SRP272593 PRJNA647375 Small RNAs are implicated in regulation of gene and transposable element expression in the protist Trichomonas vaginalis Trichomonas vaginalis is the causative agent of trichomoniasis, the most prevalent non-viral sexually transmitted infection world-wide. The ~160 Mb T. vaginalis genome is highly repeated, and more than half of the genome contains repetitive elements including transposable elements (TEs) and virally-derived repeats. An intriguing question is how the parasite controls this potentially lethal complement of "jumping genes", which can disrupt transcription of protein coding genes and genome functions. In this study, we generated RNA-Seq and small RNA-Seq datasets in triplicate for the T. vaginalis G3 reference strain, and characterized the mRNA and small RNA populations and their mapping patterns along all six chromosomes. Mapping the RNA-Seq transcripts to the genome revealed that the majority of genes in repetitive elements are not expressed. Interestingly, we identified a novel species of small RNA that map bidirectionally along the chromosomes, and are correlated with reduced protein-coding gene expression and reduced RNA-Seq coverage in repetitive elements. This novel small RNA family may play a regulatory role in gene and repetitive element expression. Our results identify a possible small RNA pathway mechanism by which the parasite regulates expression of genes and transposable elements, and raises intriguing questions as to the role repeats may play in shaping T. vaginalis genome evolution and the diversity of small RNA pathways in general.