Draft Genome Sequence and Annotation of the Obligate Bacterial Endosymbiont Caedibacter taeniospiralis, Causative Agent of the Killer Phenotype in Paramecium tetraurelia.

Draft Genome Sequence and Annotation of the Obligate Bacterial Endosymbiont Caedibacter taeniospiralis, Causative Agent of the Killer Phenotype in Paramecium tetraurelia Nestor Zaburannyi, d,e Katrin Grosser, b Gilles Gasparoni, c Rolf Müller, d,e Martina Schrallhammer, b Martin Simon a a Molecular Cell Dynamics, Centre for Human and Molecular Biology, Saarland University, Saarbrücken, Germany b Microbiology, Institute of Biology II, Albert Ludwig University of Freiburg, Freiburg, Germany c Genetics, Centre for Human and Molecular Biology, Saarland University, Saarbrücken, Germany d Department of Microbial Natural Products, Helmholtz Centre for Infection Research and Department of Pharmacy, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University, Saarbrücken, Germany e German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Hannover, Germany ABSTRACT Caedibacter taeniospiralis is an obligate endosymbiont living in the cytoplasm of Paramecium tetraurelia.C. taeniospiralis causes the so-called killer trait, eliminating intraspecific competitors of its host when released into the medium by the concerted action of the unusual protein structure R-body (refractile body) in addition to an as-yet-unknown toxin. Caedibacter taeniospiralis (Thiotrichales,Gammaproteobacteria) lives in the cytoplasm of its host, Paramecium tetraurelia (Ciliophora). This unicellular, relatively large (150- ␮ m) eukaryote separates vegetative and sexual functions, possesses germline and somatic nuclei, and is a long-established model in genetics and epigenetics research (1). A special feature of the Paramecium-Caedibacter symbiosis is the “killer trait.” A proportion of the endosymbiont population produces an unusual protein structure, the R-body (refractile body) (2). This structure, most likely acting as a delivery device for an unidentified toxin, is responsible for killing symbiont-free, sensitive paramecia after the ingestion of bacteria released from infected strains (3). Caedibacter-harboring cells are protected from the lethal effect of their symbionts. Cultivation of C. taeniospiralis outside its host has not been accomplished so far. Total DNA was isolated from exponentially growing paramecia. Their infection status was verified by fluorescence in situ hybridization, which enabled detection of intracellular C. taeniospiralis 51 T , as described elsewhere (4). To minimize contamination from food bacteria, P. tetraurelia cultures (strain 51K ⫽CCAP 1660/3F) were fed with ␤ -lactamhypersensitive Escherichia coli ΔtolC (5) and treated with 10 ␮ gml ⫺1 ampicillin before DNA isolation (6). Library preparation for whole-genome sequencing used the tagmentation procedure (7). We generated a library of ~500 to 800 bp for subsequent sequencing on an Illumina MiSeq instrument (2 ⫻300 nucleotides [nt]). After assembly using the ABySS-pe program (8), 24 contigs were assigned to the genome of C. taeniospiralis. These can be differentiated from the host genome by their nearly identical coverage and by their GC content of 41.5%, diverging to the host genome’s GC content of 28% (9). Draft genome sequences had a total sequence length of 1.3 Mb (N 50 , 55.531 bp), including the previously known plasmid, pKAP, of 41.7 kb (10). The genome contains three rRNA clusters in 16S-23S-5S configurations. Gene annotation of the draft sequence was carried out using Prodigal (11), tRNAscan-SE (12), and RNAmmer (13) software tools. Next to 36 tRNA genes, 1,080 Received 16 November 2017 Accepted 5 December 2017 Published 18 January 2018 Citation Zaburannyi N, Grosser K, Gasparoni G, Müller R, Schrallhammer M, Simon M. 2018. Draft genome sequence and annotation of the obligate bacterial endosymbiont Caedibacter taeniospiralis, causative agent of the killer phenotype in Paramecium tetraurelia. Genome Announc 6:e01418-17. https://doi.org/10.1128/ genomeA.01418-17. Copyright ©2018 Zaburannyi et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Martina Schrallhammer, [email protected], or Martin Simon, [email protected]. PROKARYOTES crossm Volume 6 Issue 3 e01418-17 genomea.asm.org 1 on February 7, 2018 by GESELLSCHAFT FUR BIOTECHNO-http://genomea.asm.org/Downloaded from protein coding sequences could be identified, of which, 787 could be functionally annotated by a similarity search against the eggNOG database with the eggNOGmapper software (14). The genome sequence of C. taeniospiralis strain 51K will improve our understanding of this organism and its symbiotic interaction with P. tetraurelia, including and in addition to the killer trait. The availability of this sequence information enables phylogenomic analyses of the genus Caedibacter and will provide a valuable resource for the identification and analysis of toxin candidates, which might have unusual biological properties that explain the need for the R-body as a delivery device. Accession number(s). This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number PGGB00000000. The version described in this paper is version PGGB01000000. ACKNOWLEDGMENTS This work was supported by the German Science Foundation (grant SI1397/3-1) and the Research Innovation Fund of the Albert Ludwig University of Freiburg. We are grateful to Jasmin Kirch and Astrid Petersen for their assistance. REFERENCES 1. Simon M, Plattner H. 2014. Unicellular eukaryotes as models in cell and molecular biology: critical appraisal to their past and future value. Int Rev Cell Mol Biol 309:141–198. https://doi.org/10.1016/B978-0-12-800255-1 .00003-X. 2. Schrallhammer M, Schweikert M. 2009. The killer effect of Paramecium and its causative agents, p 1–21. In Fujishima M (ed), Endosymbionts in Paramecium, microbiology monographs. Springer, New York, NY. 3. Schrallhammer M, Galati S, Altenbuchner J, Schweikert M, Görtz HD, Petroni G. 2012. 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Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper. Mol Biol Evol 34:2115–2122. https://doi .org/10.1093/molbev/msx148. Zaburannyi et al. Volume 6 Issue 3 e01418-17 genomea.asm.org 2 on February 7, 2018 by GESELLSCHAFT FUR BIOTECHNO-http://genomea.asm.org/Downloaded from