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Open Access Research article

Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification

Xiangyu Deng1, Adam M Phillippy2, Zengxin Li1, Steven L Salzberg2 and Wei Zhang1*

  • * Corresponding author: Wei Zhang zhangw@iit.edu

  • † Equal contributors

Author Affiliations

1 National Center for Food Safety and Technology, Illinois Institute of Technology, Summit, Illinois 60501, USA

2 Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland 20742, USA

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BMC Genomics 2010, 11:500  doi:10.1186/1471-2164-11-500

Published: 16 September 2010

Additional files

Additional file 1:

Density estimation of PF values for both present and absent genes. Barplot of the positive fraction probability densities for known present and absent genes demonstrates the vast majority of truly present genes have PF score greater than 0.9 and the vast majority of truly absent genes have PF less than 0.1. Green bars show the density of PF scores for genes found present by a tblastn search, and black bars show the density of PF scores for genes found absent by a tblastn search. PF labels give the minimum of each left-closed interval. For example, PF = 0.5 bars show the densities for the bucket PF = [0.5,0.6).

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Additional file 2:

Homologous groups with locus tax IDs in 26 L. monocytogenes genomes. A total of 3,744 homologous groups were identified from 52,776 proteins annotated in 26 L. monocytogenes genomes. Each row in this file indicates the locus and tax IDs of proteins belonging to a specific homologous group.

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Additional file 3:

Comparison of homologous genes in rhamnose metabolic pathways. Alignment of putative rhamnose utilization pathway in E. coli strain K-12, L. monocytogenes strain EGD-e, and B. subtilius strain 168. The percentage of amino acid sequence similarities is shown between homologous gene pairs. Genes encoding L-rhamnose isomerase, L-rhamnulose kinase, and rhamnulose-1-phosphate aldolase are located in the same orientation in L. monocytogenes EGD-e and E. coli K-12 genomes. The pathway is adopted from KEGG database.

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Additional file 4:

Presence or absence of 3,560 HGs in 26 L. monocytogenes genomes. Binary distribution (i.e. present: "1"; absent or divergent: "0") of 3,560 HGs in 26 L. monocytogenes genomes. Each HG is designated by the tax and locus IDs of a representative protein.

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Additional file 5:

Distribution of phylogenetically-informative LI and LII core genes in LIII. Binary distribution (i.e. present: "1"; absent or divergent: "0") of phylogenetically-informative LI and LII core genes in LIII strains were summarized in this table.

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Additional file 6:

Binary distribution of accessory genes in 26 L. monocytogenes genomes. Binary distribution (i.e. present: "1"; absent or divergent: "0") of accessory genes in 26 L. monocytogenes genomes. These genes were used to generate the minimal spanning trees.

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Additional file 7:

Minimum spanning trees that show the distribution of accessory genes in different L. monocytogenes lineages. A total of 576, 521 and 489 accessory genes were identified from F2365 (LI), EGD-e (LII), and J2-071 (LIII), respectively. The binary distribution of these accessory genes was surveyed in 28 L. monocytogenes genomes, including 4 newly sequenced strains. Each circle represents a group of accessory genes in F2365 (A, D, G), EGD-e (B, E, H), or J2-071 (C, F, I) that share a unique binary distribution (i.e. "1" for presence or "0" for absence) in all strains belonging to a specific lineage (i.e. I, II, or III). The size of each circle is proportional to the total number of genes that share the same binary distribution. Each circle is color-coded based on the number of L. monocytogenes strains (from 0 to 10, see color bar) that share the same distribution. This figure provides an overview of the genomic diversity of the three genetic lineages from a perspective of accessory gene presence or absence, where LIII displays the most diversified gene content.

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Additional file 8:

Alignment of A118-like prophage in different L. monocytogenes lineages. The x-axis gives the location on the EGD-e chromosome, and for each strain, windowed alignment identity is given on a scale of 50-100% identity on the y-axis. Strains which show no homology to the EGD-e A118-like prophage are struck through in blue line. Strains which do show homology to the prophage, but the prophage is inserted somewhere other than comK, are struck through in red line (N1-017, HCC23). This plot illustrates some interesting phylogenetic incompatibilities. For example, based on whole-genome analysis, the nearest phylogenetic neighbor to EGD-e is R2-561. Yet the comK prophage in nearly all other strains appears more similar to EGD-e than does the prophage in R2-561, which has identity < 50% for most of its length.

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Additional file 9:

Probe density versus mean log intensity of the CGH arrays. Histogram with overlaid kernel density estimation (red) of the distribution of probe intensities for sample J1-208, showing an optimal intensity cutoff of 8.82 at the minimum between the present and absent modes. Displayed distribution is for the mean intensities of the two normalized quantile replicates for strain J1-208.

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