Investigating Deep Phylogenetic Relationships among Cyanobacteria and Plastids by Small Subunit rRNA Sequence Analysis1

Abstract

Small subunit rRNA sequence data were generated for 27 strains of cyanobacteria and incorporated into a phylogenetic analysis of 1,377 aligned sequence positions from a diverse sampling of 53 cyanobacteria and 10 photosynthetic plastids. Tree inference was carried out using a maximum likelihood method with correction for site-to-site variation in evolutionary rate. Confidence in the inferred phylogenetic relationships was determined by construction of a majority-rule consensus tree based on alternative topologies not considered to be statistically significantly different from the optimal tree. The results are in agreement with earlier studies in the assignment of individual taxa to specific sequence groups. Several relationships not previously noted among sequence groups are indicated, whereas other relationships previously supported are contradicted. All plastids cluster as a strongly supported monophyletic group arising near the root of the cyanobacterial line of descent.

Gut content microbiota of introduced bigheaded carps ( Hypophthalmichthys spp.) inhabiting the largest shallow lake in Central Europe

“…The first PCR was carried out using 27F (Lane, 1991) and 1401R (Nübel et al, 1996) primers, while for the second PCR, 27F-GC and 519R (Turner et al, 1999) primers were applied (which resulted in 16S rRNA gene amplicons containing the V1-V3 variable regions to get high resolution DGGE patterns; Yu and Morrison, 2004;Youssef et al, 2009) Bacterial community profiles were revealed and compared by DGGE using 7% (w/v) polyacrylamide gel containing a 40 to 60% gradient of denaturants (100% is defined as 40% formamide and 7 M urea). The electrophoresis was carried out at 60 °C in 1× Tris-acetate-EDTA (TAE) buffer at 120 V for 14.5 hours using a phorU-2 electrophoresis system (Ingeny International, Goes, Netherlands).…”

Bacterial Diversity in Bentonites, Engineered Barrier for Deep Geological Disposal of Radioactive Wastes

“…The primers used for this reaction were the bacterial universal primers 16S8F (5'-AGAGTTTGATCCTGGCTCAG-3') [40] and 16S1492R (5'-TACGGYTACCTTGTTACGACTT-3') [41]. The PCR amplifications were performed as described by [42], using 2 µl of reaction mixture obtained combining three parallel replicates.…”

Duplication and Quadruplication of Arabidopsis thaliana Cysteinyl- and Asparaginyl-tRNA Synthetase Genes of Organellar Origin

“…The extra aaRS genes in eukaryotes are presumed to be derived from those contained in the original mitochondrial endosymbiont (for a review of mitochondrial origins, see Gray et al 1999) and subsequently transferred to the nucleus, as no known extant mitochondrial genomes encode an aaRS. Plants received a third and more recent influx of aaRS genes with the acquisition of plastids (for reviews of plastid origins, see Douglas 1998;Martin et al 1998;Turner et al 1999). Like mitochondria, plastids have lost most of their original genes, some of which have been transferred to the nucleus.…”