Total RNA was isolated from cultures after antibiotics treatment using Tri-Reagent (Sigma). After additional DNAse digestion, RNA samples were depleted for eukaryotic and bacterial rRNAs by subsequent usage of the Yeast Ribo-Kit and the gram-negative bacterial Ribo-Zero Kits (Illumina). After additional depletion of poly(A) RNAs, directional RNA libraries were generated from the left-over RNA using the NEB ultra directional RNA library prep Kit (NEB).. Dual RNA Seq of Caedibacter in Paramecium

Interest in host-symbiont interactions is continuously increasing, not only due to the recognized importance of microbiomes. Started with the detection and description of novel symbionts, attention moves to the molecular consequences and innovations of symbioses. However, molecular analysis requires genomic data which is difficult to obtain from obligate intracellular and uncultivated bacteria. We report the identification of the \textit{Caedibacter} genome, an obligate symbiont of the ciliate \textit{Paramecium}. The infection confers the host with the ability to kill other cells, and moreover with immunity against this effect. We obtained the \textit{C. taeniospiralis} genome and transcriptome by dual-Seq of DNA and RNA from infected paramecia. Comparison of codon usage and expression level indicates that genes necessary for a specific trait of this symbiosis, i.e. the delivery of an unknown toxin, result from horizontal gene transfer hinting to the relevance of DNA transfer for acquiring new characters. Prediction of secreted proteins of \textit{Caedibacter} as major agents of contact with the host implies, next to several toxin candidates, a rather un-characterized secretome which appears to be highly adapted to this symbiosis. Our data provides new insight into the molecular establishment and evolution of this obligate symbiosis and for the pathway characterization of toxicity and immunity.