Phylogenetic relationships among Acanthamoeba sequence types

(revision November 2023)

A phylogenetic tree obtained using representative isolates from various sequence types within Acanthamoeba is presented here.  This tree has been adapted from the tree that appeared in the publication of Corsaro et al. (Parasitology Research 116: 1273; 2017).

Note: The recently identified T23 sequence type appears to be a sister clade to the T10/T12/T14 clade.

 

TIMELINE FOR DISCOVERY OF SEQUENCE TYPES:

Sequence types T1 – T4 were described in the first paper to propose the Sequence Type approach to characterizing Acanthamoeba (Gast, Ledee, Fuerst and Byers, 1996).  Fifteen of 18 isolates were found to represent T4, while single isolates were observed for T1, T2 and T3.

The number of Sequence Types was expanded by to include T5-T12 in a subsequent analysis of 53 additional isolates by the Ohio State University lab (Stothard et al.,1998).  Note that no definitive member of Sequence Type T8 has been observed since the first description of the type from ATCC 30867; Acanthamoeba tubiashi).    

After 1998 a number of investigators reported the occurrence of additional Sequence Types, usually one addition at a time. 

T13: Horn et al (1999) observed several isolates that carried intracellular endocytobionts that differed from previous Sequence Types.  They suggested that they represented two new types T13 and T14.  Subsequently, it was found that the isolates represented variants of a single type  designated T13.

T14: A rare form was isolated in Pakistan and designated T14 (Gast, 2001). This type has been observed in only 3 additional isolates since its first description.

T15: Hewett et al. (2003) analyzed isolates designated as A. jacobsi and described them as representing a new sequence type, T15.  However, their analysis was based on a partial sequence of the 18S rRNA gene.  Subsequently, Corsaro  et al. (2017) obtained the almost complete 18S rRNA sequence of several A. jacobsi isolates, and confirmed that it did represent a distinct sequence type. 

T16: two different forms were initially designated T16, but only one, analyzed by Corsaro and Venditti (2010) was based on a almost complete 18S rRNA gene sequence.  This isolate was observed to be a sister clade to type T13.  

T17: Nuprasert, Putaporntip, Pariyakanok, and Jongwutiwes (2010) reported a new group I Acanthamoeba that was divergent from T7, T8 and T9.

 

SEQUENCE TYPES DESCRIBED SINCE 2010: 

T18: Qvarnstrom, Nerad, and Visvesvara (2015) described a fifth sequence type within the Group I Acanthamoeba.

T19:  In August 2014, Magnet et al. [Parasitol Res (2014) 113: 2845 – 2850] reported the sequence of a single isolate that appears to represent a new sequence type that was labeled as T19.  This isolate represents a lineage that diverges from the common ancestor of the T13-T16 group in the figure above.  The T19 lineage is identified inn the figure above.

T20:  Described by Fuerst, Booton and Crary, in J. Eukaryotic Microbiology 2014.  Sequence type T20 represents a sequence type first identified in our lab in 2005, but misidentified as a divergent T4 sequence because of the lack of a full sequence, and lack of power for comparison because of the limited number of sequences available in 2005.  Subsequent reanalyses, including  almost complete 18S sequences from isolates OSU 04-020 and OSU o4-023 indicate that they represent  an identifiable sequence type that has been seen in subsequent analyses of partial sequences from several geographic regions.

T21: This sequence type has not yet been formally described, but information appeared about the proposed new species (Acanthamoeba pyriformis sp. nov.) in a publication in December 2016.  A sequence of the 18S rRNA gene has been deposited (accession # KX840327).  In addition, information about the species is represented by the released data concerning the transcriptome of the species.  The sequence of the 18S rRNA gene contained portions equivalent to the expanded hypervariable regions that characterize Acanthamoeba 18S rRNA genes.   Initial comparisons of this sequence with the almost complete 18S rRNA genes of other Acanthamoeba taxa found none of the other taxa within Acanthamoeba showing sequence similarity to Acanthamoeba pyriformis sp. nov. greater than ~86%.  The sequence appears to be more divergent from the Group I acanthamoebae  (A. astronyxis, etc.) than to other taxa of the genus,  suggesting it may have diverged from within Acanthamoeba  Groups II or III.  No other partial or almost complete sequences have been reported that show close correspondence with this type sequence.  More extensive comparisons will be forthcoming.  When available, we will link with the sequence at GenBank (accession # KX840327).

T22: This sequence type has not yet been described formally in a publication as oof November 2023, but is represented by the nuclear 18S rRNA gene and mitochondrial 16S-like gene sequences from the genome project with accession number CDEZOOOOOO.1 (listed as representing Acanthamoeba royreba, but actually clearly representing an alternative, unidentified ATCC isolate).   These sequences suggest a distinct sequence type unseen previously (and unfortunately unidentified as to ATCC isolate because of mislabeling).  The sequences are available from this web site as pdfs for the 18S rRNA and 16S-like rRNA genes.  The T21 genome data files have also been examined for the mt-DNA genome, which also shows a distinct differentiation of these sequences from any of the other known sequence types.

T23: In 2021, two sequences were identified in Thailand that represented a new sequence type (and a newly named species of Acanthamoeba, A. bangkokensis sp. nov. (Putaporntip et al., 2021).  At present, no sequences from other genes within the genome of this new sequence type have been reported.  As of November 2023, no additional isolates have been found that would be classified within T23.

 

NOTE ON THE EXISTENCE OF UNDISCOVERED SEQUENCE TYPES:

Only one new sequence type (T23) has been described since 2017.  However, analysis of variation of partial 18S rRNA sequences suggests that additional types probably exist, especially in the Group I Acanthamoeba and possibly within some sequences now considered to be “divergent T4” (for instance in the recently described T4H sub-type).  There are also several partial sequences from isolates closest to type T11 that suggest that a very rare form exists which could represent a new sequence type.  In addition, the fact that some types (such as type T8 and type T14) have been observed either never or only once since their initial observation 20 years or more ago, suggests that additional rare sequence types can also exist, perhaps in ecological or geographic locations that have been rarely sampled.

 

Updated October 2023.