Characterisation of large and small subunit rRNA and mini-exon genes further supports the distinction of six Trypanosoma cruzi lineages

It has been proposed that isolates of Trypanosoma cruzi, the agent of Ameri can trypanosomiasis, can be ordered into two primary phylogenetic lineages, first based on multilocus enzyme electrophoresis and random amplified poly morphic DNA, and subsequently based on the 24S alpha rRNA and mini-exon gen es. Recent multilocus enzyme electrophoresis and random amplified polymorph ic DNA data have additionally shown that the major multilocus enzyme electr ophoresis/random amplified polymorphic DNA lineage II is further subdivided into five smaller lineages, designated IIa-IIe. In this study. the precise correspondence between the multilocus enzyme electrophoresis/random amplif ied polymorphic DNA and rRNA/mini-exon lineages was investigated. Using the 24S alpha rRNA and mini-exon markers in combination. five sets of strains were distinguished, corresponding to the multilocus enzyme electrophoresis/ random amplified polymorphic DNA lineages I, IIa, IIc, IId and to lineages IIb/IIe together, respectively. The previous categorisation into only two p rimary lineages based on 24S alpha rRNA and mini-exon characterisation is e xplained, in part, by the lack of representativeness of the breadth of T. c ruzi diversity in earlier study samples. Additionally, a PCR assay based on a length-variable region of the 18S rRNA gene distinguished lineage Ile fr om lineage IIb. Thus, the six multilocus enzyme electrophoresis/random ampl ified polymorphic DNA lineages could be readily identified by combining dat a from the 24S alpha rRNA. mini-exon and 18S rRNA characterisation assays, further supporting the relevance of these genetic units for T. cruzi strain classification and subspecific nomenclature. The recently proposed groups T. cruzi I and T. cruzi II correspond to multilocus enzyme electrophoresis/ random amplified polymorphic DNA lineages I and IIb, respectively. Our find ings show that T cruzi lineage characterisation based on a single marker (e ither mini-exon or 24S alpha rRNA) has insufficient resolution, and leads t o important reinterpretations of recent epidemiological and evolutionary st udies based on the oversimplified rRNA/mini-exon dichotomic classification of T cruzi isolates. (C) 2001 Australian Society for Parasitology Inc. Publ ished by Elsevier Science Ltd. All rights reserved.