Alleles within sequence types

(updated October 2023)


When we first began sequencing the 18S rRNA gene of Acanthamoeba in the early 1990’s, every sequence appeared to be unique.  Were this truly a situation that might reflect the predictions of the “infinite allele” model of population genetics?  It turned out that such was not necessarily the case, although genetic diversity of the 18S rRNA gene in Acanthamoeba appears to be substantially greater than that observed in any other eukaryotic genus (although we admit that we have not performed anything close to a comprehensive survey).   The sequence types that we defined beginning in 1996 (Gast et al.) help to describe this variation, but the degree of variability is much greater than simply the list of more than 20 sequence types.

In an attempt to better describe the degree of variation that existed in a populations sample of Acanthamoeba isolates, we defined the set of alleles within the 18S rRNA gene that were identified during a  study of a group of T3 and T4 isolates found in water samples in Hong Kong (Booton et al. J. Clin. Micro. 2002).  These alleles represented variability found within one of the regions of the 18S rRNA sequences (the ASA.S1 sub-sequence).   In detail, these alleles represent the primary nucleotide sequence of the variable region of segment DF3 (stem 29-1 of the Acanthamoeba 18S rRNA).

We initially observed 10 different alleles within samples categorized as sequence type T4 and 5 alleles within sequence type T3. In that study, we were not attempting to use the allele designations as a phylogenetic tool.  Rather, they were used simply as a means of categorizing the isolates observed in the study. 

As more data accumulated, it turned out that there were considerably more alleles within Acanthamoeba than those that we first described, especially within sequence type T4.  In accompanying pages we describe the current situation for alleles in sequence type T4, in sequence types T3 and T11, and more recently in sequence type T5.

Most recently, we have now been able to detail alleles that occur in several other sequence types.  This includes the alleles that are found within the T2-T6 sequence complex, and alleles that occur within the T15 sequence type.

A full description of the history of alleles was presented in a paper delivered at the 2019 FLAM meeting in Costa Rica, and this has appeared in a publication that evolved from that meeting (Fuerst and Booton, 2020).

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