We have compiled a separate Sequences page, which includes accession numbers and the ability to download sequences and which includes the rDNA sequences described below.
Ward & Adams (1998) have analysed rDNA sequences from some plasmodiophorid isolates and concluded that the plasmodiophorids did not group with the Fungi, nor convincingly with any other group of organisms. The principal evidence is presented below.
Sequences were obtained of the NS7 - ITS4 rDNA region (White et al., 1990) for isolates of Polymyxa graminis (3 subgroups), P. betae and Plasmodiophora brassicae as well as for the Chytridiomycete Olpidium brassicae.
The NS7-NS8 region was used to search the EMBL and Genbank databases using FASTA to find those sequences most homologous to those from the Polymyxa and Plasmodiophora isolates. The closest matches (all 75%) were to oomycetes (Phytophthora megasperma, Lagenidium giganteum, Achlya bisexualis) and diatoms (Pseudo-nitzschia multiseries).
The sequences obtained were then aligned with those from the databases for a range of eukaryotic organisms, including the only other plasmodiophorid rDNA sequence currently available, from another Plasmodiophora brassicae isolate (EMBL accession No. U18981, Castlebury & Domier). Phylogenetic analyses were done useing programs in the PHYLIP package (Felsenstein, 1993). Genetic distances between pairs of species were calculated using the program DNADIST using the Kimura two parameter method. Phylogenetic trees were constructed using a parsimony method (DNAPARS) and distance methods (DNADIST + NEIGHBOR or FITCH) using the original data set and 100 bootstrap data sets generated by the program SEQBOOT. The tree obtained using NEIGHBOR with the archezoan Giardia as the outgroup is shown in Figure 1. The results show good support (from bootstrapping) for the Polymyxa species group and the Plasmodiophora + Polymyxa group and there is some support for the separation of Polymyxa species (P. betae and P. graminis). None of the analyses associated the plasmodiophorid species with any of the other species used for comparison. As expected, the Olpidium brassicae isolate grouped with other Chytridiomycetes and the true fungi.
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| Fig. 1. The consensus phylogenetic tree of the NS7-NS8 regions obtained using NEIGHBOR analysis and displayed as a Phylogram from VIEWTREE (Page, 1996). The bootstrap values at the forks indicate the number of times out of 100 trees that this grouping occurred. The horizontal lines represent distances to the scale shown in the bottom left of the figure. |
As others have reported, the Oomycete "fungi" group with diatoms (and some algae) in a taxon variously called Straminipiles or Chromista. Some authors include these in a broadly defined "Protoctista" while others define the Protozoa more narrowly and raise this group to Kingdom status. Our data suggest that the plasmodiophorids do not group convincingly with the true Fungi, the Straminipiles, nor with any other group of organisms. They should probably be classified as Protoctista (Protista).
Additional sequences of the ITS4-ITS5 regions of one isolate each of a Ligniera sp. and of Spongospora subterranea subsp. subterranea were also obtained and analysed with the other plasmodiophorids, using Olpidium brassicae as the outgroup. The pairwise distance values between organisms supported the recognition of Ligniera as a distinct taxon with distances of 0.45-0.59 from Polymyxa, whereas the Polymyxa isolates had distances between one another of 0.16-0.32.
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