Vermamoeba gene sequences in the DNA databases

(updated November 2023)

Nuclear 18S rRNA gene sequences:

As of July, 2021 there were 992 sequences of the 18S rRNA gene, with a putative assignment to V. vermiformis, that had been deposited in the DNA databases or were available from researchers for comparison. After the first sequences were deposited in 1993/1994, no additional sequences were deposited until 2001.  The pattern of yearly deposits into the DNA databases of 18S rRNA sequences is shown in the first figure below.

Following 2003, sequences were deposited on a regular basis.  Spikes in the deposition of sequences in 2007, 2010 and 2011-2012 correspond to environmental studies of uncultured eukaryotes which identified large numbers of DNA sequences from V. vermiformis in their samples.

Sequences of the 18S rRNA gene in the DNA databases from V. vermiformis vary greatly in size.  There are proportionately many fewer “almost” complete sequences from putative V. vermiformis isolates than are found in studies from Acanthamoeba.  This may be primarily because most isolates are very similar in sequence (usually less than 1% sequence divergence between almost complete sequences).  Nevertheless, as will be documented on another page, consideration of the almost-complete sequences provides considerable information with which to better understand population/geographic variation within V. vermiformis

The distribution of the lengths of the 18SrRNA gene sequences from V. vermiformis in the DNA databases is shown in the following graph.

The sequences range from 123  to 1852 bp in length.  The greatest number of sequences (527) fall in the bin for which sequences have lengths between 501 and 600 bp.   This group far exceeds other bins.  In part this is due to the choice of a set of uniform PCR primers that produced an optimal fragment size for sequencing in the pre-Nextgen sequence era.  Another factor is that many of the surveys of uncultured eukaryotic environmental microbiome produced similar sized products.  

The distribution of sizes in the figure above is substantially different than that seen in Acanthamoeba, having fewer sequences (both in numbers and percentages) in the “almost complete group, as well as fewer in the <500 bp classes.  This latter observation derives from the fact that one of the optimal size groups in length for Acanthamoeba (300-450 bp) represents the set of fragments that include the most informative portion of the Acanthamoeba 18S rRNA gene.     

There were 38 sequences whose length (excluding introns) exceeded 1500 bp in length.  (Note that there are also five additional sequences that are assigned to the genus Hartmannella, the genus that originally contained what is now Vermamoeba, but these are not included in this analysis of V. vermiformis).  The sequences exceeding 1500 bp represent a core group that can be used to help categorize the shorter sequences into possible subgroups.  (The group exceeding 1500 bp are the “almost complete” sequences).   Information concerning the sequence variation in this select group is presented on an accompanying page.


Mitochondrial 16S-like rRNA gene sequences:

A significant number of sequences for the small subunit rRNA gene from the mitochondrial genome of Vermamoeba isolates have been obtained, supplementing information for the nuclear 18S rRNA genes.  As of November 2023, only 29 sequences have been obtained that can be attributed to the mitochondrial 16S-like rRNA gene, only 3% of the number for the nuclear equivalent.  This is actually a slightly higher percentage than for the equivalent comparison of Acanthamoeba genes (2.5%).  Nevertheless, the source of the mitochondrial gene sequences for Vermamoeba is substantially different from the sources that have provided information for the nuclear gene, or the source of the mitochondrial gene sequences in Acanthamoeba.

For the nuclear gene, the majority of sequence are obtained by using either PCR screening primers specific to Vermamoeba or using conserved universal eukaryotic primers for environmental screening and then identifying the products as representing Vermamoeba. For the mitochondrial gene, none of the sequences were derived from investigations specifically targeting the mitochondrial SSU rRNA.  Six of the 29 sequences are derived directly from complete or nearly complete mitochondrial genomes.  Seven of the 29 sequences were derived from environmental studies specifically targeting eukaryotic 16S-like genes.  The remaining 16 sequences were obtained during prokaryotic environmental screenings, and only identified with Vermamoeba during our analyses.  These 16 are all labeled as uncultured bacterium or uncultured prokaryotes.  We know of no bacterial taxa that closely match the sequences found within the Vermamoeba gene, and which would, as a consequence, lead to a false identification attributed to Vermamoeba.

The distribution of the sequence lengths for the mitochondrial 16S-like rRNA sequences is shown in the chart below.  The six sequences derived from mitochondrial genomes are represented by the bars to the right, while other bars represent the results of the various environmental studies.


Genome studies and sequences:


Through November 2023. only two whole genome studies have focused on Vermamoeba. The first whole genome sequence was reported for the isolate V. vermiformis CDC-19 (Chelkha et al,, 2020).   The total draft genome size for isolate CDC-19ATCC 50237 (>59 Mb) appears to be larger than in some other FLA, such as Naegleria grubei or Acanthamoeba castellanii Neff.  The detailed WGS results were not deposited in the traditional international DNA databases, but can be accessed through a genome page at the website of the Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Marseille.  The second genome to be obtained was that of V. vermiformis isolate TW EDP1, with a genome accession at WGS project JAGUQM. As of November 2023, no specific report of the genome has been peer-reviewed.  A report was deposited in BioRxiv in 2021.  The reported size of the reconstructed nuclear genome for  isolate TW EDP1 is 39.5 Mb, more consistent with sizes from other amoebae. 


The first mitochondrial genome sequence from V. vermiformis, for isolate BCP-EM3VF21-2, was released in 2015. This was quickly followed by a second sequence from isolate “Hartmannella” (Vermamoeba) vermiformis ATCC 50236 in 2016.  The mitochondrial genome of four additional isolates of V. vermiformis (CDC-19 ATCC 50237TW EDP1, 4391-Kostka, and a V. vermiformis contaminant of the CCAP culture Deuteramoeba algonquinensis CCAP 1503/5) have since been made available through the international DNA databases.  Sizes of all genomes appear to in the range ~51-53 kbp, approximately 10 kbp larger than mt-genome sequences from Acanthamoeba.  (note that the reported size of TW EDP1 [~67kb] appears to be inflated because of the inclusion of a series of nucleotide repeats that may be an artifact of genome reconstruction). All of the sequences appear to show the same gene order and gene content.  Analysis of gene content is provisional, since many of the ORFs reflect sequences with no known protein homology in other taxa. Comparisons of the mt-genome sequences of the six isolates suggest that substantial variation exists within Vermamoeba, but that the level of variation is much less than in Acanthamoeba.  


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