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Background   Trichomonas vaginalis  is the most prevalent non-viral sexually transmitted parasite. Although the protist is presumed to reproduce asexually, 60% of its haploid genome contains transposable elements (TEs), known contributors to genome variability. The availability of a draft genome sequence and our collection of >200 global isolates of  T. vaginalis  facilitate the study and analysis of TE population dynamics and their contribution to genomic variability in this protist.    Results  We present here a pilot study of a subset of class II  Tc1/mariner  TEs that belong to the  T. vaginalis Tvmar1  family. We report the genetic structure of 19  Tvmar1  loci, their ability to encode a full-length transposase protein, and their insertion frequencies in 94 global isolates from seven regions of the world. While most of the  Tvmar1  elements studied exhibited low insertion frequencies, two of the 19 loci (locus 1 and locus 9) show high insertion frequencies of 1.00 and 0.96, respectively. The genetic structuring of the global populations identified by principal component analysis (PCA) of the  Tvmar1  loci is in general agreement with published data based on genotyping, showing that  Tvmar1  polymorphisms are a robust indicator of  T. vaginalis  genetic history. Analysis of expression of 22 genes flanking 13  Tvmar1  loci indicated significantly altered expression of six of the genes next to five  Tvmar1  insertions, suggesting that the insertions have functional implications for  T. vaginalis  gene expression.    Conclusions  Our study is the first in  T. vaginalis  to describe  Tvmar1  population dynamics and its contribution to genetic variability of the parasite. We show that a majority of our studied  Tvmar1  insertion loci exist at very low frequencies in the global population, and insertions are variable between geographical isolates. In addition, we observe that low frequency insertion is related to reduced or abolished expression of flanking genes. While low insertion frequencies might be expected, we identified two  Tvmar1  insertion loci that are fixed across global populations. This observation indicates that  Tvmar1  insertion may have differing impacts and fitness costs in the host genome and may play varying roles in the adaptive evolution of  T. vaginalis .

The Tc1/mariner transposable element family shapes genetic variation and gene expression in the protist Trichomonas vaginalis