Redefining the differences in gene content between Yersinia pestis and Yersinia pseudotuberculosis using large-scale comparative genomics

Abstract

Yersinia pestis, the causative agent of plague, is best known for historical pandemics, but still actively causes disease in many parts of the world. Y. pestis is a recently derived clone of the pathogenic species Yersinia pseudotuberculosis, but is more associated with human infection. Numerous studies have documented genomic changes since the two species differentiated, although all of these studies used a relatively small sample set for defining these differences. In this study, we compared the complete genomic content between a diverse set of Y. pestis and Y. pseudotuberculosis genomes, and identified unique loci that could serve as diagnostic markers or for better understanding the evolution and pathogenesis of each group. Comparative genomics analyses also identified subtle variations in gene content between individual monophyletic clades within these species, based on a core genome single nucleotide polymorphism phylogeny that would have been undetected in a less comprehensive genome dataset. We also screened loci that were identified in other published studies as unique to either species and generally found a non-uniform distribution, suggesting that the assignment of these unique genes to either species should be re-evaluated in the context of current sequencing efforts. Overall, this study provides a high-resolution view into the genomic differences between Y. pestis and Y. pseudotuberculosis, demonstrating fine-scale differentiation and unique gene composition in both species.

Data Summary

1. De novo sequencing data of 118 Yersinia pestis strains are deposited in the Sequence Read Archive: http://www.ncbi.nlm.nih.gov/Traces/sra/?study = SRP003808

Impact Statement

This study employed large-scale comparative genomics to understand the genomic differences between Yersinia pseudotuberculosis and Yersinia pestis, a pathogen responsible for global human pandemics. We identified that many results from previous comparative studies were not reproduced when using a larger sample set. These results change the understanding of the evolution of Y. pestis, specifically the timing for when genomic components were gained and lost since the most recent common ancestor between the two species. Additionally, the identification of coding regions conserved in Y. pestis and missing from Y. pseudotuberculosis provides targets for functional studies to better understand the pathogenicity and spread of Y. pestis. Whilst the results of this study will primarily appeal to researchers who study Yersinia spp., the methods employed provide a framework to better understand the evolution of the pan-genome in any bacterial species.

Introduction

Yersinia pestis, the causative agent of plague, is a recently evolved clone of Yersinia pseudotuberculosis serotype O : 1b (Achtman et al., 1999). Y. pestis is best known for causing three pandemics, including the black death (Achtman et al., 2004), the plague of Justinian (Wagner et al., 2014) and the third pandemic, where Y. pestis was spread worldwide (Cui et al., 2013). Y. pestis still actively causes disease in many parts of the world, including North America (Wagner et al., 2010) and Madagascar (Ratovonjato et al., 2014). Disease caused by Y. pestis is generally treatable with antimicrobials (Bonacorsi et al., 1994), although acquired resistance has been observed in isolated cases in Madagascar (Galimand et al., 2006); details of the plasmid that confers the multidrug-resistant phenotype have been published (Welch et al., 2007).

A lot of work has focused on genomic and phenotypic differences between Y. pestis and Y. pseudotuberculosis. One of the most striking differences is the presence in most Y. pestis of two plasmids, pMT1 and pCP1, that are absent from all Y. pseudotuberculosis (Hu et al., 1998). Y. pseudotuberculosis is still pathogenic (Rosqvist et al., 1988), and Y. pestis and Y. pseudotuberculosis share genes associated with pathogenesis, including the pYV plasmid (also known as pCD1) and the ail locus (Reuter et al., 2014), which is associated with attachment and invasion. A filamentous phage, YpfΦ, has been characterized in some Y. pestis, but is absent from all known Y. pseudotuberculosis genomes (Derbise & Carniel, 2014); this phage has been associated with dissemination in mice (Derbise et al., 2007). Additionally, mutations have been described in Y. pestis compared with Y. pseudotuberculosis that have led to flea-borne transmission of Y. pestis (Sun et al., 2014) due to enhanced biofilm formation.

In this study, we compared the entire pan-genomes of both species with the large-scale blast score ratio (LS-BSR) pipeline (Sahl et al., 2014) to better understand the distribution and conservation of identified coding regions. Smaller-scale comparisons between Y. pestis and Y. pseudotuberculosis have been published (Achtman et al., 1999; Chain et al., 2004; Duan et al., 2014; Pouillot et al., 2008), but LS-BSR on a large set of genomes enabled us to rapidly compare the genomic content between species. These comparisons enabled us to identify fine-scale resolution in the global propagation of the Y. pestis clone. We also screened previously published genes against this comprehensive dataset to determine how well these previous studies captured the gene distribution across Y. pestis and Y. pseudotuberculosis.

Methods

Genomes analysed

Except where noted otherwise, our comparisons included 133 Y. pestis genomes and 13 Y. pseudotuberculosis genomes, as well as five plasmids (Table S1, available in the online Supplementary Material). To improve the assembly contiguity for 118 genomes recently published (Cui et al., 2013) and assembled with Velvet (Zerbino & Birney, 2008), raw reads were downloaded and assembled with SPAdes version 3.1.0 (Bankevich et al., 2012). This method improved the contiguity of all but one assembly and increased the assembly size (Table S2). The SPAdes assemblies are publicly available and named by the Sequence Read Archive accession number (https://github.com/jasonsahl/YP_genomes.git).

Core genome single nucleotide polymorphism (SNP) phylogeny

Genome assemblies from external genomes were aligned against the finished genome of Colorado 92 (CO92) (GenBank accession number NC_003143) with NUCmer (Delcher et al., 2003). The reference was also aligned against itself to identify duplicated regions, which were then removed for SNP comparisons. SNPs were identified from genome assemblies by a direct mapping of each query base to the corresponding reference base. Raw reads from a previously published study (Cui et al., 2013) were mapped to CO92 with bwa-mem (Li, 2013) and SNPs were called with the UnifiedGenotyper method in the Genome Analysis Toolkit (DePristo et al., 2011; McKenna et al., 2010); any SNP with a coverage of < 10 or an allele proportion < 90 % were filtered from downstream analyses. These methods were wrapped by the Northern Arizona SNP Pipeline (NASP) (http://tgennorth.github.io/NASP/) (Engelthaler et al., 2014). A phylogeny was inferred on the concatenated SNP alignment using RAxML version 8 (Stamatakis, 2014) and the ASC_GTRGAMMA model (Lewis correction) that incorporates an ascertainment bias correction. The retention index (RI) was calculated with phangorn (Schliep, 2011).

Comparative genomics

All coding regions were predicted from all genome assemblies with Prodigal (Hyatt et al., 2010). These coding regions were concatenated, then clustered and de-replicated using usearch (Edgar, 2010) at a pairwise identity of 0.9. Each cluster representative, or the cluster centroid, was then aligned against each genome using either tblastn (Altschul et al., 1997) or blat (Kent, 2002) in conjunction with LS-BSR (Sahl et al., 2014); the different methods were used to examine the conservation of either nucleotide or peptide sequences. LS-BSR values can range from 0 (no alignment) to 1 (100 % identity). To identify correlations between coding region conservation and metadata (e.g. isolation location), LS-BSR values were first multiplied by 100 in order to convert all float values to integers and these adjusted BSR (Rasko et al., 2005) values were then correlated with categorical data using a Kruskal–Wallis test implemented in qiime version 1.9.0 (Caporaso et al., 2010), which also incorporated false detection rate (FDR) adjusted P values. Categories tested included: branch location within the Y. pestis phylogeny (0–4), subclade in the Y. pestis phylogeny (e.g. 0.PE4Ba), country of strain origin, latitude of strain origin, number of nodes to the most recent common ancestor (MRCA; Y. pseudotuberculosis) and number of SNPs to the MRCA. Coding regions that showed positive correlations (FDR P < 0.05) were aligned against the GenBank (Benson et al., 2012) nr database with tblastn (Altschul et al., 1997) for annotation. Pan-genome stats were calculated with the pan_genome_stats.py script in the LS-BSR repository (https://github.com/jasonsahl/LS-BSR/tree/master/tools).

Distribution of annotated genes

From reviewing the relevant literature, we identified a panel of genes associated with Y. pestis virulence (Chain et al., 2004; Derbise et al., 2007; Lillard et al., 1997; Pouillot et al., 2008; Radnedge et al., 2002; Reuter et al., 2014; Schubert et al., 1998; Sodeinde et al., 1992; Sun et al., 2014) (Table S3), and screened these for conservation across 133 contemporary genomes of Y. pestis and 13 Y. pseudotuberculosis genomes using LS-BSR in conjunction with tblastn. In general, a gene was considered conserved if it had BSR>0.8, which is ∼80 % peptide identity over 100 % of the peptide length (Rasko et al., 2008). The conservation of genes was visualized as a heatmap correlated with a phylogeny using the Interactive Tree Of Life (iTOL) (Letunic & Bork, 2007).

Read mapping to confirm gene presence/absence

To confirm the presence or absence of specific coding regions, raw sequence reads were mapped to the reference sequence with bwa-mem. The coverage across each base was calculated with the GenomeCoverageBed method in BEDTools (Quinlan & Hall, 2010). Presence was dependent on the breadth of coverage across the reference at a minimum depth of coverage (DOC) (default value of × 3 was used); a script to wrap these methods is available (https://gist.github.com/3206314afe510b9e2cbb.git). Differences in mean DOC were visualized with Circos (Krzywinski et al., 2009).

Multiple sequence alignment analysis

For cases where individual mutations were investigated, the gene sequence was pulled out of all genome assemblies directly from blastn alignments (Altschul et al., 1990), aligned with muscle (Edgar, 2004) and visualized with Jalview (Waterhouse et al., 2009).

Results

Core genome phylogeny

A core genome SNP phylogeny was inferred to demonstrate the relationship between Y. pestis genomes screened in the current study. The resulting phylogeny (Fig. 1) was similar in clade membership to a previous study that used the same set of genomes (Cui et al., 2013). The RI (Farris, 1989) of the concatenated SNP alignment was 0.99, indicating very little homoplasy in the underlying data. A phylogeny was also inferred from an alignment including 13 Y. pseudotuberculosis genomes as well as the 133 Y. pestis genomes, rooted with Yersinia enterolitica 8081 (GenBank accession number NC_008800) (Fig. S1); for visualization, SNPs specific to Y. enterolitica were removed from the alignment. The phylogeny demonstrated the increased phylogenetic diversity in Y. pseudotuberculosis relative to Y. pestis. The RI of this alignment was 0.85, demonstrating significant homoplasy, likely resulting from recombination.

Fig. 1.

Loss of genes across Branch 2 genomes across the Y. pestis phylogeny. Differentially conserved genes were identified through associations of metadata and the LS-BSR (Sahl et al., 2014) matrix using qiime (Caporaso et al., 2010). The phylogeny was inferred with RAxML (Stamatakis, 2014) on a concatenation of SNPs identified with NASP (Engelthaler et al., 2014). The phylogeny was associated with the LS-BSR values using iTOL (Letunic & Bork, 2007).

In silico screen of the Y. pseudotuberculosis pan-genome across 133 Y. pestis genomes

To understand the pan-genome differences between Y. pseudotuberculosis and Y. pestis, the pan-genome was identified with LS-BSR for all Y. pseudotuberculosis genomes (n = 13), resulting in 5469 unique coding regions (Fig. 2a). Of these regions, seven were found to be highly conserved (BSR>0.8) in all Y. pseudotuberculosis genomes and missing (BSR < 0.4) from all Y. pestis genomes (Table 1); this demonstrated that most of the Y. pseudotuberculosis core genome was also conserved in at least one Y. pestis genome. Y. pestis has been associated with genome reduction (Chain et al., 2006) based on host adaptation, but this small number of regions represents either the limited number of ancestral genes that are no longer required by Y. pestis, genes that are no longer needed but have not been purged or the relatively short time since the split between Y. pestis and Y. pseudotuberculosis.

Fig. 2.

Pan-genome plots demonstrating the acquisition of genes with additional genomic sequencing in (a) Y. pseudotuberculosis and (b) Y. pestis. For each analysis, a number of randomly selected genomes were parsed at different genome depths from the LS-BSR (Sahl et al., 2014) matrix, and the number of coding regions with BSR>0.8 in all genomes was identified and plotted.

Table 1. Annotation of coding regions unique to either Y. pestis or Y. pseudotuberculosis.

Annotation	GenBank accession no.	Group
Hypothetical protein	WP_038824878	Y. pseudotuberculosis
Uracil transporter	WP_038824557	Y. pseudotuberculosis
Hypothetical protein	WP_011192493	Y. pseudotuberculosis
Aldehyde dehydrogenase	WP_011192485	Y. pseudotuberculosis
TonB-dependent vitamin B12 receptor	ACA70332	Y. pseudotuberculosis
Hypothetical protein	WP_038824929	Y. pseudotuberculosis
Hypothetical protein	ABS48865	Y. pseudotuberculosis
Hypothetical protein	YPO0396	Y. pestis
Integrase	YOP2083	Y. pestis
Hypothetical protein	YPO0387	Y. pestis
Hypothetical protein	YPO0388	Y. pestis
Hypothetical protein	YPO3437	Y. pestis
XRE family transcriptional regulator	WP_002214362	Y. pestis
Transcriptional regulator	YPO4031	Y. pestis
Transposase	WP_002214360	Y. pestis
Outer membrane receptor	YPO3910	Y. pestis
Hypothetical protein	YPO3948	Y. pestis
Hypothetical protein	YPO0394a	Y. pestis
Hypothetical protein	YPO0394	Y. pestis
Integrase	YPO4033	Y. pestis
Pseudogene	YPO4029	Y. pestis
Hypothetical protein	YPO0397	Y. pestis

The pan-genome of Y. pseudotuberculosis was screened across 133 Y. pestis genomes (Table S1) using the LS-BSR pipeline. Of all coding regions screened, 21 were found to have significantly lower BSR values (fdr adjusted P < 0.05) among Branch 2 genomes in the Y. pestis phylogeny when compared with other branches (Fig. 1), indicating loss of these coding regions since evolving from Y. pseudotuberculosis. Annotation of these regions using the CO92 annotation demonstrated that 19 out of 21 were known products, many involved with flagellar composition and function (Table 2); many of these coding regions have also been lost in Pestoides F (Fig. 1). One coding region was conserved in the 2.ANT lineage, but was absent from the 2.MED lineage (Fig. 1). Annotation of this sequence is associated with a toxin described in Y. pseudotuberculosis (locus tag WP_011192526); similar types of genes have recently been described as atypical toxins (Koskiniemi et al., 2013). The 2.MED lineage contains genomes collected over a long time frame (1958–2006), with almost all of them isolated from China, suggesting local adaptation, niche specialization or a lack of sampling from other parts of the world.

Table 2. Annotation of regions lost by Branch 2 genomes.

Locus	Annotation	Locus tag
fliD	Flagellar hook-associated protein	YPO0740
fliS	Flagellar protein	YPO0741
YPO0742	Hypothetical protein	YPO0742
YPO0744	Flagellar biogenesis protein	YPO0744
fliA	Flagellar biosynthesis sigma factor	YPO0745
motA	Flagellar motor protein MotA	YPO0746
motB	Hypothetical protein	YPO0747
YPO0749	Hypothetical protein	YPO0749
YPO0750	Hypothetical protein	YPO0750
YPO0751	Hypothetical protein	YPO0751
YPO0754	Hypothetical protein	YPO0754
YPO1380	MFS family transporter protein	YPO1380
YPO2315	Hypothetical protein	YPO2315
Pcp	Lipoprotein	YPO2373
YPO2375	Aldo/keto reductase	YPO2375
YPO2376	Hypothetical protein	YPO2376
sepC	Insecticial toxin	YPO2380
YPO2493	Dioxygenase subunit alpha	YPO2493

In silico screen of the Y. pestis pan-genome across Y. pseudotuberculosis genomes

Based on default values in LS-BSR, the Y. pestis pan-genome was found to consist of 5227 unique coding regions (Fig. 2b). A screen of these coding regions against all Y. pseudotuberculosis genomes demonstrated that there were 15 coding regions present in all Y. pestis genomes (BSR>0.8) and missing from all Y. pseudotuberculosis genomes (BSR < 0.4) (Table 1); none of these regions was associated with any of the known Y. pestis plasmids. In the pan-genome, there were 725 coding regions that were conserved in one or more Y. pestis genome and missing from all Y. pseudotuberculosis genomes. Of the total Y. pestis-specific coding regions, 156 of these coding regions were associated with Y. pestis plasmids (BSR>0.8). Of the remaining coding regions, 294 were only conserved in a single genome, suggesting possible contamination, sequencing artefacts or horizontally acquired genomic regions. For example, 228 of these unique regions were identified in the draft genome assembly of Orientalis IP275 and are most likely associated with a plasmid that confers resistance to multiple antimicrobials (Welch et al., 2007). The remaining Y. pestis-specific coding regions (n = 275) were conserved in two or more genomes (Table S4).

Chain et al. (2004) identified a total of 112 Y. pestis-specific genes and screened them across a panel of 19 Y. pestis strains. They found 32 of these regions to be conserved in all of their Y. pestis strains, but in none of the nine screened Y. pseudotuberculosis strains. An in silico screen of these regions (Table S3) against our collection of genomes demonstrated that only five genes were completely conserved across the Y. pestis phylogeny (BSR>0.8 in 133 genomes) (Table S5). One of the regions (WP_002213869) was conserved (BSR = 1) in two Y. pseudotuberculosis genomes (B-7194, CBKS0000000; B-7195, CBKR00000000) in our collection.

In silico screen of previously annotated genes

LS-BSR analysis demonstrated that the 11 genes from a previously described Y. pestis filamentous phage (Derbise et al., 2007) associated with mouse dissemination were conserved in all genomes within the 1.ORI group (Fig. 3); this region was also identified in one genome (YN472) from the 1.IN3 group and a portion of the phage was identified in a genome (H1958004) from the 2.MED group (Fig. 3). A read mapping analysis confirmed the presence of portions of this phage in these two genomes, although the DOC was significantly lower compared with the coverage in 1.ORI genomes. For example, in genome fig1946001 from the 1.ORI group, the mean DOC across the genome was × 58 and the coverage across the phage was × 243. In contrast, the DOC across the genome of YN472 from the 1.IN group was × 108 and only × 5 across the phage. This lower level of coverage could be due to copy number variation or cross-sample contamination during sequencing and would need to be confirmed with targeted assays. If confirmed, the presence of this phage in the 1.IN3 group would suggest that this lineage gave rise to 1.ORI, as has been proposed previously (Cui et al., 2013). All coding regions from the filamentous phage were missing (BSR < 0.4) from all Y. pseudotuberculosis genomes. Li et al. (2008) identified three of these phage ORFs in a strain that was included in our panel (A1956001), but our analysis identified these ORFs as missing (BSR = 0.0) in the genome assembly. We validated the absence of these ORFs in this assembly with read mapping.

Fig. 3.

Variable distribution of previously characterized genes across the Y. pestis phylogeny (Table S3). The phylogeny was inferred with RAxML (Stamatakis, 2014) on a concatenation of SNPs identified with NASP (Engelthaler et al., 2014). The phylogeny was associated with the LS-BSR values using iTOL (Letunic & Bork, 2007).

From a pathogenesis perspective, one of the genomic regions associated with virulence is the HPI (high pathogenicity island), a component of the pgm locus (Schubert et al., 1998). Prodigal was used to predict coding regions from this region (AL031866) and all coding regions (n = 93) were screened against all genomes with LS-BSR. The results demonstrate that a large section (∼65 coding regions) of the pgm locus was consistently missing from multiple (∼30) Y. pestis genomes (Fig. S2); the pgm was largely conserved across screened Y. pseudotuberculosis genomes. A subset of the pgm locus, the hmsHFRS operon, was reported to be necessary for the synthesis of Y. pestis biofilm in fleas (Sun et al., 2014) and therefore flea-borne transmission of the pathogen. Sun et al. (2014) further stated that both Y. pestis and Y. pseudotuberculosis contained a fully functional hmsHFRS operon. However, our LS-BSR analysis of the four hmsHFRS loci (hmsH, hmsF, hmsR and hmsS; GenBank accession number U22837) (Lillard et al., 1997) demonstrated that these genes were conserved in only a portion (106/133) of our Y. pestis panel. In contrast, these four loci were present in all of our screened Y. pseudotuberculosis genomes.

Reuter et al. (2014) reported that the chromosomal type III secretion system (abbreviated Ygt for the Yersinia genus type III secretion system) is present in all Yersinia species, but in the process of being lost from the pathogenic lineages (Reuter et al., 2014). They screened 32 regions (Table S3) of Ygt across three and 31 Y. pestis and Y. pseudotuberculosis strains, respectively, and found them to be variably distributed across these two species (range 0–84.68 %; mean ± sd 45.68 ± 32.45 %). In our global LS-BSR analysis of these 32 regions in our panel of genomes, we found 30 of 32 regions to be missing (BSR < 0.1) from all screened Y. pestis and Y. pseudotuberculosis genomes. The remaining two regions (strain YE21202, coordinates 3177984:3178778 and 3178768:3179844) were not highly conserved across the majority of genomes in both species (BSR < 0.5). These two regions were categorized as putative type III secretion proteins.

The pla gene (locus tag YPPCP1.07) on the pPCP1 plasmid encodes a cell surface protease/plasminogen activator that is essential for invasiveness at the flea-bite site following Y. pestis transmission (Sodeinde et al., 1992; Sun et al., 2014). The LS-BSR analysis demonstrated the conservation (BSR = 1) of this gene in most contemporary Y. pestis strains (n = 125/133) (Fig. 3); the absence of this locus in some genomes may represent the loss of the pPCP1 plasmid due to laboratory passage (Perry & Fetherston, 1997). The pla gene was missing from all Y. pseudotuberculosis genomes surveyed (BSR = 0).

Pouillot et al. (2008) screened 47 Y. pestis and 31 Y. pseudotuberculosis strains for five regions and four ORFs (Table S3) that were specific to Y. pseudotuberculosis. They concluded that despite their loss in Y. pestis, five out of nine of these (ORF2, ORF3, ORF4, R1, R3) were important to survival, growth or virulence in Y. pseudotuberculosis. An in silico screen of these five loci demonstrated that R1 was conserved in Y. pestis Branches 0.PE2, 0.PE3 and 0.PE4A only, suggesting independent loss in both 0.PE7 and all other branches of Y. pestis (Fig. 3). ORF2 was present in Branch 0.PE7 only (Fig. 3), suggesting that the deletion of this region happened after the split between Y. pseudotuberculosis and Y. pestis. In Y. pseudotuberculosis, ORF2 and R1 were highly conserved (BSR>0.98) across all sequenced genomes, but ORF3 and ORF4 were only conserved (BSR>0.8) in a portion of Y. pseudotuberculosis genomes (ORF3 in four of 13; ORF4 in seven of 13).

Chain et al. (2004) reported the loss of a lipid A acyltransferase gene htrB (locus tag YPTB2490) in all Y. pestis since its divergence from Y. pseudotuberculosis. However, our LS-BSR analysis demonstrated that this gene was conserved in the two most ancestral contemporary strains of Y. pestis on Branch 0.PE7 (620024 and CMCC05009) (Fig. 3). This gene was also highly conserved in all Y. pseudotuberculosis genomes (BSR ≥ 0.99). Chain et al. (2004) also reported nine coding regions (YPTB3450–YPTB3459) conserved in Y. pseudotuberculosis, representing a region that encodes several haemolysin genes absent from Y. pestis. Our in silico screen of these nine regions in our panel of Y. pestis assemblies demonstrated variation in the conservation of these regions across assemblies in both species (Table S6). Five of these regions were missing across all screened Y. pestis genomes (BSR = 0) and the remaining four demonstrate low homology across Y. pestis genomes (BSR = 0–0.86). In our screened Y. pseudotuberculosis genomes, all of these regions were completely conserved (BSR = 1) in only two of 13 genomes.

Chain et al. (2004) also reported frameshift mutations in two virulence factor genes characterized in Y. pestis, srfA and srfB (YPTB2212 and YPTB2213, respectively, both discontinued in the National Center for Biotechnology Information database) that are conserved in Y. pseudotuberculosis. The authors speculated that if these mutations influence protein function, these loci might be involved in species-specific virulence. Our in silico screen of these regions demonstrated that both loci are conserved in all Y. pestis genomes, although small deletions observed in the multiple sequence alignment could result in frameshift mutations; these deletions were observed in only a portion of Y. pseudotuberculosis genomes (Fig. S3). In Y. pseudotuberculosis, srfA was conserved in all screened genomes (mean BSR = 0.98), but srfB was not conserved (BSR < 0.51) in six out of 13 genomes.

In their 2014 paper, Sun et al. (2014) detailed three loss-of-function mutations that increased the transmissibility of Y. pestis via flea bite. We screened both the Y. pestis Kim10 and Y. pseudotuberculosis IP32953 homologues for PDE2, PDE3 and rcsA (Table S3). Whilst Sun et al. (2014) reported that PDE3 was conserved in all Y. pestis genomes except for Angola and Pestoides F strains, we found that PDE3 was also missing from genome Antigua UG05-0454, Branch 0.PE2 and Branch 0.ANT3 (Fig. S4); we also found that PDE3 was missing (BSR < 0.2) from six of 13 Y. pseudotuberculosis genomes. Sun et al. (2014) also reported a 30 bp tandem duplication in rcsA that was present in all Y. pestis except for Branch 0 strain Pestoides A. We screened the Y. pestis version of this gene (YP02449) in a multiple sequence alignment and found the duplication to be missing in additional genomes across the Y. pestis phylogeny (C1975003, M0000002, SHAN11, YN1683, Antigua, Antigua UG05, CMCC96007, CMCC11001, CMCC03001) (Fig. S5); the tandem duplication was confirmed to be missing from all Y. pseudotuberculosis genomes. Whilst PDE2 was highly conserved across all Y. pestis genomes, it was missing from one Y. pseudotuberculosis genome (B-6863), although this may be have been due to an assembly error. The reported frameshift was found in all Y. pestis genomes and none of the Y. pseudotuberculosis genomes.

Difference region (DFR) 4 is a 15 kb genomic island that is known to be lost in some Y. pestis strains (i.e. CO92) and contains genes that may play a role in virulence. Radnedge et al. (2002) investigated the presence of DFR4 in 78 Y. pestis and four Y. pseudotuberculosis strains, and found it to be conserved in only 13 of the Y. pestis strains but in all four Y. pseudotuberculosis strains. LS-BSR of 16 coding regions of DFR4 demonstrated them all to be missing from 48 genomes, including the entire 0.PE2, 0.PE3, 0.PE4A, 1.IN3, 1.ORI and 2.MED1 branches. One coding region (AAL27378) was not highly conserved in all 133 screened Y. pestis genomes (BSR < 0.7) and one (AAL27386) was conserved in 27 (33 %) of the genomes; the remaining 14 coding regions were found in 85 (64 %) Y. pestis genomes. Fourteen out of 16 coding regions were conserved in all screened Y. pseudotuberculosis genomes, whilst the other two coding regions were variably distributed.

Our LS-BSR analysis of the remaining DFRs (DFR1–3, 5 and 6) described by Radnedge et al. (2002) demonstrated that DFR5 was completely lost in all Y. pestis genomes (Table 3). In DFR2, three out of four coding regions had been lost across all Y. pestis genomes. For the remaining DFRs, two out of three regions of each DFR were demonstrated to be lost across all Y. pestis genomes, but the third was found to be conserved in a portion of Y. pestis genomes: 65 % in DFR1 (AF333796), 87 % in DFR3 (AF333802), 80 % in DFR6 (AF333812) and 99 % in DFR2 (AF333801). In Y. pseudotuberculosis, DFR5 was missing from all screened genomes and aff333802 of DFR3 was conserved in all Y. pseudotuberculosis genomes. However, similar to what was found in Y. pestis, three out of four regions in DFR2 were missing across all Y. pseudotuberculosis genomes and two out of three regions of the remaining DFRs were missing across all Y. pseudotuberculosis genomes. The remaining one region within each DFR was present in 46 % in DFR1 (AF333796), 54 % in DFR2 (AF333801) and 92 % in DFR6 (AF333812) across all Y. pseudotuberculosis genomes.

Table 3. Comparison of screening results between previous studies and the current study.

Gene/region	Locus tag(s)	Reference	Previous results (%)		Results from current study (%)
			Y. pestis	Y. pseudotuberculosis	Y. pestis* (n = 133)	Y. pseudotuberculosis* (n = 13)
Filamentous phage	YPO2271–YPO2280	Derbise et al. (2007)	na	na	100 (1.ORI)	0
Y. pestis specific genes	See Table S3	Chain et al. (2004)	100 (n = 19)	0 (n = 9)	18–100	2–15
Ygt	See Table S3	Reuter et al. (2014)	na	na	0	0
hmsHFRS	U22837	Sun et al. (2014)	100	100	80	100
Pla	YPPCP1.07	na	na	na	94	0
Y. pseudotuberculosisSpecific genes	See Table S3	Pouillot et al. (2008)	0 (n = 47)	100 (n = 31)	0–14	0–100
htrB	YPTB2490	Chain et al. (2004)	0 (n = 19)	100 (n = 9)	1.50	100
Haemolysin	YPTB3450–YPTB3459	Chain et al. (2004)	0 (n = 19)	100 (n = 9)	0–9	23–46
DFR4	AF426171	Radnedge et al. (2002)	17 (n = 78)	100 (n = 4)	0–85	38–100
DFR1	See Table S3	Radnedge et al. (2002)	79 (n = 78)	100 (n = 4)	22	14
DFR2	AF333798–AF333801	Radnedge et al. (2002)	97 (n = 78)	0 (n = 4)	25	16
DFR3	AF333802–AF333804	Radnedge et al. (2002)	72 (n = 78)	100 (n = 4)	28	32
DFR5	AF333808–AF333810	Radnedge et al. (2002)	68 (n = 78)	0 (n = 4)	0	0
DFR6	AF333811–AF333813	Radnedge et al. (2002)	90 (n = 78)	100 (n = 4)	26	30
PDE2 frameshift	YPTB1308	Sun et al. (2014)	100 (n = 29)	0	100	0
PDE3 presence	YPTB3308	Sun et al. (2014)	93 (n = 29)	na	93	54
rcsA duplication	YPTB2486	Sun et al. (2014)	97 (n = 29)	0	93	0
ail attachment locus	YE1820	Reuter et al. (2014)	70–90 (n = 3)	70–90 (n = 31)	0	0
Ymt	Y1069	Sun et al. (2014)	na	na	0–100	0
srfA frameshift	YPTB2212	Chain et al. (2004)	na	na	100	100
srfB frameshift	YPTB2213	Chain et al. (2004)	na	na	100	54

na, Results not reported.

* Presence based on BSR>0.8.

Although the focus of this work was on contemporary strains, ancient genomes are now available from the first and second pandemics (Table S1); the genome sequences from the second pandemic were generated with a capture array using CO92 as the reference, which may generate false negatives for genes not present in this genome. Reads from ancient genomes were mapped across the genes screened in this study and variable distribution was observed (Table S7). With ancient genomes, the low and variable coverage prohibits any firm conclusions about the presence or absence of screened genes.

Distribution of plasmids across Y. pestis

One of the defining features of Y. pestis is the acquisition of multiple plasmids that are absent from Y. pseudotuberculosis. We screened each coding region for each plasmid (Table S1) against 133 Y. pestis genomes to look at their distribution; by only considering coding regions, we could make no comment about the synteny of plasmid structure between different isolates. The results demonstrated that pPCP1 and pCD1 are broadly conserved across Y. pestis genomes (Table S8), although they have been intermittently lost in select genomes, likely due to laboratory passage. The pMT plasmid was also intermittently conserved, although a large region (∼16.7 kb) of the plasmid appears to be missing (Supplementary Data File 1) in a monophyletic clade within the 1.IN2 group (1.IN2h–1IN2p); annotation of missing coding regions was associated with phage-related genes. Deleted regions can easily be visualized by mapping reads across the plasmid between a genome with the region (Y. pestis C1975003) and a closely related genome missing the region (Y. pestis 5) (Fig. 4).

Fig. 4.

Variable distribution of raw sequence reads from two 1.IN genomes across the pMT plasmid. Reads were mapped to the plasmid with bwa-mem (Li, 2013) and the mean DOC was calculated with the GenomeCoverageBed method in BEDTools (Quinlan & Hall, 2010). The differences in DOC were visualized with Circos (Krzywinski et al., 2009).

Discussion

Y. pestis is the causative agent of plague and a recently derived clone of Y. pseudotuberculosis. The evolution of Y. pestis has been associated with the acquisition of virulence plasmids, mutations that allow for transmission via flea bites and the loss of genes due to host adaptation. In this study, we used publicly available genomes to comprehensively characterize the gain, loss and variable composition in the Y. pestis pan-genome following its separation from the common ancestor with Y. pseudotuberculosis.

The evolution of Y. pestis has been described as largely clonal (Achtman, 2008), likely due to the specialized habitat of Y. pestis. The core genome SNP phylogeny of Y. pestis confirmed this observation, with very little homoplasy detected. However, an analysis of the pan-genome demonstrated that the gene content can be widely variable and does not necessarily resemble the evolution of other clonal pathogens, such as Bacillus anthracis (Van Ert et al., 2007). Therefore, the evolution of Y. pestis can be thought of as a clonal expansion with regard to the core genome, with a pan-genome characterized by differential gene loss and acquisition of mobile genetic elements including plasmids and bacteriophages.

A comparison of the pan-genomes between Y. pestis and Y. pseudotuberculosis demonstrated that the Y. pseudotuberculosis pan-genome is larger (Fig. 2), suggesting either that coding regions have been lost in Y. pestis due to adaptation or the genomic diversity of Y. pseudotuberculosis is much greater. Comparative genomics identified coding regions both lost by all Y. pestis compared with Y. pseudotuberculosis, as well as coding regions unique to Y. pestis. Whilst some of these regions were associated with acquired plasmids, others were associated with the chromosome, suggesting acquisition after the differentiation from Y. pseudotuberculosis. These unique regions could serve as diagnostic markers for either field or clinical differentiation between the two species. These species-specific markers did not overlap well with previously published markers, suggesting that our larger sample set provides greater resolution into the dynamics of pan-genome structures. Annotation of Y. pestis specific coding regions was largely associated with hypothetical proteins (Table 2), which presents targets for functional studies investigating the pathogenesis, evolution and spread of Y. pestis.

Other studies have investigated the genomic differences between Y. pestis and Y. pseudotuberculosis based on smaller-scale analyses (Achtman et al., 1999; Chain et al., 2004; Duan et al., 2014; Pouillot et al., 2008). Our results demonstrate that several genomic features reported to be missing from Y. pestis, such as htrB, are conserved in a subset of Y. pestis genomes (Fig. 3). Other genomic features, such as coding regions of the pMT plasmid, are variably conserved (Fig. 4), but this result was concordant with the core genome SNP phylogeny. These observations would not have been possible without analysing a comprehensive panel of Y. pestis genomes. Additional sequencing of Y. pestis isolates from under-sampled geographical regions may further refine gene conservation and distribution in Y. pestis.

In addition to screening previously characterized genes, we also performed a de novo analysis to identify genes that were associated with different categorical data. The most associated pattern of gene conservation was in Branch 2 genomes, where several genes have been lost compared to other contemporary Y. pestis isolates. Many of these genes were associated with the flagellum, which suggests that these genes are being lost because Y. pestis does not appear to be motile (Brubaker, 1991). Continued surveillance of this pathogen will determine if these genes will be lost by additional lineages in the future.

A recent study characterized three mutations in Y. pestis compared with Y. pseudotuberculosis that result in enhanced biofilm formation and transmissibility (Sun et al., 2014). However, our analysis demonstrated variation in the presence of these mutations in the Y. pestis panel screened, suggesting that the lack of these mutations does not completely shut down the transmissibility of these isolates, other mechanisms are also responsible for biofilm formation or these strains are still transmitted by fleas, but just less efficiently. These questions will need to be addressed with additional experimentation.

Overall, this study highlights the necessity of sequencing and analysing a large number of genomes from a given species to understand the distribution of genes, especially in relation to close near-neighbours of a given species. These types of comparative studies can focus functional studies that aim at understanding the global evolution of a given species. Although this study is focused on Y. pestis, the methods can be applied to any organism to characterize the gene flow, including gain and loss, across a comprehensive set of sequenced genomes.

Supplementary Data

Supplementary Data

Abbreviations:

CO92

Colorado 92

DFR

difference region

DOC

depth of coverage

FDR

false detection rate

iToL

Interactive Tree Of Life

LS-BSR

large-scale blast score ratio

MRCA

most recent common ancestor

NASP

Northern Arizona SNP Pipeline

RI

retention index

SNP

single nucleotide polymorphism

Ygt

Yersinia genus type III secretion system