Transcriptome data sets of free-living diplomonads, Trepomonas sp. and Hexamita sp.

Most species belonging to the diplomonad genera, Trepomonas and Hexamita, are considered to have secondarily adapted to free-living lifestyles from the parasitic ancestor. Here, we report the annotated transcriptome data of Trepomonas sp. NIES-1444 and Hexamita sp. NIES-1440, the analysis of which will provide insights into the lifestyle transitions.