Comparative analysis of two genomes of Chlamydia pecorum isolates from an Alpine chamois and a water buffalo

Abstract

Background: To date, whole genome sequencing has been performed mainly for isolates of Chlamydia trachomatis, C. pneumoniae, C. psittaci and C. abortus, but only a few isolates of C. pecorum have been entirely sequenced and this makes it difficult to understand its diversity and population structure. In this study the genome of two C. pecorum strains isolated from the lung of an Alpine chamois affected with pneumonia (isolate PV7855) and the brain of a water buffalo affected with meningoencephalomyelitis (isolate PV6959), were completely sequenced with MiSeq system (Illumina) and analyzed in their most polymorphic regions.

Results: The genome length and GC content of the two isolates were found to be consistent with other C. pecorum isolates and the gene content of polymorphic membrane proteins and plasticity zone was found to be very similar. Some differences were observed in the phospholipase genes for both isolates and in the number of genes in the plasticity zone, such as the presence of some hypothetical proteins in PV6959, not present in any other genomes analyzed in this study. Interestingly, PV6959 possesses an extra pmp and has an incomplete tryptophan biosynthesis operon. Plasmids were detected in both isolates.

Conclusions: Genome sequencing of the two C. pecorum strains did not reveal differences in length and GC content despite the origin from different animal species with different clinical disease. In the plasticity zone, the differences in the genes pattern might be related to the onset of specific symptoms or infection of specific hosts. The absence of a tryptophan biosynthesis pathway in PV6959 may suggest a strict relationship between C. pecorum and its host.

Keywords: Chamois; Chlamydia pecorum; Plasmids; Plasticity zone; Polymorphic membrane protein; Water buffalo; Whole genome sequencing.

Fig. 1

Circular representation of the comparison between chromosome of C. pecorum PV6959 and PV7855. Circles from the outside in represent the positions of protein-coding genes (blue), tRNA genes (green) and rRNA genes (pink) on the positive (circle 1), and negative (circle 2) strands respectively. It is shown the position of BLAST hits detected through blastn comparisons of PV6959 and PV7855 against W73 (circle 3), PV3056/3 (circle 4), P787 (circle 5), E58 (circle 6) with default settings; and GC skew (Circle 8). The image was generated with CGView Server

Fig. 2

Circular representation of the comparison between plasmid pCpecPV6959 and pCpecPV7855. Circles from the outside inside represent the plasmids used for the comparison: pCpecWA/B31/Ileal (red), pCpecW73 (light blue), pCpecMC/MarsBar (pink), pCpecDBDeUG (yellow), pCpecPV6959 (blue) and pCpecPV7855 (aqua green). The image was generated with CGView Server

Fig. 3

Phylogeny of selected Chlamydia species (A) and whole genome NeighborNet network analysis of C pecorum (B). A The box shows the relationship between the two sequenced C. pecorum genomes and others Chlamydia species (C. trachomatis, C. psittaci, C. abortus and C. pneumoniae). The maximum-likelihood tree was reconstructed using OrthoFinder v. 2.4.0 with modeltest-ng v 0.1.7 based on the nucleotide sequences of the identified single copy orthologs genes present in all organism (753). B The box shows the phylogenetic network of a whole genome sequence alignment of C. pecorum, where the PV6959 isolate is completely separate from other strains. The scale bar indicates the expected substitutions per site. The figure was generated using SplitsTree4

Fig. 4

Comparative analysis of trp system. Trp system comparison between C. pecorum PV7855, P787 and PV6959 showing comparison of nucleotide matches between complete 6-frame translations (computed using Megablast blastn) using ACT. Grey bars represent the forward and reverse strands of DNA with CDSs marked as arrows. The scale is marked in base pairs. The red bars represent homology matches, the white ones represent the non-homology matches

Fig. 5

Polymorphic membrane proteins in C. pecorum. Genomic organization of pmps in C. pecorum with gene families (indicated under each block arrow). In PV6959 the extra pmp is indicated in green. The diagonal bars indicate the separation of the four different loci. Locus tag are available in Additional File 2 Table S1

Fig. 6

Visual representation of the genomic island of the plasticity zone in C. pecorum. Comparative analysis of the genes in the plasticity zone of C. pecorum PV7855 and PV6959. Comparison of the nucleotide matches (computed using blastn) between the genes guaB (pink) and accB (orange) in C. pecorum strains. The brown genes indicate hypothetical proteins. The orientation of coding sequences in the forward and reverse frames are indicated by the direction of the block arrows. The level of BLAST identity between the sequences is indicated by the degree of grey shading in the vertical bars. The figure was generated using EasyFig [14]

Fig. 7

Phylogenetic analysis of plasmid sequences of Chlamydia pecorum. The maximum Likelihood tree was reconstructed using MEGA v. 11, using the Tamura 3 parameter model. The tree with the highest log likelihood (−11,062,28) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. This analysis involved 23 nucleotide sequences. Codon positions included were 1st + 2nd + 3rd + Noncoding. There was a total of 7803 positions in the final dataset