Draft genome sequence of ‘Treponema phagedenis’ strain V1, isolated from bovine digital dermatitis

‘Treponema phagedenis’ is considered to be a key agent in the pathogenesis of bovine digital dermatitis, an infectious foot condition of economic and animal welfare importance. We hereby report the draft sequence of ‘T. phagedenis’ strain V1. The draft genome assembly consists of 51 scaffolds comprising 3,129,551 bp and a GC-content of 39.9 %. Putative pathogenicity related factors have been identified in the genome that can be used in future studies to gain insight into the pathogenic mechanisms of ‘T. phagedenis’. Electronic supplementary material The online version of this article (doi:10.1186/s40793-015-0059-0) contains supplementary material, which is available to authorized users.


Introduction
Digital dermatitis is a painful infection of the foot and is the leading cause of lameness in dairy cattle. Secondary effects of lameness are decreased milk production and weight loss leading to economic losses and animal welfare problems [1]. The disease is characterized by a diffuse or circumscribed superficial dermatitis of the skin at the coronary margin of the hoof. Erosive lesions are formed at the superficial layer of epidermis accompanied by pain, swelling and foul odor. Bacteria from different genera have been identified from these lesions, among them spirochetes of the genus Treponema are most prevalent [2][3][4]. Members of this genus constitute both commensal and pathogenic spirochetes. Treponema pallidum, which causes syphilis, is a well-known example of a pathogenic treponeme. A Treponema phylotype recently suggested being the same species as is the human commensal 'Treponema phagedenis' [5] which is considered to be a key agent in the pathogenesis of digital dermatitis [6][7][8][9]. 'T. phagedenis' is thought to be important for lesion development because it is found at the interface with healthy tissue [10] and has been detected in infected cattle from Europe [11], North America [12], and Asia [13]. To identify the putative pathogenicity related factors of 'T. phagedenis', we performed sequencing of the 'T. phagedenis' strain V1 chromosome [14].
'Treponema phagedenis' is a helically, right-handed coiled bacterium with bent ends that are motile [16]. The typical size of 'T. phagedenis' ranges in length from 0.8 to 15 μm and 0.3 to 0.4 μm in width, with 7 to 9 flagella attached on each end [5,12]. These bacteria are mostly host-associated, anaerobic and have fastidious growth requirements. 'Treponema phagedenis' strain V1 was isolated from a clinical sample from a digital dermatitis lesion. [14]. The sample was taken from an acute lesion in a herd with continuous problems with digital dermatitis. According to the API ZYM profile, 'T. phagedenis' strain V1 shows a positive reaction for alkaline phosphatase, C 4 esterase, C 8 esterase lipase, acid phosphatase, naptholphosphohydrolase, β-galactosidase, and N-acetyl-β-glucosaminidase. The antimicrobial susceptibility test performed on 'T. phagedenis' strain V1 shows that it is susceptible to tiamulin, valnemulin, tylosin, aivlosin and doxycycline [14]. Also, three immunogenic proteins, TmpA, Ttm, and PrrA, have been detected in 'T. phagedenis'. The presence of antibodies against these proteins has been identified in high titer in sera from cattle with digital dermatitis through indirect  relative to other 'Treponema phagedenis' strains and to the other species within the genus. Brachyspira hyodysenteriae and Brachyspira innocens are used as out-group. The evolutionary history was inferred from 1212 aligned characters [42,43]. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. Numbers above branches are support values from 1000 bootstrap replicates. 0.04 on the scale bar represents 4 substitutions in 100 bp. Evolutionary analyses were conducted using maximum Likelihood method in MEGA6 [44] enzyme-linked immunosorbent assay [17]. General features of T. phagedenis V1 are stated in Table 1.

Genome sequencing information
Genome project history 'Treponema phagedenis' strain V1 was selected for sequencing in 2009 at the Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden. The genome was assembled and annotated by the SLU-Global Bioinformatics Centre at SLU. The genome project is deposited in the Genomes OnLine Database [18] with GOLD id Gi0072982 and the draft genome assembly is deposited in the European Nucleotide Archive database with accession number (CDNC01000001-CDNC01000051) under the study accession number: PRJEB5300. The aim of the sequencing was to identify genes that are linked to pathogenicity and virulence in related bacteria, to strengthen the hypothesis that bacteria of the genus Treponema causes digital dermatitis in cattle. Almost nothing is known about virulence factors of treponemes involved in digital dermatitis. Table 2 contains the summary of the project information.

Genome sequencing and assembly
The genomic sequence was obtained using a combin-  Phylum Spirochaetes TAS [35] Class 'Spirochaetia' TAS [36] Order Spirochaetales TAS [37][38][39] Family Spirochaetaceae TAS [40] Genus Treponema TAS [6,14] Species 'Treponema phagdenis' TAS [5,14] Strain: V1  Illumina sequencing. Subsets of reads from all three libraries were generated using a custom perl script to lower the coverage before performing assembly. Four different assemblies were produced, these include (i) hybrid assembly of 454 reads and Illumina reads from 160 bp insert size library (ii) hybrid assembly of 454 reads and Illumina reads from 305 bp insert size library (iii) hybrid assembly of 454 reads and Illumina reads from 505 bp insert size library (iv) 454 reads assembly.
The resulting assemblies varied in size from 2.9 to 3.1 Mbp with the average GC content of 39 %. Assembly was performed with the GS de novo assembler version 2.5.3 (Roche) using reads from each Illumina paired end library and the 454 sequencing. Resulting assemblies were compared using the MAUVE genome alignment tool [19]. The hybrid assembly produced from 454 reads and Illumina reads from 305 bp insert size library was selected for further analysis. Selection was based on N50  Table S1. Scaffolding of the selected assembly was performed using SSPACE [20] and possible removal of gaps present in scaffolds was done using Gapfiller [21] and. Homopolymer errors were corrected manually using Consed [22].

Genome annotation
The structural and functional annotation was accomplished via the Magnifying Genome (MaGe) Annotation Platform [23]. Prediction of tRNA and rRNA genes was performed using tRNAscan-SE version 1.23 [24] and RNAmmer version 1.2 [25], respectively. Putative functions of the encoding genes were assigned automatically by MAGE′s inbuilt BlastP searches against the UniProt and Trembl, TIGR-Fam, Pfam, PRIAM, COG and Inter-Pro databases. Putative phage prediction was performed using PHAST (PHAge Search Tool) webserver [26]. Proteins with signal peptides were predicted using SignalP v 4.1 [27] and TMHMM Server, v.2.0 [28] was used to predict transmembrane helices in the protein sequences.

Genome properties
The draft genome assembly comprised 60 contigs in 51 scaffolds with a total size of 3,129,551 bp (Fig. 3) that corresponds well to the size of two previously sequenced 'T. phagedenis' strains, 4A isolated from bovine digital dermatitis and F0421 isolated from human urogenitalia, with the assembly sizes of 3,027,773 and 2,830,421 respectively. The G + C content of the assembly was 39.9 %. In total 3,222 genes were predicted, of which 3,157 were protein coding genes. Table 3 contains the general genomic features. The classification of the protein coding genes in different COG categories is shown in Table 4.

Insights from the genome sequence
Potential pathogenicity related factors Putative pathogenicity related proteins that are present in the genomes of T. pallidum [29] and T. denticola [30] were predicted in 'T. phagedenis' strain V1. Protein sequences from T. pallidum strain Nichols (accession number NC_000919) and T. denticola strain ATCC 35405 (accession number NC_002967) were used to perform blast searches against the predicted proteins of 'T. phagedenis' V1. These contained genes that encode for putative adhesins, antigens and a major sheath protein (Additional file 2: Table S2). Also, 22 CDS encoding chemotaxis and motility proteins, 17 CDS encoding transposases, 2 CDS encoding hemolysins and 3 putative prophages were predicted in the 'T. phagedenis' genome annotation.  The total is based on the total number of protein coding genes in the genome Lipoproteins are considered to be of special attention in spirochetes because of their abundance in different spirochetal genera including Treponema [31]. Several of them localize to the bacterial surface and are considered as important vaccine targets. Lipoprotein prediction was thus performed separately using the SpLip server [32] that predicted 155 probable lipoproteins. The predicted lipoproteins were then Blasted against the proteins in all bacteria. Two lipoproteins with homology to known virulence related or antigenic proteins in other treponemes were expressed in Escherichia coli and are being used in ongoing studies.