Acanthamoeba DNA databases

(updated November 2023)

DNA data exists within the international DNA databases (GenBank, DDBJ or EMBL), or  as un-submitted data that various investigators have contributed to our compilation of information. 

See the attached page on references to get links to specific publications that describe sequences that have been deposited in the DNA databases (Note: the sequence reference updates in a continuing process as sequences and references appear).

Sequence information has been collated and will be summarized on our website for several genes.   These include:

1.   The nuclear small subunit ribosomal RNA gene (18S rRNA or Rns gene) :

This gene represents the most analyzed part of the Acanthamoeba genome.  Complete, nearly complete (over 2000 nucleotides in length) or partial (less than 2000 nucleotides) sequences have been reported for over 6000 isolates of Acanthamoeba.  (summarized most recently in the literature in Fuerst, 2014, and updated in posters presented at various FLAM meetings since).

Since the publication of the first Acanthamoeba 18S rRNA gene sequence in 1986, there has been a steady increase in the number of sequences deposited in the DNA databases.  During 2013, the total number of sequences exceeded 2000, while the number exceeded 3000 during 2015.   Submissions continued to accumulate, passing the 4000 mark during 2017, and 5000 during 2019.   In the middle of 2021, the total number of nuclear SSU sequences exceeded 6000.  As we close in on 2024, Entering 2022, more tan 6700 complete or partial 18S rRNA gene sequences have been made available for analysis by the international community in the international databases or in publications.  

These numbers include ~6100 18S rRNA gene sequences that had been entered into the international DNA databases summarized here.   In addition, as part of our attempt to bring together as much information as possible, we have made outreaches to individual investigators when a report appears in the literature that involves a sequences of the Acanthamoeba 18S rRNA gene that had not been deposited in the DNA databases.  As a result of these efforts, more than 600 undeposited sequences from isolates are known that were either identical to the sequence of a known isolate or that had not been deposited in the databases.  Including these sequences leads to the ~6742 18S rRNA gene sequences that were known and classified by type at the end of 2021. 

The rate of deposition of sequences of the 18S rRNA gene into the DNA databases by the Acanthamoeba research community has varied in different years, but has seen a general pattern of increase in volume.  This is illustrated in the figure below, which summarizes the rate of deposition in the collection.  The spike in 2015 is associated with several environmental surveys that contributed more than 100 sequences each.  More than 500 sequences were also obtained in 2017 and 2019.  Numbers dropped in 2020, but rebounded with 501 sequences added during 2021. Depositions in 2022 and 2023 are among the smallest in a decade.  It is important that researchers continue to deposit sequences that they obtain, especially since there remain many questions about diversity, pathogenicity and geographic variation that remain unanswered or uninvestigated.

Detailed information on the 18S rRNA gene is given on a subpage.  Information on nearly complete  or partial sequences is provided on other pages, as is information on alleles within the T4 genotype.   For a diagram of the secondary structure of the 18S rRNA from Acanthamoeba, see the accompanying subpage.  A list of the publications that have contributed to the Acanthamoeba 18S rRNA sequence database is provided on a linked page.


2. The mitochondrial small small subunit ribosomal RNA gene (16S-like rRNA or rns gene):  Sequences have been reported for more than 200 isolates.


3.  Information from genome sequences of Acanthamoeba.  These include two types of sequences, (a) whole genome sequences (or sequence projects) and (b) genome sequences of the mitochondrial genome.  Whole genome sequences or genome reports have been obtained for 34 isolates, either as WGS files or as Sequence Read Archive (SRA) files.  Mitochondrial genome sequences have been obtained for these same isolates, as well as the sequences of three additional isolates.   A transcriptome , including all mitochondrial genes, has been obtained for one additional strain.  Information on the genomes of Acanthamoeba is provided on a separate page.


In addition, our laboratory has been analyzing information for several other segments of the genomes of multiple isolates of Acanthamoeba.  These include:

4. A region of the mitochondrial genome that included multiple tRNA genes, studied in 17 isolates.  (Ledee and Byers, 2009).  Genome sequences now allow us to double this number.

5. A portion of the mitochondrial DNA encoded Cytochrome Oxidase subunit I (COI or COX1) gene in 73 isolates. (Crary, 2013).  Genome sequences and a significant addition from the Acanthamoeba lab at the Medical University of Vienna, as well as other investigators, have pushed the numbers above 170 .

6. A portion of the coding sequences of five nuclear nuclear encoded protein coding genes in 50+ isolates (Crary, 2013).  Genome sequences have pushed this number to more than 70.

Information concerning these sequences will be provided on other pages.