{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,31]],"date-time":"2026-10-31T12:45:46Z","timestamp":1793450746720,"version":"4.5.0"},"reference-count":83,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2020,10,28]],"date-time":"2020-10-28T00:00:00Z","timestamp":1603843200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100008662","name":"Joachim Herz Foundation","doi-asserted-by":"publisher","award":["add-on fellowship for interdisciplinary life science"],"award-info":[{"award-number":["add-on fellowship for interdisciplinary life science"]}],"id":[{"id":"10.13039\/100008662","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pathogens"],"abstract":"<jats:p>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. Analyzing the most variable genomic sites, we identified a set of features of C. psittaci that in its entirety is characteristic of this species: (i) a relatively short plasticity zone of less than 30,000 nt without a tryptophan operon (also in C. abortus, C. avium, C. gallinacea, C. pneumoniae), (ii) a characteristic set of of Inc proteins comprising IncA, B, C, V, X, Y (with homologs in C. abortus, C. caviae and C. felis as closest relatives), (iii) a 502-aa SinC protein, the largest among Chlamydia spp., and (iv) an elevated number of Pmp proteins of subtype G (14 in C. psittaci, 14 in Cand. C. ibidis). In combination with future functional studies, the common and distinctive criteria revealed in this study provide important clues for understanding the complexity of host-specific behavior of individual Chlamydia spp.<\/jats:p>","DOI":"10.3390\/pathogens9110899","type":"journal-article","created":{"date-parts":[[2020,10,28]],"date-time":"2020-10-28T11:43:06Z","timestamp":1603885386000},"page":"899","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":38,"title":["Comparative Genome Analysis of 33 Chlamydia Strains Reveals Characteristic Features of Chlamydia Psittaci and Closely Related Species"],"prefix":"10.3390","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7090-8717","authenticated-orcid":false,"given":"Martin","family":"H\u00f6lzer","sequence":"first","affiliation":[{"name":"RNA Bioinformatics and High-Throughput Analysis, Friedrich-Schiller-Universit\u00e4t Jena, 07743 Jena, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lisa-Marie","family":"Barf","sequence":"additional","affiliation":[{"name":"RNA Bioinformatics and High-Throughput Analysis, Friedrich-Schiller-Universit\u00e4t Jena, 07743 Jena, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6375-6441","authenticated-orcid":false,"given":"Kevin","family":"Lamkiewicz","sequence":"additional","affiliation":[{"name":"RNA Bioinformatics and High-Throughput Analysis, Friedrich-Schiller-Universit\u00e4t Jena, 07743 Jena, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fabien","family":"Vorimore","sequence":"additional","affiliation":[{"name":"Animal Health Laboratory, Bacterial Zoonoses Unit, University Paris-Est, Anses, 94706 Maisons-Alfort, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3637-5870","authenticated-orcid":false,"given":"Marie","family":"Lataretu","sequence":"additional","affiliation":[{"name":"RNA Bioinformatics and High-Throughput Analysis, Friedrich-Schiller-Universit\u00e4t Jena, 07743 Jena, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alison","family":"Favaroni","sequence":"additional","affiliation":[{"name":"Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), 07743 Jena, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christiane","family":"Schnee","sequence":"additional","affiliation":[{"name":"Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), 07743 Jena, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karine","family":"Laroucau","sequence":"additional","affiliation":[{"name":"Animal Health Laboratory, Bacterial Zoonoses Unit, University Paris-Est, Anses, 94706 Maisons-Alfort, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manja","family":"Marz","sequence":"additional","affiliation":[{"name":"RNA Bioinformatics and High-Throughput Analysis, Friedrich-Schiller-Universit\u00e4t Jena, 07743 Jena, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1230-1786","authenticated-orcid":false,"given":"Konrad","family":"Sachse","sequence":"additional","affiliation":[{"name":"RNA Bioinformatics and High-Throughput Analysis, Friedrich-Schiller-Universit\u00e4t Jena, 07743 Jena, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2020,10,28]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12864-019-6059-5","article-title":"Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","volume":"20","author":"Sigalova","year":"2019","journal-title":"BMC Genom."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1098","DOI":"10.1128\/jcm.28.6.1098-1100.1990","article-title":"Amino acid requirements for growth of Chlamydia pneumoniae in cell cultures: Growth enhancement by lysine or methionine depletion","volume":"28","author":"Kuo","year":"1990","journal-title":"J. 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