Background: Trichomonas vaginalis is a unicellular protist that causes trichomoniasis,a common but overlooked sexually transmitted human infection,with~170 million cases occurring annually worldwide.T.vaginalis offers an interesting and exciting alternative system for studying eukaryotic gene expression,as it is divergent from the fungi and metazoan systems that have received the most attention.The original genome annotation identified approximately 60,000 potential protein encoding genes that primarily relied on sequence conservation with few transcriptional evidences.A second generation annotation based on deep transcriptomes would provide a valuable resource for further studies.