Genetic diversity and phylogeny analysis of Azolla based on DNA amplification by arbitrary primers

Abstract

The polymerase chain reaction was used to amplify random sequences of DNA from 25 accessions of Azolla to evaluate the usefulness of this technique for identification and phylogenetic analysis of this aquatic fern. Accessions were selected to represent all known species within the genus Azolla and to encompass the world-wide distribution of the fern. Primers of 10 nucleotides with 70% G + C content were used to generate randomly amplified polymorphic DNA from the symbiotic Azolla-Anabaena complex. Twenty-two primers were used and each primer gave 4-10 bands of different molecular weights for each accession. Bands were scored as present or absent for each accession and variation among accessions was quantified using Nei's genetic distances. A dendrogram summarizing phenetic relationships among the 25 accessions was generated using the unweighted pair-group method with arithmetic mean. Principal component analysis was also used to evaluate genetic similarities. Three distinct groups were identified: group 1 contains five species, group 2 contains the pinnata species, and group 3 contains the nilotica species. The analysis demonstrates that the major groups of Azolla species can be easily distinguished from one an other and, in addition, that closely related accessions within species can be identified. We further found that using 10 primers, a phylogeny that is essentially the same as that derived from 22 primers can be constructed. Our results suggest that total DNA extracted from the Azolla-Anabaena symbionts is useful for classification and phylogenetic studies of Azolla.

Random amplified polymorphic DNA analysis of eel genome

“…(2) primer S17 (3) primer OPE6 (4) primer OPB12 (A1 and A2, B1 and B2, C1 and C2 refer to two individuals of Muraenesox cinereus, Anguilla anguilla and Anguilla japonica) DISCUSSION RAPD employs single arbitrarily chosen primers and the polymerase chain reaction ( PCR), and is useful in fingerprinting complex genomes. By RAPD a set of primers can generate multiple genetic markers to distinguish closely related species or even strains [ 8], [9] . In this study, 29 random primers were applied to measure the polymorphisms between Anguilla japonica, Anguilla anguilla and Muraenesox cinersus.…”

Rapid differentiation of phenotypically and genotypically similar Synechococcus elongatus strains by PCR fingerprinting.

“…This makes it a tool of great power and general applicability. It has been shown that as few as three primers used separately provide enough polymorphic information to identify species of the symbiotic genus Anabaena and to create a phylogenetic tree with topology similar to that derived with 22 primers (van Coppenhole et al 1993). Similarly, a single 10-mer and 8-mer proved sufficient for distinguishing among 31 symbiotic cyanobacterial strains of Phaeoceros sp.…”

Cyanobacterial Associations

“…Nevertheless, in recent years, the cyanobacteria inhabiting the different Azolla species have been classified using different molecular markers either directly on isolated DNA from the intact symbiosis or by PCR analysis of intact filaments picked out from the leaf cavities (Plazinski et al, 1990;van Coppenolle et al, 1993;Caudales et al, 1995;Kim et al, 1997;Zheng et al, 1999). These investigations show that the cyanobacteria from the Azolla and Rhizosperma sections are clearly distinguishable.…”