DOI: 10.5061/dryad.np597
title: Data from: Genome sequencing and comparative analysis of three Chlamydia pecorum strains associated with different pathogenic outcomes

description: Background: Chlamydia pecorum is the causative agent of a number of acute
 diseases, but most often causes persistent, subclinical infection in
 ruminants, swine and birds. In this study, the genome sequences of three
 C. pecorum strains isolated from the faeces of a sheep with inapparent
 enteric infection (strain W73), from the synovial fluid of a sheep with
 polyarthritis (strain P787) and from a cervical swab taken from a cow with
 metritis (strain PV3056/3) were determined using Illumina/Solexa and Roche
 454 genome sequencing. Results: Gene order and synteny was almost
 identical between C. pecorum strains and C. psittaci. Differences between
 C. pecorum and other chlamydiae occurred at a number of loci, including
 the plasticity zone, which contained a MAC/perforin domain protein, two
 copies of a &gt;3400 amino acid putative cytotoxin gene and four
 (PV3056/3) or five (P787 and W73) genes encoding phospholipase D.
 Chlamydia pecorum contains an almost intact tryptophan biosynthesis operon
 encoding trpABCDFR and has the ability to sequester kynurenine from its
 host, however it lacks the genes folA, folKP and folB required for folate
 metabolism found in other chlamydiae. A total of 15 polymorphic membrane
 proteins were identified, belonging to six pmp families. Strains possess
 an intact type III secretion system composed of 18 structural genes and
 accessory proteins, however a number of putative inc effector proteins
 widely distributed in chlamydiae are absent from C. pecorum. Two genes
 encoding the hypothetical protein ORF663 and IncA contain variable numbers
 of repeat sequences that could be associated with persistence of
 infection. Conclusions: Genome sequencing of three C. pecorum strains,
 originating from animals with different disease manifestations, has
 identified differences in ORF663 and pseudogene content between strains
 and has identified genes and metabolic traits that may influence
 intracellular survival, pathogenicity and evasion of the host immune
 system.
description: Ribosomal phylogeny
 alignmentMUSCLE alignment of
 concatenated protein sequences from 48 ribosomal proteins from species of
 the family Chlamydiaceae. File is in nexus format.Ribosomal
 phylogeny.nexRibosomal tree
 fileMaximum-likelihood
 (PhyML) phylogenetic tree calculated using JTT+G substitution model with
 the concatenated sequences of 48 ribosomal proteins from species of the
 family Chlamydiaceae using PhyML. File is in Newick tree file
 format.Ribosomal
 tree.trePMP AT domain
 alignmentMUSCLE alignment of the
 autotransporter (AT) domain of polymorphic membrane proteins (PMP)
 originating from Chlamydia species. File is in nexus
 format.PMP
 AT domain.nexPMP AT domain tree
 filePhylogenetic tree of the
 autotransporter domain of polymorphic membrane proteins originating from
 Chlamydia species. Distances were calculated using a JTT+I+G substitution
 model and trees generated using PhyML. File is in Newick tree file
 format.PMP
 AT domain.treChlamydial cytotoxins
 alignmentMUSCLE alignment of
 chlamydial cytotoxoin proteins. GBlocks v 0.91 was used to eliminate
 regions that could not be unambiguously aligned resulting in an alignment
 of 2845 amino acids (75% of the original 3766 positions). File is in nexus
 format.Chlamydial_cytotoxins.nexChlamydial cytotoxins treePhylogenetic tree of cytotoxins originating from Chlamydia species. Distances were calculated using a WAG+I+G substitution model and trees generated using MrBayes. File is in Newick tree file format.Chlamydial cytotoxins.tre