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  Comparative Genome Analysis of 33 Chlamydia Strains Reveals Characteristic Features of Chlamydia Psittaci and Closely Related Species

Hölzer, M., Barf, L.-M., Lamkiewicz, K., Vorimore, F., Lataretu, M., Favaroni, A., et al. (2020). Comparative Genome Analysis of 33 Chlamydia Strains Reveals Characteristic Features of Chlamydia Psittaci and Closely Related Species. Pathogens, 9(11): 899. doi:10.3390/pathogens9110899.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0007-5B3D-0 Version Permalink: http://hdl.handle.net/21.11116/0000-0007-5B58-1
Genre: Journal Article

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https://www.mdpi.com/2076-0817/9/11/899/s1 (Supplementary material)
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Supplementary File 1: ZIP-Document (last seen Nov. 2020)
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https://osf.io/j9zas/ (Supplementary material)
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The datasets generated and/or analyzed during the current study are available in an OSF repository.
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https://github.com/hoelzer-lab/ribap (Supplementary material)
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 Creators:
Hölzer, Martin, Author
Barf, Lisa-Marie1, Author              
Lamkiewicz, Kevin, Author
Vorimore, Fabien, Author
Lataretu, Marie, Author
Favaroni, Alison, Author
Schnee, Christiane, Author
Laroucau, Karine, Author
Marz, Manja, Author
Sachse, Konrad, Author
Affiliations:
1Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society, ou_2074310              

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Free keywords: Chlamydia; Chlamydia psittaci; Chlamydia trachomatis; genome analysis; annotation tool; core genome; plasticity zone; variable genomic sites; host preference
 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. 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.

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Language(s): eng - English
 Dates: 2020-10-28
 Publication Status: Published online
 Pages: 23
 Publishing info: -
 Table of Contents: 1. Introduction
2. Results
2.1. General Characteristics of the Genome Sequences Basic genomic parameters of all 33 strains are given
2.2. Common and Unique Elements in the Genomes of Chlamydia spp.
2.3. The Plasticity Zone (PZ)
2.4. Genes Encoding Polymorphic Membrane Proteins (pmps)
2.5. Inc Proteins
2.6. The Secreted Inner Nuclear Membrane-Associated Chlamydia Protein (SINC)
2.7. Histone-Like Proteins HctA and HctB
2.8. Pseudogenes
3. Discussion
3.1. Bioinformatics Tools: New and Unique Features of the RIBAP
3.2. Core Genome vs. Dispensable Genome
3.3. The Plasticity Zone
3.4. The Family of Polymorphic Membrane Proteins (Pmps)
3.5. Inclusion Membrane Proteins
3.6. SINC Protein
3.7. Histone-Like Proteins HctA and HctB
3.8. Pseudogenes
4. Materials and Methods
4.1. Chlamydial Strains
4.2. Genome Sequencing and Genome Assembly
4.3. Pan-Genome and Core Genome Calculation Using RIBAP
4.4. Annotation
4.5. Pan- Genome Scaffold
4.6. Integer Linear Programming and GLPK
4.7. Creating a RIBAP Group
4.8. The RIBAP Output
4.9. Phylogenetic Tree Based on Core Genomes
4.10. UpSet Diagrams
4.11. Multiple Blast to Identify Homologs of Pmp, Inc and SinC Genes
4.12. Calculation of Sequence Identities
4.13. Normalization of Genomes
5. Conclusions


 Rev. Type: Peer
 Identifiers: DOI: 10.3390/pathogens9110899
Other: shh2760
 Degree: -

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Title: Pathogens
Source Genre: Journal
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Publ. Info: Basel : MDPI
Pages: - Volume / Issue: 9 (11) Sequence Number: 899 Start / End Page: - Identifier: ISSN: 2076-0817
CoNE: https://pure.mpg.de/cone/journals/resource/2076-0817