Unusual 18S rDNA of Acanthamoeba containing intron turned out to be a T5/T4 chimera

The free-living amoebae of the genus Acanthamoeba are widely investigated for their diversity and evolution. Studies usually employ biomolecular methods targeting the 18S rRNA gene, assigning strains according to a well-established genotyping system. Strains from at least four genotypes contain introns in their rDNA. By retracing the evolutionary history of these introns within the amoebae, we found that the 18S rDNA of TUMSJ-341 strain (ATCC PRA-11), assigned to the genotype T5 (A. lenticulata), proved very unusual in our analyses, not corresponding to the characteristics of the group. The sequence contains a group I intron recovered only in A. lenticulata. At BLAST, however, the intron-less 18S rDNA of TUMSJ-341 does not match with T5 strains but shows some affinity with strains from genotype T4, suggesting a new genotype. Our accurate analysis of this sequence finally revealed a mixture of variable regions, showing that such discordant results are due to the insertion into the gene of a strain T5 of a DNA fragment containing hypervariable regions specific for a T4 strain. Data presented herein indicate that this sequence is probably a chimera.