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Performance comparison of three phylogenetic markers used for cyanobacterial identification and classification

Lee, E., Monis, P., Ryan, U.M. and Paparini, A. (2012) Performance comparison of three phylogenetic markers used for cyanobacterial identification and classification. In: 3rd National Cyanobacterial Workshop, 23 - 24 August, Canberra, Australia.

Abstract

A selection of cyanobacterial isolates (n=28), obtained from twelve WA freshwater systems, was used to compare the performance of three phylogenetic markers commonly used for identification and classification of members of this phylum. Phylogenetic analysis was carried out using degenerate primers targeting the small subunit rRNA gene (16SrDNA), the γ-subunit of the DNA-dependent RNA polymerase (rpoC1) locus, and the phycocyanin (cpc) operon.

For the three markers, amplification efficiency was: 92.9%, 46.4%, and 71.4% respectively, with amplicon lengths, for each locus, ranging between 318-482, 548-663, and 484-746 bp, respectively. BLAST-searches identified the isolates as belonging to chroococcales (n=7), oscillatoriales (n=6), and nostocales (n=14), while identification of one isolate was dubious, and varied depending on the marker used.

Phylogenetic reconstructions were generated using different approaches, consisting of combinations of methods, models and parameters. Results were generally in agreement, with isolates showing similar grouping patterns, regardless of the locus considered. The 16S rDNA and rpoC1 loci, in particular, appeared to consistently provide coherent identifications and classifications. Two isolates from the oscillatoriales subgroup, however, displayed a significantly different clustering pattern when the highly variable cpc locus was used. This result was consistent even when different phylogenetic reconstruction approaches were adopted for this locus.

This study confirms the potential for different phylogenetic markers to affect proper identification and classification of cyanobacteria, and clearly advocates the implementation of complementary strategies based on the analysis of DNA and morphology. The selection of phylogenetic markers should be carefully considered to obtain reliable information. In fact, at least for some data-sets, this selection appears more critical than the phylogenetic reconstruction approach adopted.

Publication Type: Conference Item
Murdoch Affiliation: School of Veterinary and Biomedical Sciences
URI: http://researchrepository.murdoch.edu.au/id/eprint/10327
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