In this strain, all four 16S rRNA genes were identical, which is in agreement with a study of Engene and Gerwick (2011). Two operons contained nearly identical 16S-23S ITS regions with both tRNA genes, and two operons contained nearly identical 16S-23S ITS regions lacking tRNA genes. This result beta-catenin inhibitor was consistent with what we found in all other Cylindrospermum strains, and we assume that all strains had this pattern even when one of the ITS operons was not recovered. The 16S-23S ITS regions were highly similar within the Cylindrospermum taxa in clades X and Y, permitting alignment of both operon 1 and operon 2. Phylogenies of these ITS regions had high bootstrap support,

and are superior to the 16S rRNA phylogenies for elucidating relationships among species (Fig. 1, b and c). These trees were in fairly close agreement with each other and with the 16S phylogeny. The ITS phylogenies were not in disagreement with our species assignments, i.e. no species was clearly not monophyletic. Secondary structure of the conserved domains of the ITS revealed a number of species-specific patterns. The D1-D1′ helices were identical for C. muscicola SAG 44.79, C. licheniforme CCALA 995, C. badium CCALA 1000, and the five strains of

C. catenatum, although sequence differences existed (note ambiguous bases W and R, group I; Fig. 2a). Cylindrospermum pellucidum CCALA 989/CCALA 992, C. stagnale PCC 7417, and C. moravicum CCALA Opaganib supplier 993 possessed helices structurally similar to the D1-D1′ helices of the C. catenatum group, but differed in minor

ways (Fig. 2, b and c). Cronbergia also had a D1-D1′ helix similar to all of the above (Fig. 2d). Cylindrospermum stagnale PCC 7417 had a single nucleotide in the terminal loop that differed from the above group (Fig. 2, a–d), such that the terminal loop was divided into a small terminal loop and a subterminal bilateral bulge (Fig. 2h). The C. catenatum group could close the large terminal loop in this position as well, but this structure would be less thermodynamically stable (GC….GU binds, but more weakly than the AC….GU in C. stagnale PCC 7417). A major break in structure occurred between the group including C. catenatum and the group of species 上海皓元医药股份有限公司 in the clade containing C. marchicum CCALA 1001, C. alatosporum CCALA 988/CCALA 994, and C. maius CCALA 998 (Fig. 2, e–g). The Hawaiian Cylindrospermum CCALA 1002 had different helices in the two different operons, both of which showed significant divergence from the helices of other species (Fig. 2, i and j). Aulosira bohemensis was also very distinct (Fig. 2k). The V2 helix is located between the tRNAIle and tRNAAla genes, and is thus only present in those operons, which contain the tRNA genes. This helix varied considerably among strains. C. catenatum (CCALA 990, 991, 996) and C.