The use of DNA probes for taxonomic study of Dictyostelium wild isolates

The classification of 27 wild isolates assigned to Dictyostelium discoideum on the basis of morphological criteria was reexamined using probes specific for DNA sequences cloned from the type strain NC4. These probes included ones specific for ribosomal spacer DNA regions and for a ribosomal RNA coding sequence, as well as probes for two chromosomal gene families (actin and discoidin) and for the DIRS-1 transposable element. Four isolates (AC4, WS526, WS584 and ZA3A) which had previoulsy been shown to have unusual mating characteristics were distinctly different from other isolates. We interpret these differences as indicating that four atypical isolates represent species other than D. discoideum. Probes for the ribosomal spacer DNA either did not hybridize to the DNA of these four isolates or had decreased levels of hybridization to EcoRI restriction fragments of different lengths to that observed with the type strain. With the discoidin probe, all isolates had DNA fragments that hybridized but AC4, WS526, WS584 and ZA3A lacked a pair of fragments that were conserved in NC4 and other isolates. With the actin probe, AC4, WS526, WS584 and ZA3A lacked numerous fragments that the other isolates shared with NC4. The DIRS-1 probes showed strong hybridization with ZA3A and weak hybridization to the other three isolates; however, the major EcoRI fragment in WS526 and WS584 was smaller than that in NC4 while ZA3A and AC4 had fragments of similar size to that in NC4. The asexual isolates WS526 and WS584 were closely related to each other and appear to be isolates of the same species although there were some differences in the overall pattern of EcoRI restriction fragments from high copy number sequences and of restriction fragments hybridizing to the actin and discoidin gene probes. The homothallic isolates AC4 and ZA3A appear to represent two additional species; ZA3A, possibly AC4, are more closely relate to D. discoideum than the species represented by WS526 and WS584. Overall it appears that the four atypical isolates (AC4, ZA3A, WS526 and WS854) are less distantly related to D. discoideum than are isolates of D. purpureum and D. mucoroides.