Genes 2012, 3(2), 291-319; doi:10.3390/genes3020291

The Chlamydiales Pangenome Revisited: Structural Stability and Functional Coherence

1,2email, 3email, 4email, 4email, 1,5email, 6email and 1,6,7,* email
Received: 27 March 2012; in revised form: 2 May 2012 / Accepted: 8 May 2012 / Published: 16 May 2012
(This article belongs to the Special Issue Evolution and Structure of Proteins and Proteomes)
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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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MDPI and ACS Style

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.

AMA Style

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.

Chicago/Turabian Style

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.

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