__Evidence for the existence of a new genus Chlamydiifrater gen. nov. inside the family _Chlamydiaceae___ #### Core gene set In this repository we provide the 15 genomes used for comparison and the output of the [RIBAP](https://github.com/hoelzer-lab/ribap) pipeline. To reproduce our results, download the genomes, install [Nextflow](https://www.nextflow.io/) and [Docker](https://www.docker.com/get-started), and run: ```bash nextflow run hoelzer-lab/ribap -r v0.3 --fasta ‘*.fasta’ ``` To show the interactive RIBAP HTML table download and unpack the results archive and open the `ribap.html` file included in the `web` folder with any internet browser. #### Positive selection of _ompA_ We further provide the output of [PoSeiDon](https://github.com/hoelzer/poseidon), a tool that was used to screen for positive selection events in the _ompA_ gene selected from representative strains of 12 species of the genus _Chlamydia_. The _ompA_ sequences were derived from the RIBAP output (Prokka annotations) and manually corrected for annotation errors: * duplicates were found in Cfe, Cmu, Cib, Cpe but not in close proximity in the genomes * we build an alignment and removed duplicates that were not aligning well: * Cpe_E58_ompA_1 * Cfe_Fe-C56_ompA_1 * Cmu_Nigg_ompA_2 * Cib_10-1398-6_ompA_2 The ompA.fasta can be found in this repository. Clone this [version of PoSeiDon](https://github.com/hoelzer/poseidon/commit/470b0eab3fef177a2f2112171afa82099c8d5226) to reproduce the results: ```bash nextflow run poseidon.nf --fasta ompA.ffn ``` The HTML output of PoSeiDon can be also directly investigated [here](https://www.rna.uni-jena.de/supplements/poseidon/2020-06-23_chlamydia/results/ompA/html/full_aln/index.html). ### Plot ONT long-reads spanning ompA clusters To ensure correctness of repetetive ompA clustered regions in the hybrid-assembled genomes, ONT long-reads were mapped to the assemblies and regions of interest were searched for spanning long-reads. Results were visualized utilizing the matplotlib library, the underlying python script can be found under: plot_ompA_coverage.py and executed as following: ```python3 python3 plot_ompA_coverage.py ``` __If you use these data please cite__: [Vorimore, F., _et al_. "Evidence for the existence of a new genus _Chlamydiifrater_ gen. nov. inside the family _Chlamydiaceae_ with two new species isolated from flamingo (_Phoenicopterus roseus_): _Chlamydiifrater phoenicopteri_ sp. nov. and _Chlamydiifrater volucris_ sp. nov." Systematic and Applied Microbiology (2021): 126200.](https://www.sciencedirect.com/science/article/pii/S0723202021000230)