing of the cpcBA-IGS and flanking regions from 38 Synechococcus species. Phylogenetic analysis of this region was largely consistent with that obtained from 16S rDNA sequence analysis and revealed a relationship between the primary PC DNA sequence and the phycobilin content of cells.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Cyanobacteria / classification*
  • Cyanobacteria / genetics*
  • DNA Primers
  • DNA, Ribosomal / genetics*
  • Evolution, Molecular*
  • Molecular Sequence Data
  • Operon*
  • Phycobilins
  • Phycocyanin / genetics*
  • Phycocyanin / metabolism
  • Phylogeny*
  • Polymerase Chain Reaction
  • Pyrroles / metabolism
  • RNA, Ribosomal, 16S / genetics*
  • Tetrapyrroles


  • DNA Primers
  • DNA, Ribosomal
  • Phycobilins
  • Pyrroles
  • RNA, Ribosomal, 16S
  • Tetrapyrroles
  • Phycocyanin
  • phycocyanobilin

Associated data

  • GENBANK/AF216942
  • GENBANK/AF216943
  • GENBANK/AF216944
  • GENBANK/AF216945
  • GENBANK/AF216946
  • GENBANK/AF216947
  • GENBANK/AF216948
  • GENBANK/AF216949
  • GENBANK/AF216950
  • GENBANK/AF216951
  • GENBANK/AF216952
  • GENBANK/AF216953
  • GENBANK/AF216954
  • GENBANK/AF216955
  • GENBANK/AF223428
  • GENBANK/AF223429
  • GENBANK/AF223430
  • GENBANK/AF223431
  • GENBANK/AF223432
  • GENBANK/AF223433
  • GENBANK/AF223434
  • GENBANK/AF223435
  • GENBANK/AF223436
  • GENBANK/AF223437
  • GENBANK/AF223438
  • GENBANK/AF223439
  • GENBANK/AF223440
  • GENBANK/AF223441
  • GENBANK/AF223442
  • GENBANK/AF223443