Exploring LSU and ITS rDNA Sequences for Acanthamoeba Identification and Phylogeny

The identification and classification of strains of Acanthamoeba, a potentially pathogenic ubiquitous free-living amoeba, are largely based on the analysis of 18S rDNA sequences, currently delineating 23 genotypes, T1 to T23. In this study, the sequences of the ITS region, i.e., the 5.8S rDNA and the two internal transcribed spacers (ITS-1 and ITS-2), and those of the large subunit (LSU) rDNA of Acanthamoeba were recovered from amoeba genomes; the sequences are available in GenBank. The complete ITS-LSU sequences could be obtained for 15 strains belonging to 7 distinct lineages (T4A, T4D, T4F, T4G, T2, T5, and T18), and the site of the hidden break producing the 26S alpha and 26S beta was identified. For the other lines, either the LSU is partial (T2/T6, T7) or the ITS is fragmentary (T7, T10, T22). It is noteworthy that a number of sequences assigned to fungi turned out to actually be Acanthamoeba, only some of which could be affiliated with known genotypes. Analysis of the obtained sequences indicates that both ITS and LSU are promising for diagnostic and phylogenetic purposes.