pathogens Article Comparative Genome Analysis of 33 Chlamydia Strains Reveals Characteristic Features of Chlamydia Psittaci and Closely Related Species 1, , 1, ,§ 1 2 Martin Hölzer y z , Lisa-Marie Barf y , Kevin Lamkiewicz , Fabien Vorimore , Marie Lataretu 1 , Alison Favaroni 3, Christiane Schnee 3, Karine Laroucau 2, Manja Marz 1 and Konrad Sachse 1,* 1 RNA Bioinformatics and High-Throughput Analysis, Friedrich-Schiller-Universität Jena, 07743 Jena, Germany;
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[email protected] (M.M.) 2 Animal Health Laboratory, Bacterial Zoonoses Unit, University Paris-Est, Anses, 94706 Maisons-Alfort, France;
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[email protected] (K.L.) 3 Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), 07743 Jena, Germany; alison.favaroni@fli.de (A.F.); christiane.schnee@fli.de (C.S.) * Correspondence:
[email protected] These authors contributed equally. y Present affiliation: Robert Koch Institute, MF1 Bioinformatics, 13353 Berlin, Germany. z § Present affiliation: Max Planck Institute for the Science of Human History, 07743 Jena, Germany. Received: 30 September 2020; Accepted: 23 October 2020; Published: 28 October 2020 Abstract: To identify genome-based features characteristic of the avian and human pathogen Chlamydia (C.) psittaci and related chlamydiae, we analyzed whole-genome sequences of 33 strains belonging to 12 species. Using a novel genome analysis tool termed Roary ILP Bacterial Annotation Pipeline (RIBAP), this panel of strains was shown to share a large core genome comprising 784 genes and representing approximately 80% of individual genomes.