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A REASSESSMENT OF ITS/5.8S DNA SEQUENCE VARIATION AND PHYLOGENETIC SIGNAL IN THE SYNUROPHYCEAE
Author(s) -
Wee J. L.
Publication year - 2000
Publication title -
journal of phycology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.85
H-Index - 127
eISSN - 1529-8817
pISSN - 0022-3646
DOI - 10.1046/j.1529-8817.1999.00001-208.x
Subject(s) - biology , phylogenetic tree , taxon , genetics , dna sequencing , sequence (biology) , evolutionary biology , dna , phylogenetics , gene , botany
Previously, DNA sequences were determined for the entire ITS/5.8S region by direct sequencing of PCR amplification products. 28 sequences were obtained from 12 species of Synurophyceae, including Tessellaria volvocina , Chrysodidymus synuroideus , six species of Synura and four species of Mallomonas. Sequences also were determined from multiple strains of some species, including 15 strains of Synura petersenii. The length of these sequences varied from 495–598 bp. The large amount of ITS/5.8S length variation made initial attempts in determining reliable sequence alignment difficult and precluded their use in phylogenetic analyses of the class. Subsequently, the approach of Bogler & Simpson (1996) was investigated where reiterative, computer assisted alignments were generated and the quality of the alignment was evaluated by homoplasy index and consistency index values. However, these alignments also were equivocal. ITS/5.8S sequences sorted the 15 S. petersenii strains into two well supported ITS lineages. One ITS type included ten isolates from North America while isolates from the second ITS type included one each from Germany and Australia and three from North America. Results are presented here where the sequences from the 15 S. petersenii isolates were used to characterize ITS‐1 and ITS‐2 RNA transcript secondary structure. Next, this information was expanded to include ITS/5.8S sequences from the other taxa in the class. Finally, the characteristics of ITS 1 and ITS 2 RNA transcript secondary structure were used as a guide to align all of the ITS/5.8S sequences from the Synurophyceae in a final phylogenetic analysis.