Transcriptome analysis of Haloferax volcanii provirus-free strain vs wild-type H100

Four predicted proviruses have been identified in the H. volcanii genome (Halfvol1, Halfvol2, Halfvol3 and Halfvol4), which have not been extensively studied. In this work, a provirus-free strain (?Halfvol1-4) was generated in which all four proviruses were deleted. A transcriptome comparison between ?Halfvol1-4 and a wild-type strain H100 was performed to elucidate the effect and function of the proviruses in H. volcanii. RNA-seq analyses revealed that ?Halfvol1-4 showed increased expression of genes for archaella, chemotaxis and pili and down-regulation of CRISPR arrays. Overall design: We isolated total RNA from ?Halfvol1-4 and the control strain H100 in exponential growth (0.5 OD650) and subjected it to DNase treatment and rRNA depletion followed by next generation RNA sequencing (RNA-seq) (each in triplicate).