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The Chlamydiales Pangenome Revisited: Structural Stability and Functional Coherence
Institute of Agrobiotechnology, Centre for Research & Technology Hellas (CERTH), Thessaloniki GR-57001, Greece
Department of Electrical & Computer Engineering, Aristotle University of Thessaloniki,Thessaloniki GR-54124, Greece
Laboratory of Microbiology & Infectious Diseases, Faculty of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki GR-54124, Greece
Division of Medical Sciences, University of Crete Medical School, Heraklion GR-71110, Greece
Department of Genetics & Plant Breeding, Aristotle University of Thessaloniki, Thessaloniki GR-54124, Greece
Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, P.O. Box 20537, Nicosia CY-1678, Cyprus
Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
* Author to whom correspondence should be addressed.
Received: 27 March 2012; in revised form: 2 May 2012 / Accepted: 8 May 2012 / Published: 16 May 2012
Abstract: The entire publicly available set of 37 genome sequences from the bacterial order Chlamydiales has been subjected to comparative analysis in order to reveal the salient features of this pangenome and its evolutionary history. Over 2,000 protein families are detected across multiple species, with a distribution consistent to other studied pangenomes. Of these, there are 180 protein families with multiple members, 312 families with exactly 37 members corresponding to core genes, 428 families with peripheral genes with varying taxonomic distribution and finally 1,125 smaller families. The fact that, even for smaller genomes of Chlamydiales, core genes represent over a quarter of the average protein complement, signifies a certain degree of structural stability, given the wide range of phylogenetic relationships within the group. In addition, the propagation of a corpus of manually curated annotations within the discovered core families reveals key functional properties, reflecting a coherent repertoire of cellular capabilities for Chlamydiales. We further investigate over 2,000 genes without homologs in the pangenome and discover two new protein sequence domains. Our results, supported by the genome-based phylogeny for this group, are fully consistent with previous analyses and current knowledge, and point to future research directions towards a better understanding of the structural and functional properties of Chlamydiales.
Keywords: comparative genomics; pangenome analysis; Chlamydiales; protein family detection; genome annotation; genome trees
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Psomopoulos, F.E.; Siarkou, V.I.; Papanikolaou, N.; Iliopoulos, I.; Tsaftaris, A.S.; Promponas, V.J.; Ouzounis, C.A. The Chlamydiales Pangenome Revisited: Structural Stability and Functional Coherence. Genes 2012, 3, 291-319.
Psomopoulos FE, Siarkou VI, Papanikolaou N, Iliopoulos I, Tsaftaris AS, Promponas VJ, Ouzounis CA. The Chlamydiales Pangenome Revisited: Structural Stability and Functional Coherence. Genes. 2012; 3(2):291-319.
Psomopoulos, Fotis E.; Siarkou, Victoria I.; Papanikolaou, Nikolas; Iliopoulos, Ioannis; Tsaftaris, Athanasios S.; Promponas, Vasilis J.; Ouzounis, Christos A. 2012. "The Chlamydiales Pangenome Revisited: Structural Stability and Functional Coherence." Genes 3, no. 2: 291-319.